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PDBsum entry 1gim

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protein ligands metals links
Ligase PDB id
1gim
Jmol
Contents
Protein chain
431 a.a. *
Ligands
NO3
HDA
IMP
GDP
Metals
_MG
Waters ×1062
* Residue conservation analysis
PDB id:
1gim
Name: Ligase
Title: Crystal structure of adenylosuccinate synthetase from escher complexed with gdp, imp, hadacidin, no3-, and mg2+. Data co 100k (ph 6.5)
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: gift from dr. B. Bachman (genetic center, ya university)
Biol. unit: Homo-Dimer (from PDB file)
Resolution:
2.50Å     R-factor:   0.206     R-free:   0.273
Authors: B.W.Poland,H.J.Fromm,R.B.Honzatko
Key ref:
B.W.Poland et al. (1996). Crystal structures of adenylosuccinate synthetase from Escherichia coli complexed with GDP, IMP hadacidin, NO3-, and Mg2+. J Mol Biol, 264, 1013-1027. PubMed id: 9000627 DOI: 10.1006/jmbi.1996.0693
Date:
15-Jun-96     Release date:   23-Dec-96    
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
Bound ligand (Het Group name = IMP)
corresponds exactly
+
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: 10.1006/jmbi.1996.0693 J Mol Biol 264:1013-1027 (1996)
PubMed id: 9000627  
 
 
Crystal structures of adenylosuccinate synthetase from Escherichia coli complexed with GDP, IMP hadacidin, NO3-, and Mg2+.
B.W.Poland, H.J.Fromm, R.B.Honzatko.
 
  ABSTRACT  
 
Crystal structures of adenylosuccinate synthetase from Esherichia coli complexed with Mg2+, IMP, GDP, NO3- and hadacidin at 298 and 100 K have been refined to R-factors of 0.188 and 0.206 against data to 2.8 A and 2.5 A resolution, respectively. Conformational changes of up to 9 A relative to the unligated enzyme occur in loops that bind to Mg2+, GDP, IMP and hadacidin. Mg2+ binds directly to GDP, NO3-, hadacidin and the protein, but is only five-coordinated. Asp13, which approaches, but does not occupy the sixth coordination site of Mg2+, hydrogen bonds to N1 of IMP. The nitrogen atom of NO3- is approximately 2.7 A from O6 of IMP, reflecting a strong electrostatic interaction between the electron-deficient nitrogen atom and the electron-rich O6. The spatial relationships between GDP, NO3- and Mg2+ suggest an interaction between the beta,gamma-bridging oxygen atom of GTP and Mg2+ in the enzyme-substrate complex. His41 hydrogen bonds to the beta-phosphate group of GDP and approaches bound NO3-. The aldehyde group of hadacidin coordinates to the Mg2+, while its carboxyl group interacts with backbone amide groups 299 to 303 and the side-chain of Arg303. The 5'-phosphate group of IMP interacts with Asn38, Thr129, Thr239 and Arg143 (from a monomer related by 2-fold symmetry). A mechanism is proposed for the two-step reaction governed by the synthetase, in which His41 and Asp13 are essential catalytic side-chains.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. A diagram of hadacidin showing chirality, covalent linkages and names of atoms (in parentheses). Groups within circles are represented by single, unified atoms in refinement.
Figure 8.
Figure 8. Stereoview of Mg 2+ in the active site of the ligated syn- thetase at 100 K. Broken lines rep- resent donor-acceptor interactions, coordinate bonds or significant elec- trostatic interactions less than 3.2 Å . Ligands are drawn with bold lines.
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (1996, 264, 1013-1027) copyright 1996.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  16569237 D.L.Scott, G.Diez, and W.H.Goldmann (2006).
Protein-lipid interactions: correlation of a predictive algorithm for lipid-binding sites with three-dimensional structural data.
  Theor Biol Med Model, 3, 17.  
12660160 A.Yamashita, K.Maeda, and Y.Maéda (2003).
Crystal structure of CapZ: structural basis for actin filament barbed end capping.
  EMBO J, 22, 1529-1538.
PDB code: 1izn
12482871 T.Borza, C.V.Iancu, E.Pike, R.B.Honzatko, and H.J.Fromm (2003).
Variations in the response of mouse isozymes of adenylosuccinate synthetase to inhibitors of physiological relevance.
  J Biol Chem, 278, 6673-6679.  
11781326 A.Gorrell, W.Wang, E.Underbakke, Z.Hou, R.B.Honzatko, and H.J.Fromm (2002).
Determinants of L-aspartate and IMP recognition in Escherichia coli adenylosuccinate synthetase.
  J Biol Chem, 277, 8817-8821.  
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
11741996 Z.Hou, W.Wang, H.J.Fromm, and R.B.Honzatko (2002).
IMP Alone Organizes the Active Site of Adenylosuccinate Synthetase from Escherichia coli.
  J Biol Chem, 277, 5970-5976.
PDB codes: 1kjx 1kkb 1kkf
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
11371198 R.A.Farley, E.Elquza, J.Müller-Ehmsen, D.J.Kane, A.K.Nagy, V.N.Kasho, and L.D.Faller (2001).
18O-exchange evidence that mutations of arginine in a signature sequence for P-type pumps affect inorganic phosphate binding.
  Biochemistry, 40, 6361-6370.  
10428826 J.B.Thoden, F.M.Raushel, G.Wesenberg, and H.M.Holden (1999).
The binding of inosine monophosphate to Escherichia coli carbamoyl phosphate synthetase.
  J Biol Chem, 274, 22502-22507.
PDB code: 1ce8
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.  
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
9422720 C.Zeng, A.E.Aleshin, G.Chen, R.B.Honzatko, and H.J.Fromm (1998).
The roles of glycine residues in the ATP binding site of human brain hexokinase.
  J Biol Chem, 273, 700-704.  
9708979 J.Y.Choe, B.W.Poland, H.J.Fromm, and R.B.Honzatko (1998).
Role of a dynamic loop in cation activation and allosteric regulation of recombinant porcine fructose-1,6-bisphosphatase.
  Biochemistry, 37, 11441-11450.
PDB codes: 1bfl 1cnq
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 code is shown on the right.