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PDBsum entry 1hrd

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protein Protein-protein interface(s) links
Oxidoreductase PDB id
1hrd
Jmol
Contents
Protein chains
449 a.a. *
Waters ×521
* Residue conservation analysis
PDB id:
1hrd
Name: Oxidoreductase
Title: Glutamate dehydrogenase
Structure: Glutamate dehydrogenase. Chain: a, b, c. Ec: 1.4.1.2
Source: Clostridium symbiosum. Organism_taxid: 1512. Strain: hb25
Biol. unit: Homo-Hexamer (from PDB file)
Resolution:
1.96Å     R-factor:   0.172    
Authors: K.L.Britton,P.J.Baker,T.J.Stillman,D.W.Rice
Key ref:
K.S.Yip et al. (1995). The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures. Structure, 3, 1147-1158. PubMed id: 8591026 DOI: 10.1016/S0969-2126(01)00251-9
Date:
03-Apr-96     Release date:   12-Mar-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P24295  (DHE2_CLOSY) -  NAD-specific glutamate dehydrogenase
Seq:
Struc:
450 a.a.
449 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.1.4.1.2  - Glutamate dehydrogenase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-glutamate + H2O + NAD+ = 2-oxoglutarate + NH3 + NADH
L-glutamate
+ H(2)O
+ NAD(+)
= 2-oxoglutarate
+ NH(3)
+ NADH
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     oxidation-reduction process   3 terms 
  Biochemical function     oxidoreductase activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1016/S0969-2126(01)00251-9 Structure 3:1147-1158 (1995)
PubMed id: 8591026  
 
 
The structure of Pyrococcus furiosus glutamate dehydrogenase reveals a key role for ion-pair networks in maintaining enzyme stability at extreme temperatures.
K.S.Yip, T.J.Stillman, K.L.Britton, P.J.Artymiuk, P.J.Baker, S.E.Sedelnikova, P.C.Engel, A.Pasquo, R.Chiaraluce, V.Consalvi.
 
  ABSTRACT  
 
BACKGROUND: The hyperthermophile Pyrococcus furiosus is one of the most thermostable organisms known, with an optimum growth temperature of 100 degrees C. The proteins from this organism display extreme thermostability. We have undertaken the structure determination of glutamate dehydrogenase from P. furiosus in order to gain further insights into the relationship between molecular structure and thermal stability. RESULTS: The structure of P. furiosus glutamate dehydrogenase, a homohexameric enzyme, has been determined at 2.2 A resolution and compared with the structure of glutamate dehydrogenase from the mesophile Clostridium symbiosum. CONCLUSIONS: Comparison of the structures of these two enzymes has revealed one major difference: the structure of the hyperthermophilic enzyme contains a striking series of ion-pair networks on the surface of the protein subunits and buried at both interdomain and intersubunit interfaces. We propose that the formation of such extended networks may represent a major stabilizing feature associated with the adaptation of enzymes to extreme temperatures.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. Superpositions of Cs (blue) and Pf (green) GluDHs. (a) The N-terminal regions (α1–α5 in Cs, α1–α2 in Pf) are shown. Helices α2 (Cs) and α1 (Pf) superimpose well as do helices α5 (Cs) and α2 (Pf). However, α1 (Cs) is completely absent in Pf and the loop α1–α2 in Pf is much shorter, replacing α3 and α4 in Cs. (b) Superposition of the region βh–βj which, in both GluDHs, forms the recognition site for the adenine ribose moiety. Figure 3. Superpositions of Cs (blue) and Pf (green) GluDHs. (a) The N-terminal regions (α1–α5 in Cs, α1–α2 in Pf) are shown. Helices α2 (Cs) and α1 (Pf) superimpose well as do helices α5 (Cs) and α2 (Pf). However, α1 (Cs) is completely absent in Pf and the loop α1–α2 in Pf is much shorter, replacing α3 and α4 in Cs. (b) Superposition of the region βh–βj which, in both GluDHs, forms the recognition site for the adenine ribose moiety. (Figure prepared using MIDASPLUS [[4]57 and [5]58].)
Figure 5.
Figure 5. The cluster of isoleucine residues in the core of domain I in the Pf GluDH structure. Figure 5. The cluster of isoleucine residues in the core of domain I in the Pf GluDH structure. (Drawn with MIDASPLUS [[3]57 and [4]58].)
 
  The above figures are reprinted by permission from Cell Press: Structure (1995, 3, 1147-1158) copyright 1995.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19933355 C.Vamsee-Krishna, and P.S.Phale (2010).
Bypassing isophthalate inhibition by modulating glutamate dehydrogenase (GDH): purification and kinetic characterization of NADP-GDHs from isophthalate-degrading Pseudomonas aeruginosa strain PP4 and Acinetobacter lwoffii strain ISP4.
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19007309 C.Ottmann, M.Weyand, A.Wolf, J.Kuhlmann, and C.Ottmann (2009).
Applicability of superfolder YFP bimolecular fluorescence complementation in vitro.
  Biol Chem, 390, 81-90.
PDB code: 3ed8
19531491 M.Li, C.J.Smith, M.T.Walker, and T.J.Smith (2009).
Novel inhibitors complexed with glutamate dehydrogenase: allosteric regulation by control of protein dynamics.
  J Biol Chem, 284, 22988-23000.
PDB codes: 3etd 3ete 3etg
20054483 S.Wang, Y.B.Yan, and Z.Y.Dong (2009).
Contributions of the C-Terminal Helix to the Structural Stability of a Hyperthermophilic Fe-Superoxide Dismutase (TcSOD).
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18931414 H.Yamamoto, K.Takio, M.Sugahara, and N.Kunishima (2008).
Structure of a haloacid dehalogenase superfamily phosphatase PH1421 from Pyrococcus horikoshii OT3: oligomeric state and thermoadaptation mechanism.
  Acta Crystallogr D Biol Crystallogr, 64, 1068-1077.
PDB code: 1wr8
18391411 K.Shimizu, C.Kuroishi, M.Sugahara, and N.Kunishima (2008).
Structure of peptidyl-tRNA hydrolase 2 from Pyrococcus horikoshii OT3: insight into the functional role of its dimeric state.
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PDB codes: 1wn2 2d3k
18779322 M.Ge, X.Y.Xia, and X.M.Pan (2008).
Salt bridges in the hyperthermophilic protein ssh10b are resilient to temperature increases.
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18340444 M.S.Kim, and X.G.Lei (2008).
Enhancing thermostability of Escherichia coli phytase AppA2 by error-prone PCR.
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Identification of two major ammonia-releasing reactions involved in secondary natto fermentation.
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18819805 T.J.Smith, and C.A.Stanley (2008).
Untangling the glutamate dehydrogenase allosteric nightmare.
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18291415 T.S.Stolworthy, A.M.Korkegian, C.L.Willmon, A.Ardiani, J.Cundiff, B.L.Stoddard, and M.E.Black (2008).
Yeast cytosine deaminase mutants with increased thermostability impart sensitivity to 5-fluorocytosine.
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18840883 V.M.Hernández-Rocamora, B.Maestro, A.Mollá-Morales, and J.M.Sanz (2008).
Rational stabilization of the C-LytA affinity tag by protein engineering.
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18422647 Y.Koga, R.Katsumi, D.J.You, H.Matsumura, K.Takano, and S.Kanaya (2008).
Crystal structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon in a dimeric form.
  FEBS J, 275, 2632-2643.
PDB code: 2zf5
17905878 H.Sakuraba, K.Yoneda, K.Yoshihara, K.Satoh, R.Kawakami, Y.Uto, H.Tsuge, K.Takahashi, H.Hori, and T.Ohshima (2007).
Sequential aldol condensation catalyzed by hyperthermophilic 2-deoxy-d-ribose-5-phosphate aldolase.
  Appl Environ Microbiol, 73, 7427-7434.
PDB code: 1vcv
17683331 I.Matsui, and K.Harata (2007).
Implication for buried polar contacts and ion pairs in hyperthermostable enzymes.
  FEBS J, 274, 4012-4022.  
17430559 K.Mizuguchi, M.Sele, and M.V.Cubellis (2007).
Environment specific substitution tables for thermophilic proteins.
  BMC Bioinformatics, 8, S15.  
17507377 M.M.Choi, E.A.Kim, S.J.Yang, S.Y.Choi, S.W.Cho, and J.W.Huh (2007).
Amino acid changes within antenna helix are responsible for different regulatory preferences of human glutamate dehydrogenase isozymes.
  J Biol Chem, 282, 19510-19517.  
17394655 R.B.Greaves, and J.Warwicker (2007).
Mechanisms for stabilisation and the maintenance of solubility in proteins from thermophiles.
  BMC Struct Biol, 7, 18.  
17401542 R.Stokke, M.Karlström, N.Yang, I.Leiros, R.Ladenstein, N.K.Birkeland, and I.H.Steen (2007).
Thermal stability of isocitrate dehydrogenase from Archaeoglobus fulgidus studied by crystal structure analysis and engineering of chimers.
  Extremophiles, 11, 481-493.
PDB code: 2iv0
17327673 S.Yoshikawa, R.Arai, Y.Kinoshita, T.Uchikubo-Kamo, T.Wakamatsu, R.Akasaka, R.Masui, T.Terada, S.Kuramitsu, M.Shirouzu, and S.Yokoyama (2007).
Structure of archaeal glyoxylate reductase from Pyrococcus horikoshii OT3 complexed with nicotinamide adenine dinucleotide phosphate.
  Acta Crystallogr D Biol Crystallogr, 63, 357-365.
PDB codes: 2dbq 2dbr 2dbz
17407260 Y.N.Kang, A.Tran, R.H.White, and S.E.Ealick (2007).
A novel function for the N-terminal nucleophile hydrolase fold demonstrated by the structure of an archaeal inosine monophosphate cyclohydrolase.
  Biochemistry, 46, 5050-5062.
PDB codes: 2ntk 2ntl 2ntm
16369541 J.D.Pédelacq, S.Cabantous, T.Tran, T.C.Terwilliger, and G.S.Waldo (2006).
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PDB codes: 2b3p 2b3q
16929110 L.Arnfors, T.Hansen, P.Schönheit, R.Ladenstein, and W.Meining (2006).
Structure of Methanocaldococcus jannaschii nucleoside kinase: an archaeal member of the ribokinase family.
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PDB codes: 2c49 2c4e
16551626 L.J.Falomir-Lockhart, L.Laborde, P.C.Kahn, J.Storch, and B.Córsico (2006).
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16759231 M.Karlström, I.H.Steen, D.Madern, A.E.Fedöy, N.K.Birkeland, and R.Ladenstein (2006).
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Antioxidant Dps protein from the thermophilic cyanobacterium Thermosynechococcus elongatus.
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PDB code: 2c41
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Hyperthermal stability of neuroglobin and cytoglobin.
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16247799 Ihsanawati, T.Kumasaka, T.Kaneko, C.Morokuma, R.Yatsunami, T.Sato, S.Nakamura, and N.Tanaka (2005).
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PDB codes: 1vbr 1vbu
15727821 J.B.Carrigan, S.Coughlan, and P.C.Engel (2005).
Properties of the thermostable glutamate dehydrogenase of the mesophilic anaerobe Peptostreptoccus asaccharolyticus purified by a novel method after over-expression in an Escherichia coli host.
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16244435 M.I.Khan, K.Ito, H.Kim, H.Ashida, T.Ishikawa, H.Shibata, and Y.Sawa (2005).
Molecular properties and enhancement of thermostability by random mutagenesis of glutamate dehydrogenase from Bacillus subtilis.
  Biosci Biotechnol Biochem, 69, 1861-1870.  
16239727 M.Sugahara, N.Ohshima, Y.Ukita, M.Sugahara, and N.Kunishima (2005).
Structure of ATP-dependent phosphoenolpyruvate carboxykinase from Thermus thermophilus HB8 showing the structural basis of induced fit and thermostability.
  Acta Crystallogr D Biol Crystallogr, 61, 1500-1507.
PDB codes: 1j3b 1xkv
14695284 B.Liu, M.Bartlam, R.Gao, W.Zhou, H.Pang, Y.Liu, Y.Feng, and Z.Rao (2004).
Crystal structure of the hyperthermophilic inorganic pyrophosphatase from the archaeon Pyrococcus horikoshii.
  Biophys J, 86, 420-427.
PDB code: 1ude
14977044 D.Triantafillidou, E.Persidou, D.Lazarou, P.Andrikopoulos, F.Leontiadou, and T.Choli-Papadopoulou (2004).
Structural destabilization of the recombinant thermophilic TthL11 ribosomal protein by a single amino acid substitution.
  Biol Chem, 385, 31-39.  
14765110 H.Nummelin, M.C.Merckel, J.C.Leo, H.Lankinen, M.Skurnik, and A.Goldman (2004).
The Yersinia adhesin YadA collagen-binding domain structure is a novel left-handed parallel beta-roll.
  EMBO J, 23, 701-711.
PDB code: 1p9h
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Structure and implications for the thermal stability of phosphopantetheine adenylyltransferase from Thermus thermophilus.
  Acta Crystallogr D Biol Crystallogr, 60, 97.
PDB code: 1od6
14573594 J.M.Choi, E.Y.Park, J.H.Kim, S.K.Chang, and Y.Cho (2004).
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  J Biol Chem, 279, 755-764.
PDB codes: 1r6l 1r6m
15039563 M.W.Bhuiya, H.Sakuraba, K.Yoneda, T.Ohshima, T.Imagawa, N.Katunuma, and H.Tsuge (2004).
Crystallization and preliminary X-ray diffraction analysis of the hyperthermostable NAD-dependent glutamate dehydrogenase from Pyrobaculum islandicum.
  Acta Crystallogr D Biol Crystallogr, 60, 715-717.  
14718652 N.Palackal, Y.Brennan, W.N.Callen, P.Dupree, G.Frey, F.Goubet, G.P.Hazlewood, S.Healey, Y.E.Kang, K.A.Kretz, E.Lee, X.Tan, G.L.Tomlinson, J.Verruto, V.W.Wong, E.J.Mathur, J.M.Short, D.E.Robertson, and B.A.Steer (2004).
An evolutionary route to xylanase process fitness.
  Protein Sci, 13, 494-503.  
15557260 S.Sakasegawa, C.H.Hagemeier, R.K.Thauer, L.O.Essen, and S.Shima (2004).
Structural and functional analysis of the gpsA gene product of Archaeoglobus fulgidus: a glycerol-3-phosphate dehydrogenase with an unusual NADP+ preference.
  Protein Sci, 13, 3161-3171.
PDB code: 1txg
15206928 Y.Hioki, K.Ogasahara, S.J.Lee, J.Ma, M.Ishida, Y.Yamagata, Y.Matsuura, M.Ota, M.Ikeguchi, S.Kuramitsu, and K.Yutani (2004).
The crystal structure of the tryptophan synthase beta subunit from the hyperthermophile Pyrococcus furiosus. Investigation of stabilization factors.
  Eur J Biochem, 271, 2624-2635.
PDB code: 1v8z
14747705 Y.Maruyama, N.Maruyama, B.Mikami, and S.Utsumi (2004).
Structure of the core region of the soybean beta-conglycinin alpha' subunit.
  Acta Crystallogr D Biol Crystallogr, 60, 289-297.
PDB code: 1uik
12557192 A.D.Gruia, S.Fischer, and J.C.Smith (2003).
Molecular dynamics simulation reveals a surface salt bridge forming a kinetic trap in unfolding of truncated Staphylococcal nuclease.
  Proteins, 50, 507-515.  
12796486 J.M.Berrisford, J.Akerboom, A.P.Turnbull, D.de Geus, S.E.Sedelnikova, I.Staton, C.W.McLeod, C.H.Verhees, J.van der Oost, D.W.Rice, and P.J.Baker (2003).
Crystal structure of Pyrococcus furiosus phosphoglucose isomerase. Implications for substrate binding and catalysis.
  J Biol Chem, 278, 33290-33297.
PDB code: 1plz
12643278 K.Ogasahara, M.Ishida, and K.Yutani (2003).
Stimulated interaction between and subunits of tryptophan synthase from hyperthermophile enhances its thermal stability.
  J Biol Chem, 278, 8922-8928.  
12672826 T.Hatta, G.Mukerjee-Dhar, J.Damborsky, H.Kiyohara, and K.Kimbara (2003).
Characterization of a novel thermostable Mn(II)-dependent 2,3-dihydroxybiphenyl 1,2-dioxygenase from a polychlorinated biphenyl- and naphthalene-degrading Bacillus sp. JF8.
  J Biol Chem, 278, 21483-21492.  
12012341 B.Cobucci-Ponzano, M.Moracci, B.Di Lauro, M.Ciaramella, R.D'Avino, and M.Rossi (2002).
Ionic network at the C-terminus of the beta-glycosidase from the hyperthermophilic archaeon Sulfolobus solfataricus: Functional role in the quaternary structure thermal stabilization.
  Proteins, 48, 98.  
12382287 C.Charron, B.Vitoux, and A.Aubry (2002).
Comparative analysis of thermoadaptation within the archaeal glyceraldehyde-3-phosphate dehydrogenases from mesophilic Methanobacterium bryantii and thermophilic Methanothermus fervidus.
  Biopolymers, 65, 263-273.  
12060744 D.H.Shin, H.Yokota, R.Kim, and S.H.Kim (2002).
Crystal structure of conserved hypothetical protein Aq1575 from Aquifex aeolicus.
  Proc Natl Acad Sci U S A, 99, 7980-7985.
PDB code: 1lfp
11933070 G.Gianese, F.Bossa, and S.Pascarella (2002).
Comparative structural analysis of psychrophilic and meso- and thermophilic enzymes.
  Proteins, 47, 236-249.  
12473121 G.S.Bell, R.J.Russell, H.Connaris, D.W.Hough, M.J.Danson, and G.L.Taylor (2002).
Stepwise adaptations of citrate synthase to survival at life's extremes. From psychrophile to hyperthermophile.
  Eur J Biochem, 269, 6250-6260.
PDB code: 1o7x
12193607 H.Y.Yoon, E.H.Cho, H.Y.Kwon, S.Y.Choi, and S.W.Cho (2002).
Importance of glutamate 279 for the coenzyme binding of human glutamate dehydrogenase.
  J Biol Chem, 277, 41448-41454.  
11847291 K.S.Lassila, D.Datta, and S.L.Mayo (2002).
Evaluation of the energetic contribution of an ionic network to beta-sheet stability.
  Protein Sci, 11, 688-690.  
11788950 M.McMahon, and P.Mulcahy (2002).
Bioaffinity purification of NADP(+)-dependent dehydrogenases: studies with alcohol dehydrogenase from Thermoanaerobacter brockii.
  Biotechnol Bioeng, 77, 517-527.  
12136148 M.W.Bhuiya, H.Tsuge, H.Sakuraba, K.Yoneda, N.Katunuma, and T.Ohshima (2002).
Crystallization and preliminary X-ray diffraction analysis of glutamate dehydrogenase from an aerobic hyperthermophilic archaeon, Aeropyrum pernix K1.
  Acta Crystallogr D Biol Crystallogr, 58, 1338-1339.  
12381840 O.Bogin, I.Levin, Y.Hacham, S.Tel-Or, M.Peretz, F.Frolow, and Y.Burstein (2002).
Structural basis for the enhanced thermal stability of alcohol dehydrogenase mutants from the mesophilic bacterium Clostridium beijerinckii: contribution of salt bridging.
  Protein Sci, 11, 2561-2574.
PDB code: 1jqb
  16233344 S.Fujiwara (2002).
Extremophiles: developments of their special functions and potential resources.
  J Biosci Bioeng, 94, 518-525.  
12202384 S.Kumar, and R.Nussinov (2002).
Relationship between ion pair geometries and electrostatic strengths in proteins.
  Biophys J, 83, 1595-1612.  
11900534 S.Ramón-Maiques, H.G.Britton, and V.Rubio (2002).
Molecular physiology of phosphoryl group transfer from carbamoyl phosphate by a hyperthermophilic enzyme at low temperature.
  Biochemistry, 41, 3916-3924.  
11562373 A.DeLuna, A.Avendano, L.Riego, and A.Gonzalez (2001).
NADP-glutamate dehydrogenase isoenzymes of Saccharomyces cerevisiae. Purification, kinetic properties, and physiological roles.
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11551792 A.Karshikoff, and R.Ladenstein (2001).
Ion pairs and the thermotolerance of proteins from hyperthermophiles: a "traffic rule" for hot roads.
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11238984 C.Vieille, and G.J.Zeikus (2001).
Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability.
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11342043 K.Numata, Y.Hayashi-Iwasaki, J.Kawaguchi, M.Sakurai, H.Moriyama, N.Tanaka, and T.Oshima (2001).
Thermostabilization of a chimeric enzyme by residue substitutions: four amino acid residues in loop regions are responsible for the thermostability of Thermus thermophilus isopropylmalate dehydrogenase.
  Biochim Biophys Acta, 1545, 174-183.  
11389725 K.Ogasahara, N.N.Khechinashvili, M.Nakamura, T.Yoshimoto, and K.Yutani (2001).
Thermal stability of pyrrolidone carboxyl peptidases from the hyperthermophilic Archaeon, Pyrococcus furiosus.
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11488906 K.Shiraki, S.Nishikori, S.Fujiwara, H.Hashimoto, Y.Kai, M.Takagi, and T.Imanaka (2001).
Comparative analyses of the conformational stability of a hyperthermophilic protein and its mesophilic counterpart.
  Eur J Biochem, 268, 4144-4150.  
11679715 M.J.Banfield, J.S.Lott, V.L.Arcus, A.A.McCarthy, and E.N.Baker (2001).
Structure of HisF, a histidine biosynthetic protein from Pyrobaculum aerophilum.
  Acta Crystallogr D Biol Crystallogr, 57, 1518-1525.
PDB code: 1h5y
11258921 M.Nakasako, T.Fujisawa, S.Adachi, T.Kudo, and S.Higuchi (2001).
Large-scale domain movements and hydration structure changes in the active-site cleft of unligated glutamate dehydrogenase from Thermococcus profundus studied by cryogenic X-ray crystal structure analysis and small-angle X-ray scattering.
  Biochemistry, 40, 3069-3079.
PDB code: 1euz
11375518 S.E.Sedelnikova, S.H.Smits, P.M.Leonard, A.B.Brinkman, J.van der Oost, J.B.Rafferty, and D.W.Rice (2001).
Crystallization and quaternary structure analysis of an Lrp-like regulatory protein from the hyperthermophile Pyrococcus furiosus.
  Acta Crystallogr D Biol Crystallogr, 57, 886-888.  
10801491 A.Szilágyi, and P.Závodszky (2000).
Structural differences between mesophilic, moderately thermophilic and extremely thermophilic protein subunits: results of a comprehensive survey.
  Structure, 8, 493-504.  
10788490 G.Gonzalez-Blasco, J.Sanz-Aparicio, B.Gonzalez, J.A.Hermoso, and J.Polaina (2000).
Directed evolution of beta -glucosidase A from Paenibacillus polymyxa to thermal resistance.
  J Biol Chem, 275, 13708-13712.  
10632710 G.Nicastro, C.De Chiara, E.Pedone, M.Tatò, M.Rossi, and S.Bartolucci (2000).
NMR solution structure of a novel thioredoxin from Bacillus acidocaldarius possible determinants of protein stability.
  Eur J Biochem, 267, 403-413.
PDB code: 1quw
11015217 K.Takano, K.Tsuchimori, Y.Yamagata, and K.Yutani (2000).
Contribution of salt bridges near the surface of a protein to the conformational stability.
  Biochemistry, 39, 12375-12381.
PDB codes: 1eq4 1eq5 1eqe
11087953 N.Panasik, J.E.Brenchley, and G.K.Farber (2000).
Distributions of structural features contributing to thermostability in mesophilic and thermophilic alpha/beta barrel glycosyl hydrolases.
  Biochim Biophys Acta, 1543, 189-201.  
10684603 P.Strop, and S.L.Mayo (2000).
Contribution of surface salt bridges to protein stability.
  Biochemistry, 39, 1251-1255.
PDB code: 1qcv
10601858 R.Di Fraia, V.Wilquet, M.A.Ciardiello, V.Carratore, A.Antignani, L.Camardella, N.Glansdorff, and G.Di Prisco (2000).
NADP+-dependent glutamate dehydrogenase in the Antarctic psychrotolerant bacterium Psychrobacter sp. TAD1. Characterization, protein and DNA sequence, and relationship to other glutamate dehydrogenases.
  Eur J Biochem, 267, 121-131.  
10653643 S.B.Richard, D.Madern, E.Garcin, and G.Zaccai (2000).
Halophilic adaptation: novel solvent protein interactions observed in the 2.9 and 2.6 A resolution structures of the wild type and a mutant of malate dehydrogenase from Haloarcula marismortui.
  Biochemistry, 39, 992.
PDB codes: 1d3a 2hlp
10861939 S.D'Auria, P.Herman, J.R.Lakowicz, F.Tanfani, E.Bertoli, G.Manco, and M.Rossi (2000).
The esterase from the thermophilic eubacterium Bacillus acidocaldarius: structural-functional relationship and comparison with the esterase from the hyperthermophilic archaeon Archaeoglobus fulgidus.
  Proteins, 40, 473-481.  
10707024 S.Kumar, B.Ma, C.J.Tsai, and R.Nussinov (2000).
Electrostatic strengths of salt bridges in thermophilic and mesophilic glutamate dehydrogenase monomers.
  Proteins, 38, 368-383.  
11080642 T.Kajander, P.C.Kahn, S.H.Passila, D.C.Cohen, L.Lehtiö, W.Adolfsen, J.Warwicker, U.Schell, and A.Goldman (2000).
Buried charged surface in proteins.
  Structure, 8, 1203-1214.
PDB code: 1f9c
10520251 C.J.Beverung, C.J.Radke, and H.W.Blanch (1999).
Protein adsorption at the oil/water interface: characterization of adsorption kinetics by dynamic interfacial tension measurements.
  Biophys Chem, 81, 59-80.  
10651277 C.Li, J.Heatwole, S.Soelaiman, and M.Shoham (1999).
Crystal structure of a thermophilic alcohol dehydrogenase substrate complex suggests determinants of substrate specificity and thermostability.
  Proteins, 37, 619-627.
PDB code: 1bxz
10591103 D.Maes, J.P.Zeelen, N.Thanki, N.Beaucamp, M.Alvarez, M.H.Thi, J.Backmann, J.A.Martial, L.Wyns, R.Jaenicke, and R.K.Wierenga (1999).
The crystal structure of triosephosphate isomerase (TIM) from Thermotoga maritima: a comparative thermostability structural analysis of ten different TIM structures.
  Proteins, 37, 441-453.
PDB code: 1b9b
10336462 H.Sugawara, H.Yamamoto, N.Shibata, T.Inoue, S.Okada, C.Miyake, A.Yokota, and Y.Kai (1999).
Crystal structure of carboxylase reaction-oriented ribulose 1, 5-bisphosphate carboxylase/oxygenase from a thermophilic red alga, Galdieria partita.
  J Biol Chem, 274, 15655-15661.
PDB code: 1bwv
9873027 I.G.Choi, W.G.Bang, S.H.Kim, and Y.G.Yu (1999).
Extremely thermostable serine-type protease from Aquifex pyrophilus. Molecular cloning, expression, and characterization.
  J Biol Chem, 274, 881-888.  
10608805 J.Hasegawa, H.Shimahara, M.Mizutani, S.Uchiyama, H.Arai, M.Ishii, Y.Kobayashi, S.J.Ferguson, Y.Sambongi, and Y.Igarashi (1999).
Stabilization of Pseudomonas aeruginosa cytochrome c(551) by systematic amino acid substitutions based on the structure of thermophilic Hydrogenobacter thermophilus cytochrome c(552).
  J Biol Chem, 274, 37533-37537.  
10607407 J.Y.Ahn, S.Choi, and S.W.Cho (1999).
Identification of lysine residue involved in inactivation of brain glutamate dehydrogenase isoproteins by o-phthalaldehyde.
  Biochimie, 81, 1123-1129.  
  10338016 M.M.Sun, N.Tolliday, C.Vetriani, F.T.Robb, and D.S.Clark (1999).
Pressure-induced thermostabilization of glutamate dehydrogenase from the hyperthermophile Pyrococcus furiosus.
  Protein Sci, 8, 1056-1063.  
10425679 P.E.Peterson, and T.J.Smith (1999).
The structure of bovine glutamate dehydrogenase provides insights into the mechanism of allostery.
  Structure, 7, 769-782.
PDB codes: 1ch6 1hwx 3mw9
10097079 P.J.Haney, J.H.Badger, G.L.Buldak, C.I.Reich, C.R.Woese, G.J.Olsen, and C.R.Woese (1999).
Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species.
  Proc Natl Acad Sci U S A, 96, 3578-3583.  
10497207 P.J.Haney, M.Stees, and J.Konisky (1999).
Analysis of thermal stabilizing interactions in mesophilic and thermophilic adenylate kinases from the genus Methanococcus.
  J Biol Chem, 274, 28453-28458.  
  10211832 S.Aghajanian, T.P.Walsh, and P.C.Engel (1999).
Specificity of coenzyme analogues and fragments in promoting or impeding the refolding of clostridial glutamate dehydrogenase.
  Protein Sci, 8, 866-872.  
10450084 S.Hayward (1999).
Structural principles governing domain motions in proteins.
  Proteins, 36, 425-435.  
10531494 S.Higuchi, M.Nakasako, and T.Kudo (1999).
Crystallization and preliminary x-ray diffraction studies of hyperthermostable glutamate dehydrogenase from Thermococcus profundus.
  Acta Crystallogr D Biol Crystallogr, 55, 1917-1919.  
10318805 S.W.Cho, and H.Y.Yoon (1999).
Photoaffinity labeling of brain glutamate dehydrogenase isoproteins with an azido-ADP.
  J Biol Chem, 274, 13948-13953.  
10217298 S.Y.Choi, J.W.Hong, M.S.Song, S.G.Jeon, J.H.Bahn, B.R.Lee, J.Y.Ahn, and S.W.Cho (1999).
Different antigenic reactivities of bovine brain glutamate dehydrogenase isoproteins.
  J Neurochem, 72, 2162-2169.  
10206992 S.Y.Kim, K.Y.Hwang, S.H.Kim, H.C.Sung, Y.S.Han, and Y.Cho (1999).
Structural basis for cold adaptation. Sequence, biochemical properties, and crystal structure of malate dehydrogenase from a psychrophile Aquaspirillium arcticum.
  J Biol Chem, 274, 11761-11767.
PDB codes: 1b8p 1b8u 1b8v
  10386872 V.M.Leppänen, H.Nummelin, T.Hansen, R.Lahti, G.Schäfer, and A.Goldman (1999).
Sulfolobus acidocaldarius inorganic pyrophosphatase: structure, thermostability, and effect of metal ion in an archael pyrophosphatase.
  Protein Sci, 8, 1218-1231.
PDB code: 1qez
10545331 W.Grabarse, M.Vaupel, J.A.Vorholt, S.Shima, R.K.Thauer, A.Wittershagen, G.Bourenkov, H.D.Bartunik, and U.Ermler (1999).
The crystal structure of methenyltetrahydromethanopterin cyclohydrolase from the hyperthermophilic archaeon Methanopyrus kandleri.
  Structure, 7, 1257-1268.
PDB code: 1qlm
  10417229 Y.Korkhin, A.J.Kalb (Gilboa), M.Peretz, O.Bogin, Y.Burstein, and F.Frolow (1999).
Oligomeric integrity--the structural key to thermal stability in bacterial alcohol dehydrogenases.
  Protein Sci, 8, 1241-1249.  
10545321 Y.Zhao, D.Jeruzalmi, I.Moarefi, L.Leighton, R.Lasken, and J.Kuriyan (1999).
Crystal structure of an archaebacterial DNA polymerase.
  Structure, 7, 1189-1199.
PDB codes: 1d5a 1qqc
  9829940 B.R.Belitsky, and A.L.Sonenshein (1998).
Role and regulation of Bacillus subtilis glutamate dehydrogenase genes.
  J Bacteriol, 180, 6298-6305.  
9482837 B.Van den Burg, G.Vriend, O.R.Veltman, G.Venema, and V.G.Eijsink (1998).
Engineering an enzyme to resist boiling.
  Proc Natl Acad Sci U S A, 95, 2056-2060.  
9582288 C.Berthet-Colominas, L.Seignovert, M.Härtlein, M.Grotli, S.Cusack, and R.Leberman (1998).
The crystal structure of asparaginyl-tRNA synthetase from Thermus thermophilus and its complexes with ATP and asparaginyl-adenylate: the mechanism of discrimination between asparagine and aspartic acid.
  EMBO J, 17, 2947-2960.  
  9603828 C.Kujo, and T.Ohshima (1998).
Enzymological characteristics of the hyperthermostable NAD-dependent glutamate dehydrogenase from the archaeon Pyrobaculum islandicum and effects of denaturants and organic solvents.
  Appl Environ Microbiol, 64, 2152-2157.  
9770481 C.Vetriani, D.L.Maeder, N.Tolliday, K.S.Yip, T.J.Stillman, K.L.Britton, D.W.Rice, H.H.Klump, and F.T.Robb (1998).
Protein thermostability above 100 degreesC: a key role for ionic interactions.
  Proc Natl Acad Sci U S A, 95, 12300-12305.  
  9828010 E.J.Spek, A.H.Bui, M.Lu, and N.R.Kallenbach (1998).
Surface salt bridges stabilize the GCN4 leucine zipper.
  Protein Sci, 7, 2431-2437.  
10089525 G.S.Bell, R.J.Russell, M.Kohlhoff, R.Hensel, M.J.Danson, D.W.Hough, and G.L.Taylor (1998).
Preliminary crystallographic studies of triosephosphate isomerase (TIM) from the hyperthermophilic Archaeon Pyrococcus woesei.
  Acta Crystallogr D Biol Crystallogr, 54, 1419-1421.  
9849940 J.Sanz-Aparicio, J.A.Hermoso, M.Martínez-Ripoll, B.González, C.López-Camacho, and J.Polaina (1998).
Structural basis of increased resistance to thermal denaturation induced by single amino acid substitution in the sequence of beta-glucosidase A from Bacillus polymyxa.
  Proteins, 33, 567-576.
PDB code: 1e4i
  9521117 K.C.Usher, A.F.de la Cruz, F.W.Dahlquist, R.V.Swanson, M.I.Simon, and S.J.Remington (1998).
Crystal structures of CheY from Thermotoga maritima do not support conventional explanations for the structural basis of enhanced thermostability.
  Protein Sci, 7, 403-412.
PDB codes: 1tmy 2tmy 3tmy 4tmy
9753433 K.Gruber, G.Klintschar, M.Hayn, A.Schlacher, W.Steiner, and C.Kratky (1998).
Thermophilic xylanase from Thermomyces lanuginosus: high-resolution X-ray structure and modeling studies.
  Biochemistry, 37, 13475-13485.
PDB code: 1yna
9535890 K.L.Britton, T.J.Stillman, K.S.Yip, P.Forterre, P.C.Engel, and D.W.Rice (1998).
Insights into the molecular basis of salt tolerance from the study of glutamate dehydrogenase from Halobacterium salinarum.
  J Biol Chem, 273, 9023-9030.  
9558328 K.Ogasahara, E.A.Lapshina, M.Sakai, Y.Izu, S.Tsunasawa, I.Kato, and K.Yutani (1998).
Electrostatic stabilization in methionine aminopeptidase from hyperthermophile Pyrococcus furiosus.
  Biochemistry, 37, 5939-5946.  
9860869 K.Ogasahara, M.Nakamura, S.Nakura, S.Tsunasawa, I.Kato, T.Yoshimoto, and K.Yutani (1998).
The unusually slow unfolding rate causes the high stability of pyrrolidone carboxyl peptidase from a hyperthermophile, Pyrococcus furiosus: equilibrium and kinetic studies of guanidine hydrochloride-induced unfolding and refolding.
  Biochemistry, 37, 17537-17544.  
9715904 M.B.Berry, and G.N.Phillips (1998).
Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+.
  Proteins, 32, 276-288.
PDB codes: 1zin 1zio 1zip
  9829929 M.Haruki, K.Hayashi, T.Kochi, A.Muroya, Y.Koga, M.Morikawa, T.Imanaka, and S.Kanaya (1998).
Gene cloning and characterization of recombinant RNase HII from a hyperthermophilic archaeon.
  J Bacteriol, 180, 6207-6214.  
9817845 M.Hilge, S.M.Gloor, W.Rypniewski, O.Sauer, T.D.Heightman, W.Zimmermann, K.Winterhalter, and K.Piontek (1998).
High-resolution native and complex structures of thermostable beta-mannanase from Thermomonospora fusca - substrate specificity in glycosyl hydrolase family 5.
  Structure, 6, 1433-1444.
PDB codes: 1bqc 2man 3man
9746940 M.J.Danson, and D.W.Hough (1998).
Structure, function and stability of enzymes from the Archaea.
  Trends Microbiol, 6, 307-314.  
9720321 M.W.Adams, and R.M.Kelly (1998).
Finding and using hyperthermophilic enzymes.
  Trends Biotechnol, 16, 329-332.  
  9836874 O.Bogin, M.Peretz, Y.Hacham, Y.Korkhin, F.Frolow, A.J.Kalb(Gilboa), and Y.Burstein (1998).
Enhanced thermal stability of Clostridium beijerinckii alcohol dehydrogenase after strategic substitution of amino acid residues with prolines from the homologous thermophilic Thermoanaerobacter brockii alcohol dehydrogenase.
  Protein Sci, 7, 1156-1163.  
9551556 R.J.Russell, U.Gerike, M.J.Danson, D.W.Hough, and G.L.Taylor (1998).
Structural adaptations of the cold-active citrate synthase from an Antarctic bacterium.
  Structure, 6, 351-361.
PDB code: 1a59
9914256 R.Jaenicke, and G.Böhm (1998).
The stability of proteins in extreme environments.
  Curr Opin Struct Biol, 8, 738-748.  
9893953 R.Scandurra, V.Consalvi, R.Chiaraluce, L.Politi, and P.C.Engel (1998).
Protein thermostability in extremophiles.
  Biochimie, 80, 933-941.  
9893955 S.D'Auria, M.Moracci, F.Febbraio, F.Tanfani, R.Nucci, and M.Rossi (1998).
Structure-function studies on beta-glycosidase from Sulfolobus solfataricus. Molecular bases of thermostability.
  Biochimie, 80, 949-957.  
  9568903 S.Millevoi, A.Pasquo, R.Chiaraluce, V.Consalvi, L.Giangiacomo, K.L.Britton, T.J.Stillman, D.W.Rice, and P.C.Engel (1998).
A monomeric mutant of Clostridium symbiosum glutamate dehydrogenase: comparison with a structured monomeric intermediate obtained during refolding.
  Protein Sci, 7, 966-974.  
9813015 S.W.Cho, H.Y.Yoon, J.Y.Ahn, S.Y.Choi, and T.U.Kim (1998).
Identification of an NAD+ binding site of brain glutamate dehydrogenase isoproteins by photoaffinity labeling.
  J Biol Chem, 273, 31125-31130.  
9501170 V.Villeret, B.Clantin, C.Tricot, C.Legrain, M.Roovers, V.Stalon, N.Glansdorff, and J.Van Beeumen (1998).
The crystal structure of Pyrococcus furiosus ornithine carbamoyltransferase reveals a key role for oligomerization in enzyme stability at extremely high temperatures.
  Proc Natl Acad Sci U S A, 95, 2801-2806.
PDB code: 1a1s
9692946 W.Zhu, K.Sandman, G.E.Lee, J.N.Reeve, and M.F.Summers (1998).
NMR structure and comparison of the archaeal histone HFoB from the mesophile Methanobacterium formicicum with HMfB from the hyperthermophile Methanothermus fervidus.
  Biochemistry, 37, 10573-10580.  
9188741 A.V.Efimov (1997).
Structural trees for protein superfamilies.
  Proteins, 28, 241-260.  
9288930 C.Legrain, V.Villeret, M.Roovers, D.Gigot, O.Dideberg, A.Piérard, and N.Glansdorff (1997).
Biochemical characterisation of ornithine carbamoyltransferase from Pyrococcus furiosus.
  Eur J Biochem, 247, 1046-1055.  
9016716 J.R.Kiefer, C.Mao, C.J.Hansen, S.L.Basehore, H.H.Hogrefe, J.C.Braman, and L.S.Beese (1997).
Crystal structure of a thermostable Bacillus DNA polymerase I large fragment at 2.1 A resolution.
  Structure, 5, 95.
PDB codes: 1bdp 1xwl
  9165087 L.Prade, P.Hof, and B.Bieseler (1997).
Dimer interface of glutathione S-transferase from Arabidopsis thaliana: influence of the G-site architecture on the dimer interface and implications for classification.
  Biol Chem, 378, 317-320.  
9166771 M.Hennig, R.Sterner, K.Kirschner, and J.N.Jansonius (1997).
Crystal structure at 2.0 A resolution of phosphoribosyl anthranilate isomerase from the hyperthermophile Thermotoga maritima: possible determinants of protein stability.
  Biochemistry, 36, 6009-6016.
PDB code: 1nsj
9380682 O.Guipaud, E.Marguet, K.M.Noll, C.B.de la Tour, and P.Forterre (1997).
Both DNA gyrase and reverse gyrase are present in the hyperthermophilic bacterium Thermotoga maritima.
  Proc Natl Acad Sci U S A, 94, 10606-10611.  
9249030 R.Chiaraluce, R.M.Schwerdtfeger, R.Scandurra, G.Antranikian, and V.Consalvi (1997).
Acid-induced disassembly of glutamate dehydrogenase from the hyperthermophilic archaeon Pyrococcus furiosus occurs below pH 2.0.
  Eur J Biochem, 247, 224-230.  
9254593 R.J.Russell, J.M.Ferguson, D.W.Hough, M.J.Danson, and G.L.Taylor (1997).
The crystal structure of citrate synthase from the hyperthermophilic archaeon pyrococcus furiosus at 1.9 A resolution,.
  Biochemistry, 36, 9983-9994.
PDB code: 1aj8
  9416608 T.Lazaridis, I.Lee, and M.Karplus (1997).
Dynamics and unfolding pathways of a hyperthermophilic and a mesophilic rubredoxin.
  Protein Sci, 6, 2589-2605.  
9020134 T.Yano, S.S.Chu, V.D.Sled', T.Ohnishi, and T.Yagi (1997).
The proton-translocating NADH-quinone oxidoreductase (NDH-1) of thermophilic bacterium Thermus thermophilus HB-8. Complete DNA sequence of the gene cluster and thermostable properties of the expressed NQO2 subunit.
  J Biol Chem, 272, 4201-4211.  
9195883 U.Ermler, M.Merckel, R.Thauer, and S.Shima (1997).
Formylmethanofuran: tetrahydromethanopterin formyltransferase from Methanopyrus kandleri - new insights into salt-dependence and thermostability.
  Structure, 5, 635-646.
PDB code: 1ftr
9154922 V.Lounnas, and R.C.Wade (1997).
Exceptionally stable salt bridges in cytochrome P450cam have functional roles.
  Biochemistry, 36, 5402-5417.  
  8931142 D.H.Shin, H.K.Song, I.S.Seong, C.S.Lee, C.H.Chung, and S.W.Suh (1996).
Crystal structure analyses of uncomplexed ecotin in two crystal forms: implications for its function and stability.
  Protein Sci, 5, 2236-2247.
PDB codes: 1ecy 1ecz
8639325 D.W.Rice, K.S.Yip, T.J.Stillman, K.L.Britton, A.Fuentes, I.Connerton, A.Pasquo, R.Scandura, and P.C.Engel (1996).
Insights into the molecular basis of thermal stability from the structure determination of Pyrococcus furiosus glutamate dehydrogenase.
  FEMS Microbiol Rev, 18, 105-117.  
8885833 G.Scapin, S.G.Reddy, and J.S.Blanchard (1996).
Three-dimensional structure of meso-diaminopimelic acid dehydrogenase from Corynebacterium glutamicum.
  Biochemistry, 35, 13540-13551.
PDB code: 1dap
8793300 J.Mayr, A.Lupas, J.Kellermann, C.Eckerskorn, W.Baumeister, and J.Peters (1996).
A hyperthermostable protease of the subtilisin family bound to the surface layer of the archaeon Staphylothermus marinus.
  Curr Biol, 6, 739-749.  
8784186 P.L.Wang, A.Donaire, Z.H.Zhou, M.W.Adams, and G.N.La Mar (1996).
Molecular model of the solution structure for the paramagnetic four-iron ferredoxin from the hyperthermophilic archaeon Thermococcus litoralis.
  Biochemistry, 35, 11319-11328.  
8736555 S.Iwata, M.Saynovits, T.A.Link, and H.Michel (1996).
Structure of a water soluble fragment of the 'Rieske' iron-sulfur protein of the bovine heart mitochondrial cytochrome bc1 complex determined by MAD phasing at 1.5 A resolution.
  Structure, 4, 567-579.
PDB code: 1rie
8939753 S.Macedo-Ribeiro, B.Darimont, R.Sterner, and R.Huber (1996).
Small structural changes account for the high thermostability of 1[4Fe-4S] ferredoxin from the hyperthermophilic bacterium Thermotoga maritima.
  Structure, 4, 1291-1301.
PDB code: 1vjw
8880936 S.Shima, R.K.Thauer, H.Michel, and U.Ermler (1996).
Crystallization and preliminary X-ray diffraction studies of formylmethanofuran: tetrahydromethanopterin formyltransferase from Methanopyrus kandleri.
  Proteins, 26, 118-120.  
  8762133 T.Salminen, A.Teplyakov, J.Kankare, B.S.Cooperman, R.Lahti, and A.Goldman (1996).
An unusual route to thermostability disclosed by the comparison of Thermus thermophilus and Escherichia coli inorganic pyrophosphatases.
  Protein Sci, 5, 1014-1025.  
8774713 V.Consalvi, R.Chiaraluce, S.Millevoi, A.Pasquo, P.Vecchini, E.Chiancone, and R.Scandurra (1996).
Refolding pathway and association intermediates of glutamate dehydrogenase from the hyperthermophile Pyrococcus furiosus.
  Eur J Biochem, 239, 679-685.  
8747452 A.Goldman (1995).
How to make my blood boil.
  Structure, 3, 1277-1279.  
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