1HOO

STRUCTURE OF GUANINE NUCLEOTIDE (GPPCP) COMPLEX OF ADENYLOSUCCINATE SYNTHETASE FROM E. COLI AT PH 6.5 AND 25 DEGREES CELSIUS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 

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This is version 1.4 of the entry. See complete history


Literature

Refined crystal structures of guanine nucleotide complexes of adenylosuccinate synthetase from Escherichia coli.

Poland, B.W.Hou, Z.Bruns, C.Fromm, H.J.Honzatko, R.B.

(1996) J Biol Chem 271: 15407-15413

  • DOI: https://doi.org/10.1074/jbc.271.26.15407
  • Primary Citation of Related Structures:  
    1HON, 1HOO, 1HOP

  • PubMed Abstract: 

    Structures of adenylosuccinate synthetase from Escherichia coli complexed with guanosine-5'-(beta,gamma-imido) triphosphate and guanosine-5'-(beta,gamma-methylene)triphosphate in the presence and the absence of Mg2+ have been refined to R-factors below 0.2 against data to a nominal resolution of 2.7 A. Asp333 of the synthetase hydrogen bonds to the exocyclic 2-amino and endocyclic N1 groups of the guanine nucleotide base, whereas the hydroxyl of Ser414 and the backbone amide of Lys331 hydrogen bond to the 6-oxo position. The side chains of Lys331 and Pro417 pack against opposite faces of the guanine nucleotide base. The synthetase recognizes neither the N7 position of guanine nucleotides nor the ribose group. Electron density for the guanine-5'-(beta,gamma-imido) triphosphate complex is consistent with a mixture of the triphosphate nucleoside and its hydrolyzed diphosphate nucleoside bound to the active site. The base, ribose, and alpha-phosphate positions overlap, but the beta-phosphates occupy different binding sites. The binding of guanosine-5'-(beta,gamma-methylene)triphosphate to the active site is comparable with that of guanosine-5'-(beta, gamma-imido)triphosphate. No electron density, however, for the corresponding diphosphate nucleoside is observed. In addition, electron density for bound Mg2+ is absent in these nucleotide complexes. The guanine nucleotide complexes of the synthetase are compared with complexes of other GTP-binding proteins and to a preliminary structure of the complex of GDP, IMP, Mg2+, and succinate with the synthetase. The enzyme, under conditions reported here, does not undergo a conformational change in response to the binding of guanine nucleotides, and minimally IMP and/or Mg2+ must be present in order to facilitate the complete recognition of the guanine nucleotide by the synthetase.


  • Organizational Affiliation

    Department of Biochemistry and Biophysics, Iowa State University, Ames, Iowa 50011, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ADENYLOSUCCINATE SYNTHETASE
A, B
431Escherichia coliMutation(s): 0 
EC: 6.3.4.4
UniProt
Find proteins for P0A7D4 (Escherichia coli (strain K12))
Explore P0A7D4 
Go to UniProtKB:  P0A7D4
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP0A7D4
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GNP
Query on GNP

Download Ideal Coordinates CCD File 
D [auth A]PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H17 N6 O13 P3
UQABYHGXWYXDTK-UUOKFMHZSA-N
GNH
Query on GNH

Download Ideal Coordinates CCD File 
C [auth A]AMINOPHOSPHONIC ACID-GUANYLATE ESTER
C10 H16 N6 O10 P2
ZGPDMUBRWRJAQQ-UUOKFMHZSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.210 
  • R-Value Work: 0.185 
  • R-Value Observed: 0.185 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 72.6α = 90
b = 92.91β = 90
c = 119γ = 90
Software Package:
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
XENGENdata reduction
XENGENdata scaling
X-PLORphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1997-02-12
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-11-29
    Changes: Derived calculations, Other
  • Version 1.4: 2024-02-07
    Changes: Data collection, Database references, Derived calculations