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Isomerase PDB id
1aw1
Jmol
Contents
Protein chains
(+ 2 more) 255 a.a. *
Ligands
PGA ×8
Waters ×308
* Residue conservation analysis
PDB id:
1aw1
Name: Isomerase
Title: Triosephosphate isomerase of vibrio marinus complexed with 2-phosphoglycolate
Structure: Triosephosphate isomerase. Chain: a, b, d, e, g, h, j, k. Engineered: yes. Other_details: complex with 2-phosphoglycolate
Source: Moritella marina. Organism_taxid: 90736. Atcc: 15382. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.70Å     R-factor:   0.192     R-free:   0.215
Authors: D.Maes,J.P.Zeelen,R.K.Wierenga
Key ref:
M.Alvarez et al. (1998). Triose-phosphate isomerase (TIM) of the psychrophilic bacterium Vibrio marinus. Kinetic and structural properties. J Biol Chem, 273, 2199-2206. PubMed id: 9442062 DOI: 10.1074/jbc.273.4.2199
Date:
09-Oct-97     Release date:   28-Jan-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P50921  (TPIS_VIBMA) -  Triosephosphate isomerase
Seq:
Struc: 		256 a.a.
255 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.5.3.1.1  - Triose-phosphate isomerase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: D-glyceraldehyde 3-phosphate = glycerone phosphate
D-glyceraldehyde 3-phosphate
Bound ligand (Het Group name = PGA)
matches with 72.00% similarity 		= glycerone phosphate
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   4 terms 
  Biochemical function     catalytic activity     3 terms  

 

 
    Added reference    
 
 
DOI no: 10.1074/jbc.273.4.2199 J Biol Chem 273:2199-2206 (1998)
PubMed id: 9442062  
 
 
Triose-phosphate isomerase (TIM) of the psychrophilic bacterium Vibrio marinus. Kinetic and structural properties.
M.Alvarez, J.P.Zeelen, V.Mainfroid, F.Rentier-Delrue, J.A.Martial, L.Wyns, R.K.Wierenga, D.Maes.
 
  ABSTRACT  
 
The purification and characterization of triose-phosphate isomerase from the psychrophilic bacterium Vibrio marinus (vTIM) is described. Crystal structures of the vTIM-sulfate complex and the vTIM-2-phosphoglycolate complex (at a 2.7-A resolution) are also presented. The optimal growth temperature of Vibrio marinus is 15 degrees C. Stability studies show that vTIM is an unstable protein with a half-life of only 10 min at 25 degrees C. The vTIM sequence is most closely related to the sequence of Escherichia coli TIM (eTIM) (66% identity), and several unique structural features described for eTIM are also seen in vTIM, but eTIM is considerably more stable. The Td values of vTIM and eTIM, determined by calorimetric studies, are 41 and 54 degrees C, respectively. Amino acid sequence comparison reveals that vTIM has an alanine in loop 8 (at position 238), whereas all other TIM sequences known to date have a serine. The vTIM mutant A238S was produced and characterized. Compared with wild type, the catalytic efficiency of the A238S mutant is somewhat reduced, and its stability is considerably increased.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. The reaction catalyzed by triose-phosphate isomerase, and the covalent structure of the substrate analogue 2PG is shown. 		Figure 6.
Fig. 6. Superposition of the backbone of the vTIM(2PG) (green), vTIM(sulfate) (blue), and eTIM (red) structures. The sulfate^ ion and the 2PG molecule are also shown, indicating the difference^ in position of the P atom (pink), and the S atom (yellow). Loop 6 of the vTIM(2PG) structure is in the closed conformation. N and C identify the N terminus and C terminus, respectively.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1998, 273, 2199-2206) copyright 1998.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19133128 R.P.Metpally, and B.V.Reddy (2009).
Comparative proteome analysis of psychrophilic versus mesophilic bacterial species: Insights into the molecular basis of cold adaptation of proteins.
  BMC Genomics, 10, 11.  
19011975 C.L.Goonasekara, and D.H.Heeley (2008).
Conformational properties of striated muscle tropomyosins from some salmonid fishes.
  J Muscle Res Cell Motil, 29, 135-143.  
17932934 S.Wong, and M.P.Jacobson (2008).
Conformational selection in silico: loop latching motions and ligand binding in enzymes.
  Proteins, 71, 153-164.  
18759222 W.C.Too, Y.C.Liew, and L.L.Few (2008).
Cloning of glyceraldehyde-3-phosphate dehydrogenase from an Antarctic psychrophilic bacterium by inverse and splinkerette PCR.
  J Basic Microbiol, 48, 430-435.  
17697122 D.Tronelli, E.Maugini, F.Bossa, and S.Pascarella (2007).
Structural adaptation to low temperatures--analysis of the subunit interface of oligomeric psychrophilic enzymes.
  FEBS J, 274, 4595-4608.  
17919319 R.R.Gabdoulline, M.Stein, and R.C.Wade (2007).
qPIPSA: relating enzymatic kinetic parameters and interaction fields.
  BMC Bioinformatics, 8, 373.  
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.  
16756497 K.S.Siddiqui, and R.Cavicchioli (2006).
Cold-adapted enzymes.
  Annu Rev Biochem, 75, 403-433.  
  16511027 D.Dong, T.Ihara, H.Motoshima, and K.Watanabe (2005).
Crystallization and preliminary X-ray crystallographic studies of a psychrophilic subtilisin-like protease Apa1 from Antarctic Pseudoalteromonas sp. strain AS-11.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 308-311.  
15670163 J.Arnórsdóttir, M.M.Kristjánsson, and R.Ficner (2005).
Crystal structure of a subtilisin-like serine proteinase from a psychrotrophic Vibrio species reveals structural aspects of cold adaptation.
  FEBS J, 272, 832-845.
PDB codes: 1s2n 1sh7
15693622 A.H.Farrell, K.A.Hohenstein, and D.H.Shain (2004).
Molecular adaptation in the ice worm, Mesenchytraeus solifugus: divergence of energetic-associated genes.
  J Mol Evol, 59, 666-673.  
  16233714 A.Hoyoux, V.Blaise, T.Collins, S.D'Amico, E.Gratia, A.L.Huston, J.C.Marx, G.Sonan, Y.Zeng, G.Feller, and C.Gerday (2004).
Extreme catalysts from low-temperature environments.
  J Biosci Bioeng, 98, 317-330.  
15175111 S.Mahato, D.De, D.Dutta, M.Kundu, S.Bhattacharya, M.T.Schiavone, and S.K.Bhattacharya (2004).
Potential use of sugar binding proteins in reactors for regeneration of CO2 fixation acceptor D-Ribulose-1,5-bisphosphate.
  Microb Cell Fact, 3, 7.  
12562783 H.Orikoshi, N.Baba, S.Nakayama, H.Kashu, K.Miyamoto, M.Yasuda, Y.Inamori, and H.Tsujibo (2003).
Molecular analysis of the gene encoding a novel cold-adapted chitinase (ChiB) from a marine bacterium, Alteromonas sp. strain O-7.
  J Bacteriol, 185, 1153-1160.  
12876336 I.Leiros, E.Moe, O.Lanes, A.O.Smalås, and N.P.Willassen (2003).
The structure of uracil-DNA glycosylase from Atlantic cod (Gadus morhua) reveals cold-adaptation features.
  Acta Crystallogr D Biol Crystallogr, 59, 1357-1365.
PDB code: 1okb
12577270 N.Aghajari, F.Van Petegem, V.Villeret, J.P.Chessa, C.Gerday, R.Haser, and J.Van Beeumen (2003).
Crystal structures of a psychrophilic metalloprotease reveal new insights into catalysis by cold-adapted proteases.
  Proteins, 50, 636-647.
PDB codes: 1g9k 1h71
12644485 Y.Xu, G.Feller, C.Gerday, and N.Glansdorff (2003).
Metabolic enzymes from psychrophilic bacteria: challenge of adaptation to low temperatures in ornithine carbamoyltransferase from Moritella abyssi.
  J Bacteriol, 185, 2161-2168.  
11933070 G.Gianese, F.Bossa, and S.Pascarella (2002).
Comparative structural analysis of psychrophilic and meso- and thermophilic enzymes.
  Proteins, 47, 236-249.  
12112681 H.Reyes-Vivas, E.Martínez-Martínez, G.Mendoza-Hernández, G.López-Velázquez, R.Pérez-Montfort, M.Tuena de Gómez-Puyou, and A.Gómez-Puyou (2002).
Susceptibility to proteolysis of triosephosphate isomerase from two pathogenic parasites: characterization of an enzyme with an intact and a nicked monomer.
  Proteins, 48, 580-590.  
12423352 J.Arnórsdottir, R.B.Smáradóttir, O.T.Magnússon, S.H.Thorbjarnardóttir, G.Eggertsson, and M.M.Kristjánsson (2002).
Characterization of a cloned subtilisin-like serine proteinase from a psychrotrophic Vibrio species.
  Eur J Biochem, 269, 5536-5546.  
11985615 K.Mavromatis, I.Tsigos, M.Tzanodaskalaki, M.Kokkinidis, and V.Bouriotis (2002).
Exploring the role of a glycine cluster in cold adaptation of an alkaline phosphatase.
  Eur J Biochem, 269, 2330-2335.  
  12180102 R.Cavicchioli, K.S.Siddiqui, D.Andrews, and K.R.Sowers (2002).
Low-temperature extremophiles and their applications.
  Curr Opin Biotechnol, 13, 253-261.  
12171655 S.D'Amico, P.Claverie, T.Collins, D.Georlette, E.Gratia, A.Hoyoux, M.A.Meuwis, G.Feller, and C.Gerday (2002).
Molecular basis of cold adaptation.
  Philos Trans R Soc Lond B Biol Sci, 357, 917-925.  
12454456 S.Parthasarathy, H.Balaram, P.Balaram, and M.R.Murthy (2002).
Structures of Plasmodium falciparum triosephosphate isomerase complexed to substrate analogues: observation of the catalytic loop in the open conformation in the ligand-bound state.
  Acta Crystallogr D Biol Crystallogr, 58, 1992-2000.
PDB codes: 1m7o 1m7p
11151009 B.V.Norledge, A.M.Lambeir, R.A.Abagyan, A.Rottmann, A.M.Fernandez, V.V.Filimonov, M.G.Peter, and R.K.Wierenga (2001).
Modeling, mutagenesis, and structural studies on the fully conserved phosphate-binding loop (loop 8) of triosephosphate isomerase: toward a new substrate specificity.
  Proteins, 42, 383-389.
PDB code: 1dkw
11258928 H.Reyes-Vivas, G.Hernández-Alcantara, G.López-Velazquez, N.Cabrera, R.Pérez-Montfort, M.T.de Gómez-Puyou, and A.Gómez-Puyou (2001).
Factors that control the reactivity of the interface cysteine of triosephosphate isomerase from Trypanosoma brucei and Trypanosoma cruzi.
  Biochemistry, 40, 3134-3140.  
11589698 I.Tsigos, K.Mavromatis, M.Tzanodaskalaki, C.Pozidis, M.Kokkinidis, and V.Bouriotis (2001).
Engineering the properties of a cold active enzyme through rational redesign of the active site.
  Eur J Biochem, 268, 5074-5080.  
11502197 T.Oikawa, K.Yamanaka, T.Kazuoka, N.Kanzawa, and K.Soda (2001).
Psychrophilic valine dehydrogenase of the antarctic psychrophile, Cytophaga sp. KUC-1: purification, molecular characterization and expression.
  Eur J Biochem, 268, 4375-4383.  
  10675897 C.Gerday, M.Aittaleb, M.Bentahir, J.P.Chessa, P.Claverie, T.Collins, S.D'Amico, J.Dumont, G.Garsoux, D.Georlette, A.Hoyoux, T.Lonhienne, M.A.Meuwis, and G.Feller (2000).
Cold-adapted enzymes: from fundamentals to biotechnology.
  Trends Biotechnol, 18, 103-107.  
10848966 D.Georlette, Z.O.Jónsson, F.Van Petegem, J.Chessa, J.Van Beeumen, U.Hübscher, and C.Gerday (2000).
A DNA ligase from the psychrophile Pseudoalteromonas haloplanktis gives insights into the adaptation of proteins to low temperatures.
  Eur J Biochem, 267, 3502-3512.  
10672012 H.K.Leiros, N.P.Willassen, and A.O.Smalås (2000).
Structural comparison of psychrophilic and mesophilic trypsins. Elucidating the molecular basis of cold-adaptation.
  Eur J Biochem, 267, 1039-1049.  
10672035 M.Rina, C.Pozidis, K.Mavromatis, M.Tzanodaskalaki, M.Kokkinidis, and V.Bouriotis (2000).
Alkaline phosphatase from the Antarctic strain TAB5. Properties and psychrophilic adaptations.
  Eur J Biochem, 267, 1230-1238.  
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.  
  10473410 A.Galkin, L.Kulakova, H.Ashida, Y.Sawa, and N.Esaki (1999).
Cold-adapted alanine dehydrogenases from two antarctic bacterial strains: gene cloning, protein characterization, and comparison with mesophilic and thermophilic counterparts.
  Appl Environ Microbiol, 65, 4014-4020.  
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
10103004 M.M.Kristjánsson, O.T.Magnússon, H.M.Gudmundsson, G.A.Alfredsson, and H.Matsuzawa (1999).
Properties of a subtilisin-like proteinase from a psychrotrophic Vibrio species comparison with proteinase K and aqualysin I.
  Eur J Biochem, 260, 752-760.  
  9862804 N.Aghajari, G.Feller, C.Gerday, and R.Haser (1998).
Structures of the psychrophilic Alteromonas haloplanctis alpha-amylase give insights into cold adaptation at a molecular level.
  Structure, 6, 1503-1516.
PDB code: 1b0i
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.