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PDBsum entry 1cib

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protein ligands metals links
Ligase PDB id
1cib
Jmol
Contents
Protein chain
431 a.a. *
Ligands
NO3
GDP
HDA
IMP
Metals
_MG
Waters ×410
* Residue conservation analysis
PDB id:
1cib
Name: Ligase
Title: Structure of adenylosuccinate synthetase from e. Coli comple gdp, imp, hadacidin, and no3
Structure: Adenylosuccinate synthetase. Chain: a. Synonym: ampsase. Engineered: yes
Source: Escherichia coli. Organism_taxid: 83333. Strain: k-12. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PDB file)
Resolution:
2.30Å     R-factor:   0.170     R-free:   0.240
Authors: Z.Hou,M.Cashel,H.J.Fromm,R.B.Honzatko
Key ref:
Z.Hou et al. (1999). Effectors of the stringent response target the active site of Escherichia coli adenylosuccinate synthetase. J Biol Chem, 274, 17505-17510. PubMed id: 10364182 DOI: 10.1074/jbc.274.25.17505
Date:
31-Mar-99     Release date:   05-Apr-00    
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 41.67% 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.274.25.17505 J Biol Chem 274:17505-17510 (1999)
PubMed id: 10364182  
 
 
Effectors of the stringent response target the active site of Escherichia coli adenylosuccinate synthetase.
Z.Hou, M.Cashel, H.J.Fromm, R.B.Honzatko.
 
  ABSTRACT  
 
Guanosine 5'-diphosphate 3'-diphosphate (ppGpp), a pleiotropic effector of the stringent response, potently inhibits adenylosuccinate synthetase from Escherichia coli as an allosteric effector and/or as a competitive inhibitor with respect to GTP. Crystals of the synthetase grown in the presence of IMP, hadacidin, NO3-, and Mg2+, then soaked with ppGpp, reveal electron density at the GTP pocket which is consistent with guanosine 5'-diphosphate 2':3'-cyclic monophosphate. Unlike ligand complexes of the synthetase involving IMP and GDP, the coordination of Mg2+ in this complex is octahedral with the side chain of Asp13 in the inner sphere of the cation. The cyclic phosphoryl group interacts directly with the side chain of Lys49 and indirectly through bridging water molecules with the side chains of Asn295 and Arg305. The synthetase either directly facilitates the formation of the cyclic nucleotide or scavenges trace amounts of the cyclic nucleotide from solution. Regardless of its mode of generation, the cyclic nucleotide binds far more tightly to the active site than does ppGpp. Conceivably, synthetase activity in vivo during the stringent response may be sensitive to the relative concentrations of several effectors, which together exercise precise control over the de novo synthesis of AMP.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Schematic of ppG2':3'p showing atom labels.
Figure 3.
Fig. 3. Stereoview of interactions between ppG2':3'p and the active site. Ligands (only hadacidin (Had), nitrate, ppG2':3'p, and Mg^2+ are shown) are drawn with bold lines. Donor-acceptor interactions (corresponding distances listed in Table II) are presented with dashed lines.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (1999, 274, 17505-17510) copyright 1999.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
19366688 K.Podzelinska, S.M.He, M.Wathier, A.Yakunin, M.Proudfoot, B.Hove-Jensen, D.L.Zechel, and Z.Jia (2009).
Structure of PhnP, a phosphodiesterase of the carbon-phosphorus lyase pathway for phosphonate degradation.
  J Biol Chem, 284, 17216-17226.  
19702577 M.Montero, G.Eydallin, A.M.Viale, G.Almagro, F.J.Muñoz, M.Rahimpour, M.T.Sesma, E.Baroja-Fernández, and J.Pozueta-Romero (2009).
Escherichia coli glycogen metabolism is controlled by the PhoP-PhoQ regulatory system at submillimolar environmental Mg2+ concentrations, and is highly interconnected with a wide variety of cellular processes.
  Biochem J, 424, 129-141.  
19447912 Y.Natori, K.Tagami, K.Murakami, S.Yoshida, O.Tanigawa, Y.Moh, K.Masuda, T.Wada, S.Suzuki, H.Nanamiya, Y.Tozawa, and F.Kawamura (2009).
Transcription activity of individual rrn operons in Bacillus subtilis mutants deficient in (p)ppGpp synthetase genes, relA, yjbM, and ywaC.
  J Bacteriol, 191, 4555-4561.  
18535838 K.Mizusawa, S.Masuda, and H.Ohta (2008).
Expression profiling of four RelA/SpoT-like proteins, homologues of bacterial stringent factors, in Arabidopsis thaliana.
  Planta, 228, 553-562.  
18178586 S.Masuda, K.Mizusawa, T.Narisawa, Y.Tozawa, H.Ohta, and K.Takamiya (2008).
The bacterial stringent response, conserved in chloroplasts, controls plant fertilization.
  Plant Cell Physiol, 49, 135-141.  
15066282 T.Hogg, U.Mechold, H.Malke, M.Cashel, and R.Hilgenfeld (2004).
Conformational antagonism between opposing active sites in a bifunctional RelA/SpoT homolog modulates (p)ppGpp metabolism during the stringent response [corrected].
  Cell, 117, 57-68.
PDB code: 1vj7
11282471 D.Chatterji, and A.K.Ojha (2001).
Revisiting the stringent response, ppGpp and starvation signaling.
  Curr Opin Microbiol, 4, 160-165.  
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.