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PDBsum entry 1ama

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protein ligands links
Transferase(aminotransferase) PDB id
1ama
Jmol
Contents
Protein chain
401 a.a. *
Ligands
PLA
Waters ×312
* Residue conservation analysis
PDB id:
1ama
Name: Transferase(aminotransferase)
Title: Domain closure in mitochondrial aspartate aminotransferase
Structure: Aspartate aminotransferase. Chain: a. Engineered: yes
Source: Gallus gallus. Chicken. Organism_taxid: 9031. Organ: heart. Expressed in: unidentified. Expression_system_taxid: 32644
Biol. unit: Dimer (from PQS)
Resolution:
2.30Å     R-factor:   0.159    
Authors: M.G.Vincent,J.-C.Genovesio-Taverne,J.N.Jansonius
Key ref:
C.A.McPhalen et al. (1992). Domain closure in mitochondrial aspartate aminotransferase. J Mol Biol, 227, 197-213. PubMed id: 1522585 DOI: 10.1016/0022-2836(92)90691-C
Date:
05-Feb-92     Release date:   31-Oct-93    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P00508  (AATM_CHICK) -  Aspartate aminotransferase, mitochondrial
Seq:
Struc:
423 a.a.
401 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 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 57.69% similarity
   Enzyme class 2: E.C.2.6.1.7  - Kynurenine--oxoglutarate transaminase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
      Reaction: L-kynurenine + 2-oxoglutarate = 4-(2-aminophenyl)-2,4-dioxobutanoate + L-glutamate
L-kynurenine
+ 2-oxoglutarate
= 4-(2-aminophenyl)-2,4-dioxobutanoate
+ 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     mitochondrion   2 terms 
  Biological process     small molecule metabolic process   9 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
    reference    
 
 
DOI no: 10.1016/0022-2836(92)90691-C J Mol Biol 227:197-213 (1992)
PubMed id: 1522585  
 
 
Domain closure in mitochondrial aspartate aminotransferase.
C.A.McPhalen, M.G.Vincent, D.Picot, J.N.Jansonius, A.M.Lesk, C.Chothia.
 
  ABSTRACT  
 
The subunits of the dimeric enzyme aspartate aminotransferase have two domains: one large and one small. The active site lies in a cavity that is close to both the subunit interface and the interface between the two domains. On binding the substrate the domains close together. This closure completely buries the substrate in the active site and moves two arginine side-chains so they form salt bridges with carboxylate groups of the substrate. The salt bridges hold the substrate close to the pyridoxal 5'-phosphate cofactor and in the right position and orientation for the catalysis of the transamination reaction. We describe here the structural changes that produce the domain movements and the closure of the active site. Structural changes occur at the interface between the domains and within the small domain itself. On closure, the core of the small domain rotates by 13 degrees relative to the large domain. Two other regions of the small domain, which form part of the active site, move somewhat differently. A loop, residues 39 to 49, above the active site moves about 1 A less than the core of the small domain. A helix within the small domain forms the "door" of the active site. It moves with the core of the small domain and, in addition, shifts by 1.2 A, rotates by 10 degrees, and switches its first turn from the alpha to the 3(10) conformation. This results in the helix closing the active site. The domain movements are produced by a co-ordinated series of small changes. Within one subunit the polypeptide chain passes twice between the large and small domains. One link involves a peptide in an extended conformation. The second link is in the middle of a long helix that spans both domains. At the interface this helix is kinked and, on closure, the angle of the kink changes to accommodate the movement of the small domain. The interface between the domains is formed by 15 residues in the large domain packing against 12 residues in the small domain and the manner in which these residues pack is essentially the same in the open and closed structures. Domain movements involve changes in the main-chain and side-chain torsion angles in the residues on both sides of the interface. Most of these changes are small; only a few side-chains switch to new conformations.(ABSTRACT TRUNCATED AT 400 WORDS)
 
  Selected figure(s)  
 
Figure 1.
Fig. 1.
Figure 3.
Figure 3. he magnitude of the structural changes that occur on domain closure. (a) The differences in the positions of C'' atoms in the open and closed forms of AATase. The differences are those measured after the open and closed forms of the subunit have been superposed by a fit of the main-cain atoms in the large domain regions that have the same structure in the 2 forms (see the text and Fig. l(b)). (b) St ructural differences within the small domain tht occur on omain closure. The differences shown here are those found after the small domains in the open and closed forms of the subunit have been superposed by a fit of the regions that have the same structure in the 2 forms (see the text). Residues 15 to 31 iffer in position because thy move more than the core of the small domain; residues 39 to 47 differ because they move less (see the text).
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1992, 227, 197-213) copyright 1992.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

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Use of 1H-15N heteronuclear multiple-quantum coherence NMR spectroscopy to study the active site of aspartate aminotransferase.
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Protein folding: the endgame.
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Refinement and comparisons of the crystal structures of pig cytosolic aspartate aminotransferase and its complex with 2-methylaspartate.
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9370432 T.B.Woolf (1997).
Molecular dynamics of individual alpha-helices of bacteriorhodopsin in dimyristol phosphatidylocholine. I. Structure and dynamics.
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8856080 P.Kasper, M.Sterk, P.Christen, and H.Gehring (1996).
Molecular-dynamics simulation of domain movements in aspartate aminotransferase.
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Time-resolved fluorescence of tryptophan synthase.
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Crystal structures and solution studies of oxime adducts of mitochondrial aspartate aminotransferase.
  Eur J Biochem, 236, 1025-1032.
PDB codes: 1oxo 1oxp
  8528073 J.J.Onuffer, and J.F.Kirsch (1995).
Redesign of the substrate specificity of Escherichia coli aspartate aminotransferase to that of Escherichia coli tyrosine aminotransferase by homology modeling and site-directed mutagenesis.
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7588727 L.Birolo, E.Sandmeier, P.Christen, and R.A.John (1995).
The roles of Tyr70 and Tyr225 in aspartate aminotransferase assessed by analysing the effects of mutations on the multiple reactions of the substrate analogue serine o-sulphate.
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Active site model for gamma-aminobutyrate aminotransferase explains substrate specificity and inhibitor reactivities.
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7780027 W.R.Fiori, and G.L.Millhauser (1995).
Exploring the peptide 3(10)-helix reversible alpha-helix equilibrium with double label electron spin resonance.
  Biopolymers, 37, 243-250.  
8110969 S.E.Huston, and G.R.Marshall (1994).
Alpha/3(10)-helix transitions in alpha-methylalanine homopeptides: conformational transition pathway and potential of mean force.
  Biopolymers, 34, 75-90.  
8404895 A.Garnier, and R.A.John (1993).
Probes of ligand-induced conformational change in aspartate aminotransferase.
  Eur J Biochem, 216, 763-768.  
  8428572 S.Subramaniam, M.Gerstein, D.Oesterhelt, and R.Henderson (1993).
Electron diffraction analysis of structural changes in the photocycle of bacteriorhodopsin.
  EMBO J, 12, 1-8.  
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.