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PDBsum entry 1nht

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protein ligands metals links
Ligase PDB id
1nht
Jmol
Contents
Protein chain
431 a.a. *
Ligands
GDP
HDA
PGS
Metals
_MG
Waters ×1362
* Residue conservation analysis
PDB id:
1nht
Name: Ligase
Title: Entrapment of 6-thiophosphoryl-imp in the active site of cry adenylosuccinate synthetase from escherichia coli data coll 100k
Structure: Adenylosuccinate synthetase. Chain: a. Ec: 6.3.4.4
Source: Escherichia coli. Organism_taxid: 562. Strain: pur a strain h1238. Atcc: coli genetic stock center, strain number 5408. Other_details: a gift from dr. B. Bachman, genetic center, university
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
2.50Å     R-factor:   0.206     R-free:   0.255
Authors: B.W.Poland,C.A.Bruns,H.J.Fromm,R.B.Honzatko
Key ref:
B.W.Poland et al. (1997). Entrapment of 6-thiophosphoryl-IMP in the active site of crystalline adenylosuccinate synthetase from Escherichia coli. J Biol Chem, 272, 15200-15205. PubMed id: 9182542 DOI: 10.1074/jbc.272.24.15200
Date:
12-Jan-97     Release date:   08-Oct-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A7D4  (PURA_ECOLI) -  Adenylosuccinate synthetase
Seq:
Struc:
432 a.a.
431 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.3.4.4  - Adenylosuccinate synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
AMP and GMP Biosynthesis
      Reaction: GTP + IMP + L-aspartate = GDP + phosphate + N6-(1,2-dicarboxyethyl)- AMP
GTP
+ IMP
+
L-aspartate
Bound ligand (Het Group name = HDA)
matches with 41.00% similarity
=
GDP
Bound ligand (Het Group name = GDP)
corresponds exactly
+ phosphate
+ N(6)-(1,2-dicarboxyethyl)- AMP
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     membrane   3 terms 
  Biological process     'de novo' AMP biosynthetic process   5 terms 
  Biochemical function     nucleotide binding     6 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.272.24.15200 J Biol Chem 272:15200-15205 (1997)
PubMed id: 9182542  
 
 
Entrapment of 6-thiophosphoryl-IMP in the active site of crystalline adenylosuccinate synthetase from Escherichia coli.
B.W.Poland, C.Bruns, H.J.Fromm, R.B.Honzatko.
 
  ABSTRACT  
 
Crystal structures of adenylosuccinate synthetase from Escherichia coli complexed with Mg2+, 6-thiophosphoryl-IMP, GDP, and hadacidin at 298 and 100 K have been refined to R-factors of 0.171 and 0.206 against data to 2.8 and 2.5 A resolution, respectively. Interactions of GDP, Mg2+ and hadacidin are similar to those observed for the same ligands in the complex of IMP, GDP, NO3-, Mg2+ and hadacidin (Poland, B. W., Fromm, H. J. & Honzatko, R. B. (1996). J. Mol. Biol. 264, 1013-1027). Although crystals were grown from solutions containing 6-mercapto-IMP and GTP, the electron density at the active site is consistent with 6-thiophosphoryl-IMP and GDP. Asp-13 and Gln-224 probably work in concert to stabilize the 6-thioanion of 6-mercapto-IMP, which in turn is the nucleophile in the displacement of GDP from the gamma-phosphate of GTP. Once formed, 6-thiophosphoryl-IMP is stable in the active site of the enzyme under the conditions of the structural investigation. The direct observation of 6-thiophosphoryl-IMP in the active site is consistent with the putative generation of 6-phosphoryl-IMP along the reaction pathway of the synthetase.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Stereo view of bound ligands in relation to a trace of -carbons of adenylosuccinate synthetase.
Figure 6.
Fig. 6. Proposed mechanism for the phosphotransfer reaction governed by the synthetase, involving 6-mercapto-IMP as a substrate. L-Aspartate is not shown here but is putatively coordinated to Mg2+ as shown in Fig. 7.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1997, 272, 15200-15205) copyright 1997.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
10346917 J.Y.Choe, B.W.Poland, H.J.Fromm, and R.B.Honzatko (1999).
Mechanistic implications from crystalline complexes of wild-type and mutant adenylosuccinate synthetases from Escherichia coli.
  Biochemistry, 38, 6953-6961.
PDB codes: 1cg0 1cg1 1cg3 1cg4
10231526 P.Lee, A.Gorrell, H.J.Fromm, and R.F.Colman (1999).
Implication of arginine-131 and arginine-303 in the substrate site of adenylosuccinate synthetase of Escherichia coli by affinity labeling with 6-(4-bromo-2,3-dioxobutyl)thioadenosine 5'-monophosphate.
  Biochemistry, 38, 5754-5763.  
9636022 J.B.Thoden, S.G.Miran, J.C.Phillips, A.J.Howard, F.M.Raushel, and H.M.Holden (1998).
Carbamoyl phosphate synthetase: caught in the act of glutamine hydrolysis.
  Biochemistry, 37, 8825-8831.
PDB code: 1a9x
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.