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PDBsum entry 1bjw

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Aminotransferase PDB id
1bjw
Jmol
Contents
Protein chains
382 a.a. *
Ligands
PO4 ×2
Waters ×308
* Residue conservation analysis
PDB id:
1bjw
Name: Aminotransferase
Title: Aspartate aminotransferase from thermus thermophilus
Structure: Aspartate aminotransferase. Chain: a, b. Engineered: yes
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
1.80Å     R-factor:   0.215     R-free:   0.269
Authors: T.Nakai,K.Okada,S.Kuramitsu,K.Hirotsu,Riken Structural Genomics/proteomics Initiative (Rsgi)
Key ref:
T.Nakai et al. (1999). Structure of Thermus thermophilus HB8 aspartate aminotransferase and its complex with maleate. Biochemistry, 38, 2413-2424. PubMed id: 10029535 DOI: 10.1021/bi9819881
Date:
30-Jun-98     Release date:   22-Jul-99    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q56232  (AAT_THET8) -  Aspartate aminotransferase
Seq:
Struc:
385 a.a.
382 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.6.1.1  - Aspartate transaminase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-aspartate + 2-oxoglutarate = oxaloacetate + L-glutamate
L-aspartate
+ 2-oxoglutarate
= oxaloacetate
+ L-glutamate
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-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     biosynthetic process   1 term 
  Biochemical function     catalytic activity     6 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi9819881 Biochemistry 38:2413-2424 (1999)
PubMed id: 10029535  
 
 
Structure of Thermus thermophilus HB8 aspartate aminotransferase and its complex with maleate.
T.Nakai, K.Okada, S.Akutsu, I.Miyahara, S.Kawaguchi, R.Kato, S.Kuramitsu, K.Hirotsu.
 
  ABSTRACT  
 
The three-dimensional structures of pyridoxal 5'-phosphate-type aspartate aminotransferase (AspAT) from Thermus thermophilus HB8 and pyridoxamine 5'-phosphate type one in complex with maleate have been determined by X-ray crystallography at 1.8 and 2.6 A resolution, respectively. The enzyme is a homodimer, and the polypeptide chain of the subunit is folded into one arm, one small domain, and one large domain. AspATs from many species were classified into aminotransferase subgroups Ia and Ib. The enzyme belongs to subgroup Ib, its sequence being less than 16% identical to the primary sequences of Escherichia coli, pig cytosolic, and chicken mitochondrial AspATs, which belong to subgroup Ia whose sequences are more than 40% identical and whose three-dimensional structures are quite similar with the active site residues almost completely conserved. The first X-ray analysis of AspAT subgroup Ib indicated that the overall and the active site structures are essentially conserved between the AspATs of subgroup Ia and the enzyme of subgroup Ib, but there are two distinct differences between them. (1) In AspAT subgroup Ia, substrate (or inhibitor) binding induces a large movement of the small domain as a whole to close the active site. However, in the enzyme of subgroup Ib, only the N-terminal region (Lys13-Val30) of the small domain approaches the active site to interact with the maleate. (2) In AspAT subgroup Ia, Arg292 recognizes the side chain carboxylate of the substrate; however, residue 292 of the enzyme in subgroup Ib is not Arg, and in place of Arg292, Lys109 forms a salt bridge with the side chain carboxylate. The thermostability of the enzyme is attained at least in part by the high content of Pro residues in the beta-turns and the marked increase in the number of salt bridges on the molecular surface compared with the mesophilic AspAT.
 

Literature references that cite this PDB file's key reference Google scholar

  PubMed id Reference
  21332942 H.J.Wu, Y.Yang, S.Wang, J.Q.Qiao, Y.F.Xia, Y.Wang, W.D.Wang, S.F.Gao, J.Liu, P.Q.Xue, and X.W.Gao (2011).
Cloning, expression and characterization of a new aspartate aminotransferase from Bacillus subtilis B3.
  FEBS J, 278, 1345-1357.  
21102469 H.Maeda, H.Yoo, and N.Dudareva (2011).
Prephenate aminotransferase directs plant phenylalanine biosynthesis via arogenate.
  Nat Chem Biol, 7, 19-21.  
20509863 R.Schwaiger, C.Schwarz, K.Furtwängler, V.Tarasov, A.Wende, and D.Oesterhelt (2010).
Transcriptional control by two leucine-responsive regulatory proteins in Halobacterium salinarum R1.
  BMC Mol Biol, 11, 40.  
18831049 T.Tomita, T.Miyagawa, T.Miyazaki, S.Fushinobu, T.Kuzuyama, and M.Nishiyama (2009).
Mechanism for multiple-substrates recognition of alpha-aminoadipate aminotransferase from Thermus thermophilus.
  Proteins, 75, 348-359.
PDB codes: 2zp7 3cbf
18056996 F.Rossi, S.Garavaglia, V.Montalbano, M.A.Walsh, and M.Rizzi (2008).
Crystal Structure of Human Kynurenine Aminotransferase II, a Drug Target for the Treatment of Schizophrenia.
  J Biol Chem, 283, 3559-3566.
PDB code: 2vgz
18560158 H.Sakuraba, K.Yoneda, K.Takeuchi, H.Tsuge, N.Katunuma, and T.Ohshima (2008).
Structure of an archaeal alanine:glyoxylate aminotransferase.
  Acta Crystallogr D Biol Crystallogr, 64, 696-699.
PDB code: 2zc0
17683331 I.Matsui, and K.Harata (2007).
Implication for buried polar contacts and ion pairs in hyperthermostable enzymes.
  FEBS J, 274, 4012-4022.  
17323931 Q.Wu, Y.N.Liu, H.Chen, E.J.Molitor, and H.W.Liu (2007).
A retro-evolution study of CDP-6-deoxy-D-glycero-L-threo-4-hexulose-3-dehydrase (E1) from Yersinia pseudotuberculosis: implications for C-3 deoxygenation in the biosynthesis of 3,6-dideoxyhexoses.
  Biochemistry, 46, 3759-3767.  
16894611 B.Popovic, X.Tang, D.Y.Chirgadze, F.Huang, T.L.Blundell, and J.B.Spencer (2006).
Crystal structures of the PLP- and PMP-bound forms of BtrR, a dual functional aminotransferase involved in butirosin biosynthesis.
  Proteins, 65, 220-230.
PDB codes: 2c7t 2c81
16990263 Q.Han, H.Robinson, Y.G.Gao, N.Vogelaar, S.R.Wilson, M.Rizzi, and J.Li (2006).
Crystal structures of Aedes aegypti alanine glyoxylate aminotransferase.
  J Biol Chem, 281, 37175-37182.
PDB codes: 2huf 2hui 2huu
16640556 S.Sivaraman, and J.F.Kirsch (2006).
The narrow substrate specificity of human tyrosine aminotransferase--the enzyme deficient in tyrosinemia type II.
  FEBS J, 273, 1920-1929.  
  16511030 H.Chon, H.Matsumura, S.Shimizu, N.Maeda, Y.Koga, K.Takano, and S.Kanaya (2005).
Overproduction and preliminary crystallographic study of a human kynurenine aminotransferase II homologue from Pyrococcus horikoshii OT3.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 319-322.  
16138312 H.Chon, H.Matsumura, Y.Koga, K.Takano, and S.Kanaya (2005).
Crystal structure of a human kynurenine aminotransferase II homologue from Pyrococcus horikoshii OT3 at 2.20 A resolution.
  Proteins, 61, 685-688.
PDB code: 1x0m
15853804 Q.Han, Y.G.Gao, H.Robinson, H.Ding, S.Wilson, and J.Li (2005).
Crystal structures of Aedes aegypti kynurenine aminotransferase.
  FEBS J, 272, 2198-2206.
PDB codes: 1yiy 1yiz
15498941 A.Paiardini, F.Bossa, and S.Pascarella (2004).
Evolutionarily conserved regions and hydrophobic contacts at the superfamily level: The case of the fold-type I, pyridoxal-5'-phosphate-dependent enzymes.
  Protein Sci, 13, 2992-3005.  
15364907 F.Rossi, Q.Han, J.Li, J.Li, and M.Rizzi (2004).
Crystal structure of human kynurenine aminotransferase I.
  J Biol Chem, 279, 50214-50220.
PDB codes: 1w7l 1w7m 1w7n
14761974 M.Goto, R.Omi, I.Miyahara, A.Hosono, H.Mizuguchi, H.Hayashi, H.Kagamiyama, and K.Hirotsu (2004).
Crystal structures of glutamine:phenylpyruvate aminotransferase from Thermus thermophilus HB8: induced fit and substrate recognition.
  J Biol Chem, 279, 16518-16525.
PDB codes: 1v2d 1v2e 1v2f
15103638 R.Schwarzenbacher, L.Jaroszewski, F.von Delft, P.Abdubek, E.Ambing, T.Biorac, L.S.Brinen, J.M.Canaves, J.Cambell, H.J.Chiu, X.Dai, A.M.Deacon, M.DiDonato, M.A.Elsliger, S.Eshagi, R.Floyd, A.Godzik, C.Grittini, S.K.Grzechnik, E.Hampton, C.Karlak, H.E.Klock, E.Koesema, J.S.Kovarik, A.Kreusch, P.Kuhn, S.A.Lesley, I.Levin, D.McMullan, T.M.McPhillips, M.D.Miller, A.Morse, K.Moy, J.Ouyang, R.Page, K.Quijano, A.Robb, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, J.Vincent, X.Wang, B.West, G.Wolf, Q.Xu, K.O.Hodgson, J.Wooley, and I.A.Wilson (2004).
Crystal structure of an aspartate aminotransferase (TM1255) from Thermotoga maritima at 1.90 A resolution.
  Proteins, 55, 759-763.
PDB code: 1o4s
15103612 Y.Katsura, M.Shirouzu, H.Yamaguchi, R.Ishitani, O.Nureki, S.Kuramitsu, H.Hayashi, and S.Yokoyama (2004).
Crystal structure of a putative aspartate aminotransferase belonging to subgroup IV.
  Proteins, 55, 487-492.
PDB code: 1iug
12723595 H.Kim, K.Ikegami, M.Nakaoka, M.Yagi, H.Shibata, and Y.Sawa (2003).
Characterization of aspartate aminotransferase from the cyanobacterium Phormidium lapideum.
  Biosci Biotechnol Biochem, 67, 490-498.  
  16233433 H.Kim, M.Nakaoka, M.Yagi, H.Ashida, K.Hamada, H.Shibata, and Y.Sawa (2003).
Cloning, structural analysis and expression of the gene encoding aspartate aminotransferase from the thermophilic cyanobacterium Phormidium lapideum.
  J Biosci Bioeng, 95, 421-424.  
12595727 J.K.Yang, C.Chang, S.J.Cho, J.Y.Lee, Y.G.Yu, S.H.Eom, and S.W.Suh (2003).
Crystallization and preliminary X-ray analysis of the Mj0684 gene product, a putative aspartate aminotransferase, from Methanococcus jannaschii.
  Acta Crystallogr D Biol Crystallogr, 59, 563-565.  
12717026 V.R.Sobrado, M.Montemartini-Kalisz, H.M.Kalisz, M.C.De La Fuente, H.J.Hecht, and C.Nowicki (2003).
Involvement of conserved asparagine and arginine residues from the N-terminal region in the catalytic mechanism of rat liver and Trypanosoma cruzi tyrosine aminotransferases.
  Protein Sci, 12, 1039-1050.  
11939774 C.G.Cheong, C.B.Bauer, K.R.Brushaber, J.C.Escalante-Semerena, and I.Rayment (2002).
Three-dimensional structure of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica.
  Biochemistry, 41, 4798-4808.
PDB codes: 1kus 1lkc
12145272 J.B.Kwok, R.Kapoor, T.Gotoda, Y.Iwamoto, Y.Iizuka, N.Yamada, K.E.Isaacs, V.V.Kushwaha, W.B.Church, P.R.Schofield, and V.Kapoor (2002).
A missense mutation in kynurenine aminotransferase-1 in spontaneously hypertensive rats.
  J Biol Chem, 277, 35779-35782.  
11238984 C.Vieille, and G.J.Zeikus (2001).
Hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability.
  Microbiol Mol Biol Rev, 65, 1.  
11933245 H.Kagamiyama, and H.Hayashi (2001).
Release of enzyme strain during catalysis reduces the activation energy barrier.
  Chem Rec, 1, 385-394.  
11294630 K.Haruyama, T.Nakai, I.Miyahara, K.Hirotsu, H.Mizuguchi, H.Hayashi, and H.Kagamiyama (2001).
Structures of Escherichia coli histidinol-phosphate aminotransferase and its complexes with histidinol-phosphate and N-(5'-phosphopyridoxyl)-L-glutamate: double substrate recognition of the enzyme.
  Biochemistry, 40, 4633-4644.
PDB codes: 1gew 1gex 1gey
10673430 G.Schneider, H.Käck, and Y.Lindqvist (2000).
The manifold of vitamin B6 dependent enzymes.
  Structure, 8, R1-R6.  
10880431 H.I.Krupka, R.Huber, S.C.Holt, and T.Clausen (2000).
Crystal structure of cystalysin from Treponema denticola: a pyridoxal 5'-phosphate-dependent protein acting as a haemolytic enzyme.
  EMBO J, 19, 3168-3178.
PDB codes: 1c7n 1c7o
11106504 L.Feng, M.K.Geck, A.C.Eliot, and J.F.Kirsch (2000).
Aminotransferase activity and bioinformatic analysis of 1-aminocyclopropane-1-carboxylate synthase.
  Biochemistry, 39, 15242-15249.  
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.