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PDBsum entry 1loo

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Ligase PDB id
1loo
Jmol
Contents
Protein chain
431 a.a. *
Ligands
GTP
Waters ×100
* Residue conservation analysis
PDB id:
1loo
Name: Ligase
Title: Crystal structure of the mouse-muscle adenylosuccinate synth ligated with gtp
Structure: Adenylosuccinate synthetase. Chain: a. Engineered: yes
Source: Mus musculus. House mouse. Organism_taxid: 10090. Gene: adss1. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Biol. unit: Dimer (from PDB file)
Resolution:
2.20Å     R-factor:   0.244     R-free:   0.276
Authors: C.V.Iancu,T.Borza,H.J.Fromm,R.B.Honzatko
Key ref:
C.V.Iancu et al. (2002). IMP, GTP, and 6-phosphoryl-IMP complexes of recombinant mouse muscle adenylosuccinate synthetase. J Biol Chem, 277, 26779-26787. PubMed id: 12004071 DOI: 10.1074/jbc.M203730200
Date:
06-May-02     Release date:   28-Aug-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P28650  (PURA1_MOUSE) -  Adenylosuccinate synthetase isozyme 1
Seq:
Struc:
457 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
Bound ligand (Het Group name = GTP)
corresponds exactly
+ IMP
+ L-aspartate
= GDP
+ 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   2 terms 
  Biological process     'de novo' AMP biosynthetic process   5 terms 
  Biochemical function     nucleotide binding     7 terms  

 

 
    reference    
 
 
DOI no: 10.1074/jbc.M203730200 J Biol Chem 277:26779-26787 (2002)
PubMed id: 12004071  
 
 
IMP, GTP, and 6-phosphoryl-IMP complexes of recombinant mouse muscle adenylosuccinate synthetase.
C.V.Iancu, T.Borza, H.J.Fromm, R.B.Honzatko.
 
  ABSTRACT  
 
Prokaryotes have a single form of adenylosuccinate synthetase that controls the committed step of AMP biosynthesis, but vertebrates have two isozymes of the synthetase. The basic isozyme, which predominates in muscle, participates in the purine nucleotide cycle, has an active site conformation different from that of the Escherichia coli enzyme, and exhibits significant differences in ligand recognition. Crystalline complexes presented here of the recombinant basic isozyme from mouse show the following. GTP alone binds to the active site without inducing a conformational change. IMP in combination with an acetate anion induces major conformational changes and organizes the active site for catalysis. IMP, in the absence of GTP, binds to the GTP pocket of the synthetase. The combination of GTP and IMP results in the formation of a stable complex of 6-phosphoryl-IMP and GDP in the presence or absence of hadacidin. The response of the basic isozyme to GTP alone differs from that of synthetases from plants, and yet the conformation of the mouse basic and E. coli synthetases in their complexes with GDP, 6-phosphoryl-IMP, and hadacidin are nearly identical. Hence, reported differences in ligand recognition among synthetases probably arise from conformational variations observed in partially ligated enzymes.
 
  Selected figure(s)  
 
Figure 2.
Fig. 2. Stereoview of GTP bound to the active site. Electron density is from an omit map (coefficients of 2F[obs] F[calc], [calc] phases) contoured at 3 using a cutoff radius of 1 Å. Dashed lines represent donor-acceptor interactions.
Figure 6.
Fig. 6. Stereoview of the 6PIMP·GDP·hadacidin complex. One molecule of 6PIMP, GDP, and hadacidin bind to the single, symmetry-unique subunit in this crystal form ( top). Electron density is from an omit map (coefficients of 2F[obs] F[calc], [calc] phases) contoured at 3 using a cutoff radius of 1 Å. Dashed lines represent donor-acceptor interactions. Only the new interactions, relative to GDP·6PIMP complex, are shown. Additional details are in "Results."
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 26779-26787) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20059543 K.S.Chakrabarti, K.G.Thakur, B.Gopal, and S.P.Sarma (2010).
X-ray crystallographic and NMR studies of pantothenate synthetase provide insights into the mechanism of homotropic inhibition by pantoate.
  FEBS J, 277, 697-712.
PDB code: 3guz
17634986 E.R.Jefferson, T.P.Walsh, and G.J.Barton (2008).
A comparison of SCOP and CATH with respect to domain-domain interactions.
  Proteins, 70, 54-62.  
18981424 F.R.Fischer, P.A.Wood, F.H.Allen, and F.Diederich (2008).
Orthogonal dipolar interactions between amide carbonyl groups.
  Proc Natl Acad Sci U S A, 105, 17290-17294.  
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.