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PDBsum entry 1ajs

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Aminotransferase PDB id
1ajs
Jmol
Contents
Protein chains
412 a.a. *
Ligands
PLA
Waters ×331
* Residue conservation analysis
PDB id:
1ajs
Name: Aminotransferase
Title: Refinement and comparison of the crystal structures of pig cytosolic aspartate aminotransferase and its complex with 2-methylaspartate
Structure: Aspartate aminotransferase. Chain: a. Other_details: the coenzyme pyridoxal 5'-phosphate in subunit a forms a schiff base with the substrate analog 2- methylaspartate, and forms the external aldimine. But due to crystal lattice packings the coenzyme in subunit b is still in the internal aldimine with the side chain of lys 258.. Aspartate aminotransferase.
Source: Sus scrofa. Pig. Organism_taxid: 9823. Organism_taxid: 9823
Biol. unit: Dimer (from PDB file)
Resolution:
1.60Å     R-factor:   0.173    
Authors: S.Rhee,M.M.Silva,C.C.Hyde,P.H.Rogers,C.M.Metzler, D.E.Metzler,A.Arnone
Key ref:
S.Rhee et al. (1997). Refinement and comparisons of the crystal structures of pig cytosolic aspartate aminotransferase and its complex with 2-methylaspartate. J Biol Chem, 272, 17293-17302. PubMed id: 9211866 DOI: 10.1074/jbc.272.28.17293
Date:
08-May-97     Release date:   20-Aug-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00503  (AATC_PIG) -  Aspartate aminotransferase, cytoplasmic
Seq:
Struc:
413 a.a.
412 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 3 residue positions (black crosses)

 Enzyme reactions 
   Enzyme class 1: 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
Bound ligand (Het Group name = PLA) matches with 57.00% similarity
   Enzyme class 2: E.C.2.6.1.3  - Cysteine transaminase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: L-cysteine + 2-oxoglutarate = mercaptopyruvate + L-glutamate
L-cysteine
+ 2-oxoglutarate
= mercaptopyruvate
+ L-glutamate
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     biosynthetic process   15 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.272.28.17293 J Biol Chem 272:17293-17302 (1997)
PubMed id: 9211866  
 
 
Refinement and comparisons of the crystal structures of pig cytosolic aspartate aminotransferase and its complex with 2-methylaspartate.
S.Rhee, M.M.Silva, C.C.Hyde, P.H.Rogers, C.M.Metzler, D.E.Metzler, A.Arnone.
 
  ABSTRACT  
 
Two high resolution crystal structures of cytosolic aspartate aminotransferase from pig heart provide additional insights into the stereochemical mechanism for ligand-induced conformational changes in this enzyme. Structures of the homodimeric native structure and its complex with the substrate analog 2-methylaspartate have been refined, respectively, with 1.74-A x-ray diffraction data to an R value of 0.170, and with 1.6-A data to an R value of 0.173. In the presence of 2-methylaspartate, one of the subunits (subunit 1) shows a ligand-induced conformational change that involves a large movement of the small domain (residues 12-49 and 327-412) to produce a "closed" conformation. No such transition is observed in the other subunit (subunit 2), because crystal lattice contacts lock it in an "open" conformation like that adopted by subunit 1 in the absence of substrate. By comparing the open and closed forms of cAspAT, we propose a stereochemical mechanism for the open-to-closed transition that involves the electrostatic neutralization of two active site arginine residues by the negative charges of the incoming substrate, a large change in the backbone (phi,psi) conformational angles of two key glycine residues, and the entropy-driven burial of a stretch of hydrophobic residues on the N-terminal helix. The calculated free energy for the burial of this "hydrophobic plug" appears to be sufficient to serve as the driving force for domain closure.
 
  Selected figure(s)  
 
Figure 8.
Fig. 8. Atom labeling convention and definition of torsional angles for the internal aldimine.
Figure 9.
Fig. 9. Changes in the solvent-accessible surface area of subunit 1 residues (A) and subunit 2 residues (B) that are associated^ with the open-to-closed transition in subunit 1.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1997, 272, 17293-17302) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22505263 A.A.Lebedev, P.Young, M.N.Isupov, O.V.Moroz, A.A.Vagin, and G.N.Murshudov (2012).
JLigand: a graphical tool for the CCP4 template-restraint library.
  Acta Crystallogr D Biol Crystallogr, 68, 431-440.  
  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.  
20977429 Q.Han, H.Robinson, T.Cai, D.A.Tagle, and J.Li (2011).
Biochemical and structural characterization of mouse mitochondrial aspartate aminotransferase, a newly identified kynurenine aminotransferase-IV.
  Biosci Rep, 31, 323-332.
PDB codes: 3pd6 3pdb
19826765 Q.Han, T.Cai, D.A.Tagle, and J.Li (2010).
Structure, expression, and function of kynurenine aminotransferases in human and rodent brains.
  Cell Mol Life Sci, 67, 353-368.
PDB code: 3hlm
18931110 N.J.Zelyas, H.Cai, T.Kwong, and S.E.Jensen (2008).
Alanylclavam biosynthetic genes are clustered together with one group of clavulanic acid biosynthetic genes in Streptomyces clavuligerus.
  J Bacteriol, 190, 7957-7965.  
18620547 Q.Han, T.Cai, D.A.Tagle, H.Robinson, and J.Li (2008).
Substrate specificity and structure of human aminoadipate aminotransferase/kynurenine aminotransferase II.
  Biosci Rep, 28, 205-215.
PDB code: 3dc1
18186649 Q.Han, Y.G.Gao, H.Robinson, and J.Li (2008).
Structural insight into the mechanism of substrate specificity of aedes kynurenine aminotransferase.
  Biochemistry, 47, 1622-1630.
PDB codes: 2r5c 2r5e
17154432 A.K.Hirsch, F.R.Fischer, and F.Diederich (2007).
Phosphate recognition in structural biology.
  Angew Chem Int Ed Engl, 46, 338-352.  
17683331 I.Matsui, and K.Harata (2007).
Implication for buried polar contacts and ion pairs in hyperthermostable enzymes.
  FEBS J, 274, 4012-4022.  
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
15889412 K.Hirotsu, M.Goto, A.Okamoto, and I.Miyahara (2005).
Dual substrate recognition of aminotransferases.
  Chem Rec, 5, 160-172.  
15189157 C.Bustamante, Y.R.Chemla, N.R.Forde, and D.Izhaky (2004).
Mechanical processes in biochemistry.
  Annu Rev Biochem, 73, 705-748.  
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
12912902 G.Capitani, D.De Biase, C.Aurizi, H.Gut, F.Bossa, and M.G.Grütter (2003).
Crystal structure and functional analysis of Escherichia coli glutamate decarboxylase.
  EMBO J, 22, 4027-4037.
PDB codes: 1pmm 1pmo
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.  
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.  
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
12119022 C.G.Cheong, J.C.Escalante-Semerena, and I.Rayment (2002).
Structural studies of the L-threonine-O-3-phosphate decarboxylase (CobD) enzyme from Salmonella enterica: the apo, substrate, and product-aldimine complexes.
  Biochemistry, 41, 9079-9089.
PDB codes: 1l4b 1l4e 1l4f 1l4g 1l4h 1l4k 1l4l 1l4m 1l4n 1l5f 1l5k 1l5l 1l5m 1l5n 1l5o 1lc5 1lc7 1lc8
11933245 H.Kagamiyama, and H.Hayashi (2001).
Release of enzyme strain during catalysis reduces the activation energy barrier.
  Chem Rec, 1, 385-394.  
11148029 H.Mizuguchi, H.Hayashi, K.Okada, I.Miyahara, K.Hirotsu, and H.Kagamiyama (2001).
Strain is more important than electrostatic interaction in controlling the pKa of the catalytic group in aspartate aminotransferase.
  Biochemistry, 40, 353-360.
PDB codes: 1g4v 1g4x 1g7w 1g7x
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
11264579 N.Yennawar, J.Dunbar, M.Conway, S.Hutson, and G.Farber (2001).
The structure of human mitochondrial branched-chain aminotransferase.
  Acta Crystallogr D Biol Crystallogr, 57, 506-515.
PDB codes: 1ekf 1ekp 1ekv
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.  
11112527 M.M.Islam, H.Hayashi, H.Mizuguchi, and H.Kagamiyama (2000).
The substrate activation process in the catalytic reaction of Escherichia coli aromatic amino acid aminotransferase.
  Biochemistry, 39, 15418-15428.  
10698925 T.Clausen, A.Schlegel, R.Peist, E.Schneider, C.Steegborn, Y.S.Chang, A.Haase, G.P.Bourenkov, H.D.Bartunik, and W.Boos (2000).
X-ray structure of MalY from Escherichia coli: a pyridoxal 5'-phosphate-dependent enzyme acting as a modulator in mal gene expression.
  EMBO J, 19, 831-842.
PDB code: 1d2f
10684605 T.Fujii, M.Maeda, H.Mihara, T.Kurihara, N.Esaki, and Y.Hata (2000).
Structure of a NifS homologue: X-ray structure analysis of CsdB, an Escherichia coli counterpart of mammalian selenocysteine lyase.
  Biochemistry, 39, 1263-1273.
PDB code: 1c0n
10079072 A.A.Morollo, G.A.Petsko, and D.Ringe (1999).
Structure of a Michaelis complex analogue: propionate binds in the substrate carboxylate site of alanine racemase.
  Biochemistry, 38, 3293-3301.
PDB code: 2sfp
9930977 A.Okamoto, S.Ishii, K.Hirotsu, and H.Kagamiyama (1999).
The active site of Paracoccus denitrificans aromatic amino acid aminotransferase has contrary properties: flexibility and rigidity.
  Biochemistry, 38, 1176-1184.
PDB codes: 2ay1 2ay2 2ay3 2ay4 2ay5 2ay6 2ay7 2ay8 2ay9
10029535 T.Nakai, K.Okada, S.Akutsu, I.Miyahara, S.Kawaguchi, R.Kato, S.Kuramitsu, and K.Hirotsu (1999).
Structure of Thermus thermophilus HB8 aspartate aminotransferase and its complex with maleate.
  Biochemistry, 38, 2413-2424.
PDB codes: 1bjw 1bkg
10417420 T.P.Ko, S.P.Wu, W.Z.Yang, H.Tsai, and H.S.Yuan (1999).
Crystallization and preliminary crystallographic analysis of the Escherichia coli tyrosine aminotransferase.
  Acta Crystallogr D Biol Crystallogr, 55, 1474-1477.
PDB code: 3tat
  10595543 W.Blankenfeldt, C.Nowicki, M.Montemartini-Kalisz, H.M.Kalisz, and H.J.Hecht (1999).
Crystal structure of Trypanosoma cruzi tyrosine aminotransferase: substrate specificity is influenced by cofactor binding mode.
  Protein Sci, 8, 2406-2417.
PDB code: 1bw0
9790670 H.Hayashi, H.Mizuguchi, and H.Kagamiyama (1998).
The imine-pyridine torsion of the pyridoxal 5'-phosphate Schiff base of aspartate aminotransferase lowers its pKa in the unliganded enzyme and is crucial for the successive increase in the pKa during catalysis.
  Biochemistry, 37, 15076-15085.  
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.