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PDBsum entry 1g7x

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Transferase PDB id
1g7x
Jmol
Contents
Protein chain
396 a.a. *
Ligands
PLP
Waters ×187
* Residue conservation analysis
PDB id:
1g7x
Name: Transferase
Title: Aspartate aminotransferase active site mutant n194a/r292l/r3
Structure: Aspartate aminotransferase. Chain: a. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562
Biol. unit: Dimer (from PDB file)
Resolution:
2.20Å     R-factor:   0.229    
Authors: H.Mizuguchi,H.Hayashi,K.Okada,I.Miyahara,K.Hirotsu,H.Kagamiy
Key ref:
H.Mizuguchi et al. (2001). Strain is more important than electrostatic interaction in controlling the pKa of the catalytic group in aspartate aminotransferase. Biochemistry, 40, 353-360. PubMed id: 11148029 DOI: 10.1021/bi001403e
Date:
15-Nov-00     Release date:   29-Nov-00    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
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 3 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 = PLP) matches with 93.75% 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    
 
 
DOI no: 10.1021/bi001403e Biochemistry 40:353-360 (2001)
PubMed id: 11148029  
 
 
Strain is more important than electrostatic interaction in controlling the pKa of the catalytic group in aspartate aminotransferase.
H.Mizuguchi, H.Hayashi, K.Okada, I.Miyahara, K.Hirotsu, H.Kagamiyama.
 
  ABSTRACT  
 
Systematic single and multiple replacement studies have been applied to Escherichia coli aspartate aminotransferase to probe the electrostatic effect of the two substrate-binding arginine residues, Arg292 and Arg386, and the structural effect of the pyridoxal 5'-phosphate-Asn194-Arg386 hydrogen-bond linkage system (PLP-N-R) on the pK(a) value of the Schiff base formed between pyridoxal 5'-phosphate (PLP) and Lys258. The electrostatic effects of the two arginine residues cannot be assessed by simple mutational studies of the residues. PLP-N-R lowers the pK(a) value of the PLP-Lys258 Schiff base by keeping it in the distorted conformation, which is unfavorable for protonation. Mutation of Arg386 eliminates its hydrogen bond with Asn194 and partially disrupts PLP-N-R, thereby relaxing the strain of the Schiff base. On the other hand, mutation of Arg292, the large domain residue that interacts with the small domain residue Asp15, makes the domain opening easier. Because PLP-N-R lies between the two domains, the domain opening increases the strain of the Schiff base. Therefore, the true electrostatic effects of Arg292 and Arg386 could be derived from mutational analysis of the enzyme in which PLP-N-R had been completely disrupted by the Asn194Ala mutation. Through the analyses, we could dissect the electrostatic and structural effects of the arginine mutations on the Schiff base pK(a). The positive charges of the two arginine residues and the PLP-N-R-mediated strain of the Schiff base lower the Schiff base pK(a) by 0.7 and 1.7, respectively. Thus, the electrostatic effect of the arginine residues is not as strong as has historically been thought, and this finding substantiates our recent finding that the imine-pyridine torsion of the Schiff base is the primary determinant (2.8 unit decrease) of the extremely low pK(a) value of the Schiff base [Hayashi, H., Mizuguchi, H., and Kagamiyama, H. (1998) Biochemistry 37, 15076-15085].
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20871599 M.Höhne, S.Schätzle, H.Jochens, K.Robins, and U.T.Bornscheuer (2010).
Rational assignment of key motifs for function guides in silico enzyme identification.
  Nat Chem Biol, 6, 807-813.  
17989071 Y.Yoshikane, N.Yokochi, M.Yamasaki, K.Mizutani, K.Ohnishi, B.Mikami, H.Hayashi, and T.Yagi (2008).
Crystal structure of pyridoxamine-pyruvate aminotransferase from Mesorhizobium loti MAFF303099.
  J Biol Chem, 283, 1120-1127.
PDB codes: 2z9u 2z9v 2z9w 2z9x
15608117 A.P.Dubnovitsky, E.G.Kapetaniou, and A.C.Papageorgiou (2005).
Enzyme adaptation to alkaline pH: atomic resolution (1.08 A) structure of phosphoserine aminotransferase from Bacillus alcalophilus.
  Protein Sci, 14, 97.
PDB codes: 1w23 1w3u
15883191 A.P.Dubnovitsky, R.B.Ravelli, A.N.Popov, and A.C.Papageorgiou (2005).
Strain relief at the active site of phosphoserine aminotransferase induced by radiation damage.
  Protein Sci, 14, 1498-1507.
PDB codes: 2bhx 2bi1 2bi2 2bi3 2bi5 2bi9 2bia 2bie 2big
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
12488449 H.Hayashi, H.Mizuguchi, I.Miyahara, Y.Nakajima, K.Hirotsu, and H.Kagamiyama (2003).
Conformational change in aspartate aminotransferase on substrate binding induces strain in the catalytic group and enhances catalysis.
  J Biol Chem, 278, 9481-9488.
PDB codes: 1ix6 1ix7 1ix8
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.  
11967363 E.Deu, K.A.Koch, and J.F.Kirsch (2002).
The role of the conserved Lys68*:Glu265 intersubunit salt bridge in aspartate aminotransferase kinetics: multiple forced covariant amino acid substitutions in natural variants.
  Protein Sci, 11, 1062-1073.  
11248682 A.Matharu, H.Hayashi, H.Kagamiyama, B.Maras, and R.A.John (2001).
Contributions of the substrate-binding arginine residues to maleate-induced closure of the active site of Escherichia coli aspartate aminotransferase.
  Eur J Biochem, 268, 1640-1645.  
11933245 H.Kagamiyama, and H.Hayashi (2001).
Release of enzyme strain during catalysis reduces the activation energy barrier.
  Chem Rec, 1, 385-394.  
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.