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PDBsum entry 1aj8

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protein ligands Protein-protein interface(s) links
Lyase PDB id
1aj8
Jmol
Contents
Protein chains
371 a.a. *
Ligands
COA ×2
CIT ×2
Waters ×482
* Residue conservation analysis
PDB id:
1aj8
Name: Lyase
Title: Citrate synthase from pyrococcus furiosus
Structure: Citrate synthase. Chain: a, b. Engineered: yes
Source: Pyrococcus furiosus. Organism_taxid: 2261. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
Resolution:
1.90Å     R-factor:   0.191     R-free:   0.232
Authors: R.J.M.Russell,J.M.C.Ferguson,D.W.Hough,M.J.Danson,G.L.Taylor
Key ref:
R.J.Russell et al. (1997). The crystal structure of citrate synthase from the hyperthermophilic archaeon pyrococcus furiosus at 1.9 A resolution,. Biochemistry, 36, 9983-9994. PubMed id: 9254593 DOI: 10.1021/bi9705321
Date:
16-May-97     Release date:   19-Nov-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q53554  (CISY_PYRFU) -  Citrate synthase
Seq:
Struc:
377 a.a.
371 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.3.3.16  - Citrate synthase (unknown stereospecificity).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Acetyl-CoA + H2O + oxaloacetate = citrate + CoA
Acetyl-CoA
Bound ligand (Het Group name = COA)
matches with 90.00% similarity
+ H(2)O
+ oxaloacetate
=
citrate
Bound ligand (Het Group name = CIT)
corresponds exactly
+ CoA
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     metabolic process   3 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi9705321 Biochemistry 36:9983-9994 (1997)
PubMed id: 9254593  
 
 
The crystal structure of citrate synthase from the hyperthermophilic archaeon pyrococcus furiosus at 1.9 A resolution,.
R.J.Russell, J.M.Ferguson, D.W.Hough, M.J.Danson, G.L.Taylor.
 
  ABSTRACT  
 
The crystal structure of the closed form of citrate synthase, with citrate and CoA bound, from the hyperthermophilic Archaeon Pyrococcus furiosus has been determined to 1.9 A. This has allowed direct structural comparisons between the same enzyme from organisms growing optimally at 37 degrees C (pig), 55 degrees C (Thermoplasma acidophilum) and now 100 degrees C (Pyrococcus furiosus). The three enzymes are homodimers and share a similar overall fold, with the dimer interface comprising primarily an eight alpha-helical sandwich of four antiparallel pairs of helices. The active sites show similar modes of substrate binding; moreover, the structural equivalence of the amino acid residues implicated in catalysis implies that the mechanism proceeds via the same acid-base catalytic process. Given the overall structural and mechanistic similarities, it has been possible to make detailed structural comparisons between the three citrate synthases, and a number of differences can be identified in passing from the mesophilic to thermophilic to hyperthermophilic citrate synthases. The most significant of these are an increased compactness of the enzyme, a more intimate association of the subunits, an increase in intersubunit ion pairs, and a reduction in thermolabile residues. Compactness is achieved by the shortening of a number of loops, an increase in the number of atoms buried from solvent, an optimized packing of side chains in the interior, and an absence of cavities. The intimate subunit association in the dimeric P. furiosus enzyme is achieved by greater complementarity of the monomers and by the C-terminal region of each monomer folding over the surface of the other monomer, in contrast to the pig enzyme where the C-terminus has a very different fold. The increased number of intersubunit ion pairs is accompanied by an increase in the number involved in networks. Interestingly, all loop regions in the P. furiosus enzyme either are shorter or contain additional ion pairs compared with the pig enzyme. The possible relevance of these structural features to enzyme hyperthermostability is discussed.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21153672 D.Chakravorty, S.Parameswaran, V.K.Dubey, and S.Patra (2011).
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20970504 S.Chittori, H.S.Savithri, and M.R.Murthy (2011).
Crystal structure of Salmonella typhimurium 2-methylcitrate synthase: Insights on domain movement and substrate specificity.
  J Struct Biol, 174, 58-68.
PDB code: 3o8j
21424517 V.Moore, A.Kanu, O.Byron, G.Campbell, M.J.Danson, D.W.Hough, and S.J.Crennell (2011).
Contribution of inter-subunit interactions to the thermostability of Pyrococcus furiosus citrate synthase.
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19763902 O.Prakash, and N.Jaiswal (2010).
alpha-Amylase: an ideal representative of thermostable enzymes.
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19768676 A.Ruggiero, M.Masullo, D.Marasco, M.R.Ruocco, P.Grimaldi, P.Arcari, A.Zagari, and L.Vitagliano (2009).
The dimeric structure of Sulfolobus solfataricus thioredoxin A2 and the basis of its thermostability.
  Proteins, 77, 1004-1008.
PDB code: 3hhv
18344010 C.C.Deocaris, S.Takano, D.Priyandoko, Z.Kaul, T.Yaguchi, D.C.Kraft, K.Yamasaki, S.C.Kaul, and R.Wadhwa (2008).
Glycerol stimulates innate chaperoning, proteasomal and stress-resistance functions: implications for geronto-manipulation.
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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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17710363 X.X.Zhou, Y.B.Wang, Y.J.Pan, and W.F.Li (2008).
Differences in amino acids composition and coupling patterns between mesophilic and thermophilic proteins.
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17400551 C.Ma, S.Remani, J.Sun, R.Kotaria, J.A.Mayor, D.E.Walters, and R.S.Kaplan (2007).
Identification of the substrate binding sites within the yeast mitochondrial citrate transport protein.
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17395198 D.R.Boutz, D.Cascio, J.Whitelegge, L.J.Perry, and T.O.Yeates (2007).
Discovery of a thermophilic protein complex stabilized by topologically interlinked chains.
  J Mol Biol, 368, 1332-1344.
PDB code: 2ibp
17486291 E.Ahrman, N.Gustavsson, C.Hultschig, W.C.Boelens, and C.S.Emanuelsson (2007).
Small heat shock proteins prevent aggregation of citrate synthase and bind to the N-terminal region which is absent in thermostable forms of citrate synthase.
  Extremophiles, 11, 659-666.  
17567739 E.Ahrman, W.Lambert, J.A.Aquilina, C.V.Robinson, and C.S.Emanuelsson (2007).
Chemical cross-linking of the chloroplast localized small heat-shock protein, Hsp21, and the model substrate citrate synthase.
  Protein Sci, 16, 1464-1478.  
17498304 E.Chea, and D.R.Livesay (2007).
How accurate and statistically robust are catalytic site predictions based on closeness centrality?
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17400742 F.Li, C.H.Hagemeier, H.Seedorf, G.Gottschalk, and R.K.Thauer (2007).
Re-citrate synthase from Clostridium kluyveri is phylogenetically related to homocitrate synthase and isopropylmalate synthase rather than to Si-citrate synthase.
  J Bacteriol, 189, 4299-4304.  
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.
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17683334 L.D.Unsworth, J.van der Oost, and S.Koutsopoulos (2007).
Hyperthermophilic enzymes--stability, activity and implementation strategies for high temperature applications.
  FEBS J, 274, 4044-4056.  
17933930 M.A.Salameh, and J.Wiegel (2007).
Purification and characterization of two highly thermophilic alkaline lipases from Thermosyntropha lipolytica.
  Appl Environ Microbiol, 73, 7725-7731.  
17766385 R.A.Goldstein (2007).
Amino-acid interactions in psychrophiles, mesophiles, thermophiles, and hyperthermophiles: insights from the quasi-chemical approximation.
  Protein Sci, 16, 1887-1895.  
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.  
17944946 S.Koutsopoulos, J.van der Oost, and W.Norde (2007).
Kinetically controlled refolding of a heat-denatured hyperthermostable protein.
  FEBS J, 274, 5915-5923.  
17235516 V.Spiwok, P.Lipovová, T.Skálová, J.Dusková, J.Dohnálek, J.Hasek, N.J.Russell, and B.Králová (2007).
Cold-active enzymes studied by comparative molecular dynamics simulation.
  J Mol Model, 13, 485-497.  
16720405 J.G.Bragg, D.Thomas, and P.Baudouin-Cornu (2006).
Variation among species in proteomic sulphur content is related to environmental conditions.
  Proc Biol Sci, 273, 1293-1300.  
16759231 M.Karlström, I.H.Steen, D.Madern, A.E.Fedöy, N.K.Birkeland, and R.Ladenstein (2006).
The crystal structure of a hyperthermostable subfamily II isocitrate dehydrogenase from Thermotoga maritima.
  FEBS J, 273, 2851-2868.
PDB code: 1zor
16294337 O.A.Adekoya, R.Helland, N.P.Willassen, and I.Sylte (2006).
Comparative sequence and structure analysis reveal features of cold adaptation of an enzyme in the thermolysin family.
  Proteins, 62, 435-449.  
16934982 R.Lieph, F.A.Veloso, and D.S.Holmes (2006).
Thermophiles like hot T.
  Trends Microbiol, 14, 423-426.  
15526298 A.Seto, K.Murayama, M.Toyama, A.Ebihara, N.Nakagawa, S.Kuramitsu, M.Shirouzu, and S.Yokoyama (2005).
ATP-induced structural change of dephosphocoenzyme A kinase from Thermus thermophilus HB8.
  Proteins, 58, 235-242.
PDB code: 1uf9
15951512 L.Brocchieri, and S.Karlin (2005).
Protein length in eukaryotic and prokaryotic proteomes.
  Nucleic Acids Res, 33, 3390-3400.  
16357204 R.Khayat, L.Tang, E.T.Larson, C.M.Lawrence, M.Young, and J.E.Johnson (2005).
Structure of an archaeal virus capsid protein reveals a common ancestry to eukaryotic and bacterial viruses.
  Proc Natl Acad Sci U S A, 102, 18944-18949.
PDB code: 2bbd
15933031 S.H.Baik, F.Michel, N.Aghajari, R.Haser, and S.Harayama (2005).
Cooperative effect of two surface amino acid mutations (Q252L and E170K) in glucose dehydrogenase from Bacillus megaterium IWG3 on stabilization of its oligomeric state.
  Appl Environ Microbiol, 71, 3285-3293.
PDB code: 1rwb
16106445 S.Koutsopoulos, J.van der Oost, and W.Norde (2005).
Temperature-dependent structural and functional features of a hyperthermostable enzyme using elastic neutron scattering.
  Proteins, 61, 377-384.  
15848038 W.F.Li, X.X.Zhou, and P.Lu (2005).
Structural features of thermozymes.
  Biotechnol Adv, 23, 271-281.  
15858262 Y.Eisenberg-Domovich, V.P.Hytönen, M.Wilchek, E.A.Bayer, M.S.Kulomaa, and O.Livnah (2005).
High-resolution crystal structure of an avidin-related protein: insight into high-affinity biotin binding and protein stability.
  Acta Crystallogr D Biol Crystallogr, 61, 528-538.
PDB codes: 1y52 1y53 1y55
14973185 A.Paz, D.Mester, I.Baca, E.Nevo, and A.Korol (2004).
Adaptive role of increased frequency of polypurine tracts in mRNA sequences of thermophilic prokaryotes.
  Proc Natl Acad Sci U S A, 101, 2951-2956.  
14997520 S.Kumar, and R.Nussinov (2004).
Different roles of electrostatics in heat and in cold: adaptation by citrate synthase.
  Chembiochem, 5, 280-290.  
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
15169774 Y.Tanaka, K.Tsumoto, Y.Yasutake, M.Umetsu, M.Yao, H.Fukada, I.Tanaka, and I.Kumagai (2004).
How oligomerization contributes to the thermostability of an archaeon protein. Protein L-isoaspartyl-O-methyltransferase from Sulfolobus tokodaii.
  J Biol Chem, 279, 32957-32967.
PDB code: 1vbf
12824188 D.J.Stokell, L.J.Donald, R.Maurus, N.T.Nguyen, G.Sadler, K.Choudhary, P.G.Hultin, G.D.Brayer, and H.W.Duckworth (2003).
Probing the roles of key residues in the unique regulatory NADH binding site of type II citrate synthase of Escherichia coli.
  J Biol Chem, 278, 35435-35443.
PDB codes: 1owb 1owc
12879490 F.Severcan, and P.I.Haris (2003).
Fourier transform infrared spectroscopy suggests unfolding of loop structures precedes complete unfolding of pig citrate synthase.
  Biopolymers, 69, 440-447.  
12529358 H.Sakuraba, H.Tsuge, I.Shimoya, R.Kawakami, S.Goda, Y.Kawarabayasi, N.Katunuma, H.Ago, M.Miyano, and T.Ohshima (2003).
The first crystal structure of archaeal aldolase. Unique tetrameric structure of 2-deoxy-d-ribose-5-phosphate aldolase from the hyperthermophilic archaea Aeropyrum pernix.
  J Biol Chem, 278, 10799-10806.
PDB code: 1n7k
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.  
12653995 N.Hakulinen, O.Turunen, J.Jänis, M.Leisola, and J.Rouvinen (2003).
Three-dimensional structures of thermophilic beta-1,4-xylanases from Chaetomium thermophilum and Nonomuraea flexuosa. Comparison of twelve xylanases in relation to their thermal stability.
  Eur J Biochem, 270, 1399-1412.
PDB codes: 1h1a 1m4w
12837801 X.Wang, X.He, S.Yang, X.An, W.Chang, and D.Liang (2003).
Structural basis for thermostability of beta-glycosidase from the thermophilic eubacterium Thermus nonproteolyticus HG102.
  J Bacteriol, 185, 4248-4255.
PDB code: 1np2
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.  
11846788 C.Schnarrenberger, and W.Martin (2002).
Evolution of the enzymes of the citric acid cycle and the glyoxylate cycle of higher plants. A case study of endosymbiotic gene transfer.
  Eur J Biochem, 269, 868-883.  
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
12487631 M.Dumontier, K.Michalickova, and C.W.Hogue (2002).
Species-specific protein sequence and fold optimizations.
  BMC Bioinformatics, 3, 39.  
11238984 C.Vieille, and G.J.Zeikus (2001).
Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability.
  Microbiol Mol Biol Rev, 65, 1.  
11166567 F.H.Arnold, P.L.Wintrode, K.Miyazaki, and A.Gershenson (2001).
How enzymes adapt: lessons from directed evolution.
  Trends Biochem Sci, 26, 100-106.  
11533060 I.H.Steen, D.Madern, M.Karlström, T.Lien, R.Ladenstein, and N.K.Birkeland (2001).
Comparison of isocitrate dehydrogenase from three hyperthermophiles reveals differences in thermostability, cofactor specificity, oligomeric state, and phylogenetic affiliation.
  J Biol Chem, 276, 43924-43931.  
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.
  Eur J Biochem, 268, 3233-3242.  
11266590 S.Matsumiya, Y.Ishino, and K.Morikawa (2001).
Crystal structure of an archaeal DNA sliding clamp: proliferating cell nuclear antigen from Pyrococcus furiosus.
  Protein Sci, 10, 17-23.
PDB code: 1ge8
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.  
10694395 L.C.Kurz, G.Drysdale, M.Riley, M.A.Tomar, J.Chen, R.J.Russell, and M.J.Danson (2000).
Kinetics and mechanism of the citrate synthase from the thermophilic archaeon Thermoplasma acidophilum.
  Biochemistry, 39, 2283-2296.  
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.  
  10338022 A.Ayed, and H.W.Duckworth (1999).
A stable intermediate in the equilibrium unfolding of Escherichia coli citrate synthase.
  Protein Sci, 8, 1116-1126.  
10021406 D.W.Hough, and M.J.Danson (1999).
Extremozymes.
  Curr Opin Chem Biol, 3, 39-46.  
  10430556 I.K.Cann, and Y.Ishino (1999).
Archaeal DNA replication: identifying the pieces to solve a puzzle.
  Genetics, 152, 1249-1267.  
  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.  
10447894 S.Kaspar, R.Perozzo, S.Reinelt, M.Meyer, K.Pfister, L.Scapozza, and M.Bott (1999).
The periplasmic domain of the histidine autokinase CitA functions as a highly specific citrate receptor.
  Mol Microbiol, 33, 858-872.  
10449718 T.Knöchel, A.Ivens, G.Hester, A.Gonzalez, R.Bauerle, M.Wilmanns, K.Kirschner, and J.N.Jansonius (1999).
The crystal structure of anthranilate synthase from Sulfolobus solfataricus: functional implications.
  Proc Natl Acad Sci U S A, 96, 9479-9484.
PDB code: 1qdl
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.  
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.  
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.  
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.  
9860830 M.W.Bauer, and R.M.Kelly (1998).
The family 1 beta-glucosidases from Pyrococcus furiosus and Agrobacterium faecalis share a common catalytic mechanism.
  Biochemistry, 37, 17170-17178.  
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.  
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
The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB code is shown on the right.