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PDBsum entry 1cq8

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protein ligands links
Transferase PDB id
1cq8
Jmol
Contents
Protein chain
396 a.a. *
Ligands
PY6
Waters ×109
* Residue conservation analysis
PDB id:
1cq8
Name: Transferase
Title: Aspartate aminotransferase (E.C. 2.6.1.1) complexed with c6- 5p-phosphate
Structure: Aspartate aminotransferase (2.6.1.1). Chain: a. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.40Å     R-factor:   0.213     R-free:   0.270
Authors: J.Ishijima,T.Nakai,S.Kawaguchi,K.Hirotsu,S.Kuramitsu
Key ref:
J.Ishijima et al. (2000). Free energy requirement for domain movement of an enzyme. J Biol Chem, 275, 18939-18945. PubMed id: 10858450 DOI: 10.1074/jbc.275.25.18939
Date:
06-Aug-99     Release date:   20-Dec-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

 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 = PY6) 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    
 
 
DOI no: 10.1074/jbc.275.25.18939 J Biol Chem 275:18939-18945 (2000)
PubMed id: 10858450  
 
 
Free energy requirement for domain movement of an enzyme.
J.Ishijima, T.Nakai, S.Kawaguchi, K.Hirotsu, S.Kuramitsu.
 
  ABSTRACT  
 
Domain movement is sometimes essential for substrate recognition by an enzyme. X-ray crystallography of aminotransferase with a series of aliphatic substrates showed that the domain movement of aspartate aminotransferase was changed dramatically from an open to a closed form by the addition of only one CH(2) to the side chain of the C4 substrate CH(3)(CH(2))C((alpha))H(NH(3)(+))COO(-). These crystallographic results and reaction kinetics (Kawaguchi, S., Nobe, Y., Yasuoka, J., Wakamiya, T., Kusumoto, S., and Kuramitsu, S. (1997) J. Biochem. (Tokyo) 122, 55-63; Kawaguchi, S. and Kuramitsu, S. (1998) J. Biol. Chem. 273, 18353-18364) enabled us to estimate the free energy required for the domain movement.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. The mechanisms of domain movement. The -helix 1 (Ile^17-Arg25) and the loop region (Ala^26-Ile^37) of the C3-PLP or C4-PLP complex in the open form (these residues are colored pink and the others gray) change to the closed form on binding of C5-PLP or C6-PLP (colored green). Ile^17 and Ile^37 are anchored at the active site by hydrophobic interactions with the substrate. Leu18 is located at the N-terminal end of -helix 1 and pulls the helix into the active pocket to shield the active site from the solvent. This tugging of residues from Ile^17 to Ile^37 changes the enzyme from the open to the closed form.
Figure 3.
Fig. 3. Stereoviews of AspAT bound to substrate analogs. Only Arg292* and the substrate analogs are indicated for clarity. a, the substrate analog is C4-PLP (the moiety of coenzyme is labeled as PLP and that of substrate as C4). The active-site conformation of the C4-PLP complex is almost identical to that of substrate-free AspAT (8, 9). b, the substrate analog is C5-PLP. Each substrate analog and the side chain of Arg292* are superimposed onto the (F[o] F[c]) omit map contoured at 2.5 (a) and 3 (b) with these atoms omitted. c, the structure of the C3-PLP complex (magenta), C4-PLP complex (yellow), C5-PLP complex (cyan), and C6-PLP complex (green). Note that the side chain orientation of Arg292* changes drastically depending on substrate. These figures were produced using the program O (23).
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2000, 275, 18939-18945) copyright 2000.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21278708 U.Kanjee, I.Gutsche, E.Alexopoulos, B.Zhao, M.El Bakkouri, G.Thibault, K.Liu, S.Ramachandran, J.Snider, E.F.Pai, and W.A.Houry (2011).
Linkage between the bacterial acid stress and stringent responses: the structure of the inducible lysine decarboxylase.
  EMBO J, 30, 931-944.
PDB codes: 3n75 3q16
20551137 P.Carbonell, and J.L.Faulon (2010).
Molecular signatures-based prediction of enzyme promiscuity.
  Bioinformatics, 26, 2012-2019.  
19338303 Q.Han, H.Robinson, T.Cai, D.A.Tagle, and J.Li (2009).
Structural insight into the inhibition of human kynurenine aminotransferase I/glutamine transaminase K.
  J Med Chem, 52, 2786-2793.
PDB codes: 3fvs 3fvu 3fvx
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.