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Ligase PDB id
1juy
Jmol
Contents
Protein chain
431 a.a. *
Ligands
_PI
GDP
H5P
HDA
Metals
_MG
Waters ×699
* Residue conservation analysis
PDB id:
1juy
Name: Ligase
Title: Refined crystal structure of adenylosuccinate synthetase from escherichia coli complexed with hydantocidin 5'- phosphate gdp, hpo4(2-), mg2+, and hadacidin
Structure: Adenylosuccinate synthetase. Chain: a. Ec: 6.3.4.4
Source: Escherichia coli. Organism_taxid: 562. Strain: pur a strain h1238 (a gift from dr. B. Bachman (genetic center, yale university)). Atcc: 5408, coli genetic stock center
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
2.50Å     R-factor:   0.195     R-free:   0.250
Authors: B.W.Poland,S.-F.Lee,M.V.Subramanian,D.L.Siehl,R.J.Anderson, H.J.Fromm,R.B.Honzatko
Key ref:
B.W.Poland et al. (1996). Refined crystal structure of adenylosuccinate synthetase from Escherichia coli complexed with hydantocidin 5'-phosphate, GDP, HPO4(2-), Mg2+, and hadacidin. Biochemistry, 35, 15753-15759. PubMed id: 8961938 DOI: 10.1021/bi961758r
Date:
25-Sep-96     Release date:   24-Jun-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0A7D4  (PURA_ECOLI) -  Adenylosuccinate synthetase
Seq:
Struc: 		432 a.a.
432 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
Bound ligand (Het Group name = PI)
corresponds exactly 		+ 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   2 terms 
  Biological process     nucleobase, nucleoside and nucleotide interconversion   3 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi961758r Biochemistry 35:15753-15759 (1996)
PubMed id: 8961938  
 
 
Refined crystal structure of adenylosuccinate synthetase from Escherichia coli complexed with hydantocidin 5'-phosphate, GDP, HPO4(2-), Mg2+, and hadacidin.
B.W.Poland, S.F.Lee, M.V.Subramanian, D.L.Siehl, R.J.Anderson, H.J.Fromm, R.B.Honzatko.
 
  ABSTRACT  
 
A crystal structure of adenylosuccinate synthetase from Escherichia coli, complexed with 5'-phosphate, GDP, HPO4(2-), Mg2+, and hadacidin at 100 K, has been refined to an Rfactor of 0.195 against data to 2.6 A resolution. Bond lengths and angles deviate from expected values by 0.012 A and 1.86 degrees, respectively. Lys 16 and backbone amides 15-17 and 42 interact with the phosphates of GDP, while Ser 414, Asp 333, and backbone amides 331 and 416 interact with the base. Mg2+ is octahedrally coordinated. Oxygen atoms from GDP, phosphate, and hadacidin define the equatorial plane of coordination of the Mg2+, while backbone carbonyl 40 and the side chain of Asp 13 are the apical ligands. HPO4(2-) hydrogen bonds with Lys 16, His 41, backbone amides 13, 40, and 224, and the base moiety of the hydantocidin inhibitor. The carboxylate of hadacidin interacts with Arg 303 and Thr 301; its N-formyl group coordinates to Mg2+, and its hydroxyl group hydrogen bonds with Asp 13. The 5'-phosphate of the hydantocidin inhibitor interacts with Asn 38, Thr 129, and Thr 239 but is approximately 3.5 A from Arg 143 (related by molecular 2-fold symmetry). The base moiety of hydantocidin 5'-phosphate hydrogen bonds to Gln 224 and participates in a hydrogen-bonded network that includes the phosphate molecule, several water molecules, and Asp 13. Hydantocidin 5'-phosphate, GDP, HPO4(2-), and Mg2+ may represent a set of synergistic inhibitors even more effective than the combination of IMP, GDP, NO3-, and Mg2+.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
12004071 C.V.Iancu, T.Borza, H.J.Fromm, and R.B.Honzatko (2002).
IMP, GTP, and 6-phosphoryl-IMP complexes of recombinant mouse muscle adenylosuccinate synthetase.
  J Biol Chem, 277, 26779-26787.
PDB codes: 1iwe 1lny 1lon 1loo
12186864 C.V.Iancu, T.Borza, H.J.Fromm, and R.B.Honzatko (2002).
Feedback inhibition and product complexes of recombinant mouse muscle adenylosuccinate synthetase.
  J Biol Chem, 277, 40536-40543.
PDB codes: 1mez 1mf0 1mf1
11560929 C.V.Iancu, T.Borza, J.Y.Choe, H.J.Fromm, and R.B.Honzatko (2001).
Recombinant mouse muscle adenylosuccinate synthetase: overexpression, kinetics, and crystal structure.
  J Biol Chem, 276, 42146-42152.
PDB code: 1j4b
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.  
10364182 Z.Hou, M.Cashel, H.J.Fromm, and R.B.Honzatko (1999).
Effectors of the stringent response target the active site of Escherichia coli adenylosuccinate synthetase.
  J Biol Chem, 274, 17505-17510.
PDB codes: 1ch8 1cib
9632649 W.Wang, A.Gorrell, Z.Hou, R.B.Honzatko, and H.J.Fromm (1998).
Ambiguities in mapping the active site of a conformationally dynamic enzyme by directed mutation. Role of dynamics in structure-function correlations in Escherichia coli adenylosuccinate synthetase.
  J Biol Chem, 273, 16000-16004.  
9182542 B.W.Poland, C.Bruns, H.J.Fromm, and R.B.Honzatko (1997).
Entrapment of 6-thiophosphoryl-IMP in the active site of crystalline adenylosuccinate synthetase from Escherichia coli.
  J Biol Chem, 272, 15200-15205.
PDB codes: 1ksz 1nht
9202000 W.Wang, Z.Hou, R.B.Honzatko, and H.J.Fromm (1997).
Relationship of conserved residues in the IMP binding site to substrate recognition and catalysis in Escherichia coli adenylosuccinate synthetase.
  J Biol Chem, 272, 16911-16916.  
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.