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PDBsum entry 1vq3

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protein Protein-protein interface(s) links
Ligase PDB id
1vq3
Jmol
Contents
Protein chains
86 a.a. *
Waters ×301
* Residue conservation analysis
PDB id:
1vq3
Name: Ligase
Title: Crystal structure of phosphoribosylformylglycinamidine synth subunit (ec 6.3.5.3) (tm1244) from thermotoga maritima at 1 resolution
Structure: Phosphoribosylformylglycinamidine synthase, purs chain: a, b, c, d. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 243274. Strain: msb8. Gene: tm1244. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Tetramer (from PQS)
Resolution:
1.90Å     R-factor:   0.180     R-free:   0.234
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
I.I.Mathews et al. (2006). Crystal structure of phosphoribosylformyl-glycinamidine synthase II, PurS subunit (TM1244) from Thermotoga maritima at 1.90 A resolution. Proteins, 65, 249-254. PubMed id: 16865708 DOI: 10.1002/prot.21024
Date:
15-Dec-04     Release date:   28-Dec-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9X0X1  (Q9X0X1_THEMA) -  Phosphoribosylformylglycinamidine synthase subunit PurS
Seq:
Struc:
82 a.a.
86 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.6.3.5.3  - Phosphoribosylformylglycinamidine synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Purine Biosynthesis (early stages)
      Reaction: ATP + N2-formyl-N1-(5-phospho-D-ribosyl)glycinamide + L-glutamine + H2O = ADP + phosphate + 2-(formamido)-N(1)-(5-phospho-D- ribosyl)acetamidine + L-glutamate
ATP
+ N(2)-formyl-N(1)-(5-phospho-D-ribosyl)glycinamide
+ L-glutamine
+ H(2)O
= ADP
+ phosphate
+ 2-(formamido)-N(1)-(5-phospho-D- ribosyl)acetamidine
+ L-glutamate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     purine nucleotide biosynthetic process   2 terms 
  Biochemical function     nucleotide binding     4 terms  

 

 
    reference    
 
 
DOI no: 10.1002/prot.21024 Proteins 65:249-254 (2006)
PubMed id: 16865708  
 
 
Crystal structure of phosphoribosylformyl-glycinamidine synthase II, PurS subunit (TM1244) from Thermotoga maritima at 1.90 A resolution.
I.I.Mathews, S.S.Krishna, R.Schwarzenbacher, D.McMullan, L.Jaroszewski, M.D.Miller, P.Abdubek, S.Agarwalla, E.Ambing, H.L.Axelrod, J.M.Canaves, D.Carlton, H.J.Chiu, T.Clayton, M.DiDonato, L.Duan, M.A.Elsliger, S.K.Grzechnik, J.Hale, E.Hampton, J.Haugen, K.K.Jin, H.E.Klock, E.Koesema, J.S.Kovarik, A.Kreusch, P.Kuhn, I.Levin, A.T.Morse, E.Nigoghossian, L.Okach, S.Oommachen, J.Paulsen, K.Quijano, R.Reyes, C.L.Rife, G.Spraggon, R.C.Stevens, H.van den Bedem, A.White, G.Wolf, Q.Xu, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, I.A.Wilson.
 
  ABSTRACT  
 
No abstract given.

 
  Selected figure(s)  
 
Figure 2.
Figure 2. Domain delineation of PurS. (A) Structural representative of the ferredoxin-like fold: the anticodon-binding domain of PheRS (PDB code: 1pys, chain B). (B) Dimeric unit of PurS colored according to chains (chain A: blue, chain B: red). The PurS domain-swapped dimer structure contains two domains (separated by a black horizontal bar), each of which resembles the ferredoxin-like fold. The ferredoxin-like fold is made of four -strands and two -helices, and in PurS these structural elements are contributed from the two chains of the dimer by a domain swap of -helix H1 and -strand 2. The elements are labeled according to the ferredoxin-like fold.
Figure 3.
Figure 3. (A) Structural alignment of PurS (blue) with the N-terminal domain of lgPurL (gray) from S. typhimurium C[ ]atoms from the dimer of TM1244 were used for the alignment with lgPurL. The largest structural difference corresponds to strand 3 of chain A, which is replaced by a long loop (see arrow) that acts as a linker between the adjacent PurS-like domains in lgPurL. (B) Stereo ribbon diagram of a superposition of lgPurL from S. typhimurium (FGAR-AT; gray) with PurS (TM1244; blue) and smPurL (TM1246; orange). Ligands of lgPurL are shown as CPK (Corey, Pauling, and Kultun) color scheme. The arrow indicates the expected location of the PurQ protein (TM1245) in FGAR-AT from T. maritima.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 65, 249-254) copyright 2006.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
18260100 H.L.Axelrod, D.McMullan, S.S.Krishna, M.D.Miller, M.A.Elsliger, P.Abdubek, E.Ambing, T.Astakhova, D.Carlton, H.J.Chiu, T.Clayton, L.Duan, J.Feuerhelm, S.K.Grzechnik, J.Hale, G.W.Han, J.Haugen, L.Jaroszewski, K.K.Jin, H.E.Klock, M.W.Knuth, E.Koesema, A.T.Morse, E.Nigoghossian, L.Okach, S.Oommachen, J.Paulsen, K.Quijano, R.Reyes, C.L.Rife, H.van den Bedem, D.Weekes, A.White, G.Wolf, Q.Xu, K.O.Hodgson, J.Wooley, A.M.Deacon, A.Godzik, S.A.Lesley, and I.A.Wilson (2008).
Crystal structure of AICAR transformylase IMP cyclohydrolase (TM1249) from Thermotoga maritima at 1.88 A resolution.
  Proteins, 71, 1042-1049.
PDB code: 1zcz
18597481 M.Morar, A.A.Hoskins, J.Stubbe, and S.E.Ealick (2008).
Formylglycinamide ribonucleotide amidotransferase from Thermotoga maritima: structural insights into complex formation.
  Biochemistry, 47, 7816-7830.
PDB code: 3d54
18712276 Y.Zhang, M.Morar, and S.E.Ealick (2008).
Structural biology of the purine biosynthetic pathway.
  Cell Mol Life Sci, 65, 3699-3724.  
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.