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PDBsum entry 1nsj

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Isomerase PDB id
1nsj
Jmol
Contents
Protein chain
205 a.a. *
Ligands
PO4
Waters ×106
* Residue conservation analysis
PDB id:
1nsj
Name: Isomerase
Title: Crystal structure of phosphoribosyl anthranilate isomerase from thermotoga maritima
Structure: Phosphoribosyl anthranilate isomerase. Chain: a. Synonym: prai. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Gene: trpf. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.00Å     R-factor:   0.192     R-free:   0.243
Authors: M.Hennig,J.N.J.Jansonius
Key ref:
M.Hennig et al. (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. PubMed id: 9166771 DOI: 10.1021/bi962718q
Date:
13-Sep-96     Release date:   12-Mar-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q56320  (TRPF_THEMA) -  N-(5'-phosphoribosyl)anthranilate isomerase
Seq:
Struc:
205 a.a.
205 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.5.3.1.24  - Phosphoribosylanthranilate isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Tryptophan Biosynthesis
      Reaction: N-(5-phospho-beta-D-ribosyl)anthranilate = 1-(2-carboxyphenylamino)-1- deoxy-D-ribulose 5-phosphate
N-(5-phospho-beta-D-ribosyl)anthranilate
= 1-(2-carboxyphenylamino)-1- deoxy-D-ribulose 5-phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     metabolic process   5 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1021/bi962718q Biochemistry 36:6009-6016 (1997)
PubMed id: 9166771  
 
 
Crystal structure at 2.0 A resolution of phosphoribosyl anthranilate isomerase from the hyperthermophile Thermotoga maritima: possible determinants of protein stability.
M.Hennig, R.Sterner, K.Kirschner, J.N.Jansonius.
 
  ABSTRACT  
 
The structural basis of thermostability of proteins is of great scientific and biotechnological interest. Differences in the X-ray structues of orthologous proteins from hyperthermophilic and mesophilic organisms can indicate crucial stabilizing interactions. To this end the crystal structure of dimeric phosphoribosyl anthranilate isomerase from the hyperthermophile Thermotoga maritima (tPRAI) was determined using phases derived from the isomorphous replacement method and was refined at 2.0 A resolution. The comparison to the known 2.0 A structure of PRAI from Escherichia coli (ePRAI) shows that tPRAI has the complete TIM- or (beta alpha)8-barrel fold, whereas helix alpha5 in ePRAI is replaced by a loop. The subunits of tPRAI associate via the N-terminal faces of their central beta-barrels. Two long, symmetry-related loops that protrude reciprocally into cavities of the other subunit provide for multiple hydrophobic interactions. Moreover, the side chains of the N-terminal methionines and the C-terminal leucines of both subunits are immobilized in a hydrophobic cluster, and the number of salt bridges is increased in tPRAI. These features appear to be mainly responsible for the high thermostability of tPRAI. In contrast to other hyperthermostable enzymes, tPRAI at 25 degrees C is catalytically more efficient than ePRAI, mainly due to its small K(M) value for the substrate [Sterner, R., Kleemann, G. R., Szadkowski, H., Lustig, A., Hennig, M., & Kirschner, K. (1996) Protein Sci. 5, 2000-2008]. The increased number of hydrogen bonds between the phosphate ion and tPRAI compared to ePRAI could be responsible for this effect.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21321225 A.V.Due, J.Kuper, A.Geerlof, J.P.Kries, and M.Wilmanns (2011).
Bisubstrate specificity in histidine/tryptophan biosynthesis isomerase from Mycobacterium tuberculosis by active site metamorphosis.
  Proc Natl Acad Sci U S A, 108, 3554-3559.
PDB codes: 2y85 2y88 2y89
20936671 N.Pirakitikulr, N.Ostrov, P.Peralta-Yahya, and V.W.Cornish (2010).
PCRless library mutagenesis via oligonucleotide recombination in yeast.
  Protein Sci, 19, 2336-2346.  
19247785 P.Del Vecchio, M.Elias, L.Merone, G.Graziano, J.Dupuy, L.Mandrich, P.Carullo, B.Fournier, D.Rochu, M.Rossi, P.Masson, E.Chabriere, and G.Manco (2009).
Structural determinants of the high thermal stability of SsoPox from the hyperthermophilic archaeon Sulfolobus solfataricus.
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17492665 Y.Tanaka, T.Sasaki, I.Kumagai, Y.Yasutake, M.Yao, I.Tanaka, and K.Tsumoto (2007).
Molecular properties of two proteins homologous to PduO-type ATP:cob(I)alamin adenosyltransferase from Sulfolobus tokodaii.
  Proteins, 68, 446-457.
PDB code: 1wvt
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
16436711 V.Cottier, A.Barberis, and U.Lüthi (2006).
Novel yeast cell-based assay to screen for inhibitors of human cytomegalovirus protease in a high-throughput format.
  Antimicrob Agents Chemother, 50, 565-571.  
15857781 B.Höcker (2005).
Directed evolution of (betaalpha)(8)-barrel enzymes.
  Biomol Eng, 22, 31-38.  
15624211 D.Y.Zhu, Y.Q.Zhu, R.H.Huang, Y.Xiang, N.Yang, H.X.Lu, G.P.Li, Q.Jin, and D.C.Wang (2005).
Crystal structure of the copper homeostasis protein (CutCm) from Shigella flexneri at 1.7 A resolution: the first structure of a new sequence family of TIM barrels.
  Proteins, 58, 764-768.
PDB codes: 1x7i 1x8c
16080154 K.Miyazono, Y.Sawano, and M.Tanokura (2005).
Crystal structure and structural stability of acylphosphatase from hyperthermophilic archaeon Pyrococcus horikoshii OT3.
  Proteins, 61, 196-205.  
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
14993684 H.Wright, F.Barona-Gómez, D.A.Hodgson, and V.Fülöp (2004).
Expression, purification and preliminary crystallographic analysis of phosphoribosyl isomerase (PriA) from Streptomyces coelicolor.
  Acta Crystallogr D Biol Crystallogr, 60, 534-536.  
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
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
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.  
11842090 E.Pohl, N.Brunner, M.Wilmanns, and R.Hensel (2002).
The crystal structure of the allosteric non-phosphorylating glyceraldehyde-3-phosphate dehydrogenase from the hyperthermophilic archaeum Thermoproteus tenax.
  J Biol Chem, 277, 19938-19945.
PDB code: 1ky8
12070156 N.Maeda, T.Kanai, H.Atomi, and T.Imanaka (2002).
The unique pentagonal structure of an archaeal Rubisco is essential for its high thermostability.
  J Biol Chem, 277, 31656-31662.  
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
11756459 S.Hettwer, and R.Sterner (2002).
A novel tryptophan synthase beta-subunit from the hyperthermophile Thermotoga maritima. Quaternary structure, steady-state kinetics, and putative physiological role.
  J Biol Chem, 277, 8194-8201.  
11298741 A.Ivens, O.Mayans, H.Szadkowski, M.Wilmanns, and K.Kirschner (2001).
Purification, characterization and crystallization of thermostable anthranilate phosphoribosyltransferase from Sulfolobus solfataricus.
  Eur J Biochem, 268, 2246-2252.  
11551792 A.Karshikoff, and R.Ladenstein (2001).
Ion pairs and the thermotolerance of proteins from hyperthermophiles: a "traffic rule" for hot roads.
  Trends Biochem Sci, 26, 550-556.  
11551466 B.Höcker, C.Jürgens, M.Wilmanns, and R.Sterner (2001).
Stability, catalytic versatility and evolution of the (beta alpha)(8)-barrel fold.
  Curr Opin Biotechnol, 12, 376-381.  
11238984 C.Vieille, and G.J.Zeikus (2001).
Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability.
  Microbiol Mol Biol Rev, 65, 1.  
11395407 J.A.Gerlt, and P.C.Babbitt (2001).
Divergent evolution of enzymatic function: mechanistically diverse superfamilies and functionally distinct suprafamilies.
  Annu Rev Biochem, 70, 209-246.  
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.  
11248013 N.Kallenbach (2001).
Breaking open a protein barrel.
  Proc Natl Acad Sci U S A, 98, 2958-2960.  
10944186 C.Jürgens, A.Strom, D.Wegener, S.Hettwer, M.Wilmanns, and R.Sterner (2000).
Directed evolution of a (beta alpha)8-barrel enzyme to catalyze related reactions in two different metabolic pathways.
  Proc Natl Acad Sci U S A, 97, 9925-9930.  
10745009 R.Thoma, M.Hennig, R.Sterner, and K.Kirschner (2000).
Structure and function of mutationally generated monomers of dimeric phosphoribosylanthranilate isomerase from Thermotoga maritima.
  Structure, 8, 265-276.
PDB code: 1dl3
10966577 X.Zhou, F.Alber, G.Folkers, G.H.Gonnet, and G.Chelvanayagam (2000).
An analysis of the helix-to-strand transition between peptides with identical sequence.
  Proteins, 41, 248-256.  
10383424 M.Alvarez, J.Wouters, D.Maes, V.Mainfroid, F.Rentier-Delrue, L.Wyns, E.Depiereux, and J.A.Martial (1999).
Lys13 plays a crucial role in the functional adaptation of the thermophilic triose-phosphate isomerase from Bacillus stearothermophilus to high temperatures.
  J Biol Chem, 274, 19181-19187.
PDB code: 2btm
  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.  
  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
  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.  
9690987 F.T.Robb, and D.L.Maeder (1998).
Novel evolutionary histories and adaptive features of proteins from hyperthermophiles
  Curr Opin Biotechnol, 9, 288-291.  
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.  
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
9914256 R.Jaenicke, and G.Böhm (1998).
The stability of proteins in extreme environments.
  Curr Opin Struct Biol, 8, 738-748.  
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 codes are shown on the right.