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PDBsum entry 1arh

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protein ligands Protein-protein interface(s) links
Transferase (aminotransferase) PDB id
1arh
Jmol
Contents
Protein chains
396 a.a. *
Ligands
PPD ×2
Waters ×371
* Residue conservation analysis
PDB id:
1arh
Name: Transferase (aminotransferase)
Title: Aspartate aminotransferase, y225r/r386a mutant
Structure: Aspartate aminotransferase. Chain: a, b. Synonym: aspartate transaminase. Engineered: yes. Mutation: yes. Other_details: 600 times increased beta-decarboxylase activity
Source: Escherichia coli. Organism_taxid: 562. Strain: ty103. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.30Å     R-factor:   0.219    
Authors: V.N.Malashkevich,J.N.Jansonius
Key ref: R.Graber et al. (1995). Changing the reaction specificity of a pyridoxal-5'-phosphate-dependent enzyme. Eur J Biochem, 232, 686-690. PubMed id: 7556224
Date:
23-Aug-95     Release date:   14-Nov-95    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P00509  (AAT_ECOLI) -  Aspartate aminotransferase
Seq:
Struc:
396 a.a.
396 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 2 residue positions (black crosses)

 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
Bound ligand (Het Group name = PPD) matches with 60.00% similarity
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   4 terms 
  Biochemical function     catalytic activity     8 terms  

 

 
    reference    
 
 
Eur J Biochem 232:686-690 (1995)
PubMed id: 7556224  
 
 
Changing the reaction specificity of a pyridoxal-5'-phosphate-dependent enzyme.
R.Graber, P.Kasper, V.N.Malashkevich, E.Sandmeier, P.Berger, H.Gehring, J.N.Jansonius, P.Christen.
 
  ABSTRACT  
 
The electron distribution in the coenzyme-substrate adduct of aspartate aminotransferase was changed by replacing active-site Arg386 with alanine and introducing a new arginine residue nearby. [Y225R, R386A]Aspartate aminotransferase decarboxylates L-aspartate to L-alanine (kcat = 0.04 s-1), while its transaminase activity towards dicarboxylic amino acids is decreased by three orders of magnitude (kcat = 0.19 s-1). Molecular-dynamics simulations based on the crystal structure of the mutant enzyme suggest that a new hydrogen bond to the imine N atom of the pyridoxal-5'-phosphate- aspartate adduct and an altered electrostatic potential around its beta-carboxylate group underlie the 650,000-fold increase in the ratio of beta-decarboxylase/transaminase activity.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21210729 R.Day, X.Qu, R.Swanson, Z.Bohannan, R.Bliss, and J.Tsai (2011).
Relative packing groups in template-based structure prediction: cooperative effects of true positive constraints.
  J Comput Biol, 18, 17-26.  
  20014435 P.H.Lodha, A.F.Jaworski, and S.M.Aitken (2010).
Characterization of site-directed mutants of residues R58, R59, D116, W340 and R372 in the active site of E. coli cystathionine beta-lyase.
  Protein Sci, 19, 383-391.  
18175322 L.Qu, J.Wan, Y.Cao, Y.Zhang, R.Chen, and Y.Huang (2008).
Analyzing and modeling the inhibitory effect of phosphatidic acid on the GTP-gamma-S binding activity of Goalpha.
  Proteins, 71, 1732-1743.  
17300176 S.Lima, R.Khristoforov, C.Momany, and R.S.Phillips (2007).
Crystal structure of Homo sapiens kynureninase.
  Biochemistry, 46, 2735-2744.
PDB code: 2hzp
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.  
10691982 R.Talwar, J.R.Jagath, N.A.Rao, and H.S.Savithri (2000).
His230 of serine hydroxymethyltransferase facilitates the proton abstraction step in catalysis.
  Eur J Biochem, 267, 1441-1446.  
10671998 R.Talwar, N.A.Rao, and H.S.Savithri (2000).
A change in reaction specificity of sheep liver serine hydroxymethyltransferase. Induction of NADH oxidation upon mutation of His230 to Tyr.
  Eur J Biochem, 267, 929-934.  
10398410 A.Huber, S.Demartis, and D.Neri (1999).
The use of biosensor technology for the engineering of antibodies and enzymes.
  J Mol Recognit, 12, 198-216.  
9880502 B.Mouratou, P.Kasper, H.Gehring, and P.Christen (1999).
Conversion of tyrosine phenol-lyase to dicarboxylic amino acid beta-lyase, an enzyme not found in nature.
  J Biol Chem, 274, 1320-1325.  
10099128 P.J.O'Brien, and D.Herschlag (1999).
Catalytic promiscuity and the evolution of new enzymatic activities.
  Chem Biol, 6, R91.  
10531314 R.Graber, P.Kasper, V.N.Malashkevich, P.Strop, H.Gehring, J.N.Jansonius, and P.Christen (1999).
Conversion of aspartate aminotransferase into an L-aspartate beta-decarboxylase by a triple active-site mutation.
  J Biol Chem, 274, 31203-31208.  
9268327 R.A.Vacca, S.Giannattasio, R.Graber, E.Sandmeier, E.Marra, and P.Christen (1997).
Active-site Arg --> Lys substitutions alter reaction and substrate specificity of aspartate aminotransferase.
  J Biol Chem, 272, 21932-21937.  
9265632 Y.Park, J.Luo, P.G.Schultz, and J.F.Kirsch (1997).
Noncoded amino acid replacement probes of the aspartate aminotransferase mechanism.
  Biochemistry, 36, 10517-10525.  
8797848 R.Contestabile, and R.A.John (1996).
The mechanism of high-yielding chiral syntheses catalysed by wild-type and mutant forms of aspartate aminotransferase.
  Eur J Biochem, 240, 150-155.  
  8976563 W.M.Jones, P.W.van Ophem, M.A.Pospischil, D.Ringe, G.Petsko, K.Soda, and J.M.Manning (1996).
The ubiquitous cofactor NADH protects against substrate-induced inhibition of a pyridoxal enzyme.
  Protein Sci, 5, 2545-2551.  
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 code is shown on the right.