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PDBsum entry 1gso

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protein links
Ligase PDB id
1gso
Jmol
Contents
Protein chain
419 a.a. *
Waters ×299
* Residue conservation analysis
PDB id:
1gso
Name: Ligase
Title: Glycinamide ribonucleotide synthetase (gar-syn) from e. Coli.
Structure: Protein (glycinamide ribonucleotide synthetase). Chain: a. Synonym: purd gen product. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Strain: tx635. Cell_line: b834(de3)
Resolution:
1.60Å     R-factor:   0.209     R-free:   0.247
Authors: W.Wang,T.J.Kappock,J.Stubbe,S.E.Ealick
Key ref:
W.Wang et al. (1998). X-ray crystal structure of glycinamide ribonucleotide synthetase from Escherichia coli. Biochemistry, 37, 15647-15662. PubMed id: 9843369 DOI: 10.1021/bi981405n
Date:
08-Sep-98     Release date:   09-Dec-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P15640  (PUR2_ECOLI) -  Phosphoribosylamine--glycine ligase
Seq:
Struc:
429 a.a.
419 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.6.3.4.13  - Phosphoribosylamine--glycine ligase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Purine Biosynthesis (early stages)
      Reaction: ATP + 5-phospho-D-ribosylamine + glycine = ADP + phosphate + N1- (5-phospho-D-ribosyl)glycinamide
ATP
+ 5-phospho-D-ribosylamine
+ glycine
= ADP
+ phosphate
+ N(1)- (5-phospho-D-ribosyl)glycinamide
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     response to DNA damage stimulus   5 terms 
  Biochemical function     catalytic activity     9 terms  

 

 
    reference    
 
 
DOI no: 10.1021/bi981405n Biochemistry 37:15647-15662 (1998)
PubMed id: 9843369  
 
 
X-ray crystal structure of glycinamide ribonucleotide synthetase from Escherichia coli.
W.Wang, T.J.Kappock, J.Stubbe, S.E.Ealick.
 
  ABSTRACT  
 
Glycinamide ribonucleotide synthetase (GAR-syn) catalyzes the second step of the de novo purine biosynthetic pathway; the conversion of phosphoribosylamine, glycine, and ATP to glycinamide ribonucleotide (GAR), ADP, and Pi. GAR-syn containing an N-terminal polyhistidine tag was expressed as the SeMet incorporated protein for crystallographic studies. In addition, the protein as isolated contains a Pro294Leu mutation. This protein was crystallized, and the structure solved using multiple-wavelength anomalous diffraction (MAD) phase determination and refined to 1.6 A resolution. GAR-syn adopts an alpha/beta structure that consists of four domains labeled N, A, B, and C. The N, A, and C domains are clustered to form a large central core structure whereas the smaller B domain is extended outward. Two hinge regions, which might readily facilitate interdomain movement, connect the B domain and the main core. A search of structural databases showed that the structure of GAR-syn is similar to D-alanine:D-alanine ligase, biotin carboxylase, and glutathione synthetase, despite low sequence similarity. These four enzymes all utilize similar ATP-dependent catalytic mechanisms even though they catalyze different chemical reactions. Another ATP-binding enzyme with low sequence similarity but unknown function, synapsin Ia, was also found to share high structural similarity with GAR-syn. Interestingly, the GAR-syn N domain shows similarity to the N-terminal region of glycinamide ribonucleotide transformylase and several dinucleotide-dependent dehydrogenases. Models of ADP and GAR binding were generated based on structure and sequence homology. On the basis of these models, the active site lies in a cleft between the large domain and the extended B domain. Most of the residues that facilitate ATP binding belong to the A or B domains. The N and C domains appear to be largely responsible for substrate specificity. The structure of GAR-syn allows modeling studies of possible channeling complexes with PPRP amidotransferase.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20693694 H.Xu (2010).
Enhancing MAD F(A) data for substructure determination.
  Acta Crystallogr D Biol Crystallogr, 66, 945-949.  
20631005 M.Welin, J.G.Grossmann, S.Flodin, T.Nyman, P.Stenmark, L.Trésaugues, T.Kotenyova, I.Johansson, P.Nordlund, and L.Lehtiö (2010).
Structural studies of tri-functional human GART.
  Nucleic Acids Res, 38, 7308-7319.
PDB codes: 2qk4 2v9y
19007868 A.J.Knox, C.Graham, J.Bleskan, G.Brodsky, and D.Patterson (2009).
Mutations in the Chinese hamster ovary cell GART gene of de novo purine synthesis.
  Gene, 429, 23-30.  
19301155 D.Banerjee, and K.Nandagopal (2009).
Phylogenetic Analysis and in Silico Characterization of the GARS-AIRS-GART Gene which Codes for a tri-Functional Enzyme Protein Involved in de novo Purine Biosynthesis.
  Mol Biotechnol, 42, 306-319.  
19384989 H.Li, W.Fast, and S.J.Benkovic (2009).
Structural and functional modularity of proteins in the de novo purine biosynthetic pathway.
  Protein Sci, 18, 881-892.  
19089987 P.Zhou, F.Tian, F.Lv, and Z.Shang (2009).
Geometric characteristics of hydrogen bonds involving sulfur atoms in proteins.
  Proteins, 76, 151-163.  
18712276 Y.Zhang, M.Morar, and S.E.Ealick (2008).
Structural biology of the purine biosynthetic pathway.
  Cell Mol Life Sci, 65, 3699-3724.  
18069798 Y.Zhang, R.H.White, and S.E.Ealick (2008).
Crystal structure and function of 5-formaminoimidazole-4-carboxamide ribonucleotide synthetase from Methanocaldococcus jannaschii.
  Biochemistry, 47, 205-217.
PDB codes: 2r7k 2r7l 2r7m 2r7n 2r84 2r85 2r86 2r87
16251194 H.Arulanantham, N.J.Kershaw, K.S.Hewitson, C.E.Hughes, J.E.Thirkettle, and C.J.Schofield (2006).
ORF17 from the clavulanic acid biosynthesis gene cluster catalyzes the ATP-dependent formation of N-glycyl-clavaminic acid.
  J Biol Chem, 281, 279-287.  
16481318 M.E.Fraser, K.Hayakawa, M.S.Hume, D.G.Ryan, and E.R.Brownie (2006).
Interactions of GTP with the ATP-grasp domain of GTP-specific succinyl-CoA synthetase.
  J Biol Chem, 281, 11058-11065.
PDB codes: 2fp4 2fpg 2fpi 2fpp
15983421 H.Xu, C.M.Weeks, and H.A.Hauptman (2005).
Optimizing statistical Shake-and-Bake for Se-atom substructure determination.
  Acta Crystallogr D Biol Crystallogr, 61, 976-981.  
15901709 S.Gopal, I.Borovok, A.Ofer, M.Yanku, G.Cohen, W.Goebel, J.Kreft, and Y.Aharonowitz (2005).
A multidomain fusion protein in Listeria monocytogenes catalyzes the two primary activities for glutathione biosynthesis.
  J Bacteriol, 187, 3839-3847.  
14990577 A.Dinescu, T.R.Cundari, V.S.Bhansali, J.L.Luo, and M.E.Anderson (2004).
Function of conserved residues of human glutathione synthetase: implications for the ATP-grasp enzymes.
  J Biol Chem, 279, 22412-22421.  
14500881 K.Matsuda, T.Nishioka, K.Kinoshita, T.Kawabata, and N.Go (2003).
Finding evolutionary relations beyond superfamilies: fold-based superfamilies.
  Protein Sci, 12, 2239-2251.  
11006546 T.J.Kappock, S.E.Ealick, and J.Stubbe (2000).
Modular evolution of the purine biosynthetic pathway.
  Curr Opin Chem Biol, 4, 567-572.  
10508786 C.Li, T.J.Kappock, J.Stubbe, T.M.Weaver, and S.E.Ealick (1999).
X-ray crystal structure of aminoimidazole ribonucleotide synthetase (PurM), from the Escherichia coli purine biosynthetic pathway at 2.5 A resolution.
  Structure, 7, 1155-1166.
PDB code: 1cli
10574791 I.I.Mathews, T.J.Kappock, J.Stubbe, and S.E.Ealick (1999).
Crystal structure of Escherichia coli PurE, an unusual mutase in the purine biosynthetic pathway.
  Structure, 7, 1395-1406.
PDB codes: 1d7a 1qcz
10584075 S.Roy (1999).
Multifunctional enzymes and evolution of biosynthetic pathways: retro-evolution by jumps.
  Proteins, 37, 303-309.  
9914248 J.L.Smith (1998).
Glutamine PRPP amidotransferase: snapshots of an enzyme in action.
  Curr Opin Struct Biol, 8, 686-694.  
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.