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PDBsum entry 1vk3

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protein metals links
Ligase PDB id
1vk3
Jmol
Contents
Protein chain
586 a.a. *
Metals
_CL
Waters ×221
* Residue conservation analysis
PDB id:
1vk3
Name: Ligase
Title: Crystal structure of phosphoribosylformylglycinamidine synthase ii (tm1246) from thermotoga maritima at 2.15 a resolution
Structure: Phosphoribosylformylglycinamidine synthase ii. Chain: a. Synonym: fgam synthase ii. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Gene: purl, tm1246. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
2.15Å     R-factor:   0.190     R-free:   0.254
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
I.I.Mathews et al. (2006). Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 A resolution. Proteins, 63, 1106-1111. PubMed id: 16544324 DOI: 10.1002/prot.20650
Date:
23-Apr-04     Release date:   11-May-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9X0X3  (PURL_THEMA) -  Phosphoribosylformylglycinamidine synthase subunit PurL
Seq:
Struc:
 
Seq:
Struc:
603 a.a.
586 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 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     glutamine metabolic process   4 terms 
  Biochemical function     catalytic activity     7 terms  

 

 
    reference    
 
 
DOI no: 10.1002/prot.20650 Proteins 63:1106-1111 (2006)
PubMed id: 16544324  
 
 
Crystal structure of phosphoribosylformylglycinamidine synthase II (smPurL) from Thermotoga maritima at 2.15 A resolution.
I.I.Mathews, S.S.Krishna, R.Schwarzenbacher, D.McMullan, P.Abdubek, E.Ambing, J.M.Canaves, H.J.Chiu, A.M.Deacon, M.DiDonato, M.A.Elsliger, A.Godzik, C.Grittini, S.K.Grzechnik, J.Hale, E.Hampton, G.W.Han, J.Haugen, L.Jaroszewski, H.E.Klock, E.Koesema, A.Kreusch, P.Kuhn, S.A.Lesley, I.Levin, M.D.Miller, K.Moy, E.Nigoghossian, J.Paulsen, K.Quijano, R.Reyes, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, A.White, G.Wolf, Q.Xu, K.O.Hodgson, J.Wooley, I.A.Wilson.
 
  ABSTRACT  
 
No abstract given.

 
  Selected figure(s)  
 
Figure 2.
Figure 2. Domain arrangement and structural alignment of smPurL and lgPurL. A: Domain arrangement of PurM, ThiL, smPurL, and lgPurL proteins. PurM and ThiL are homodimers. smPurL (gray) and the central domain of lgPurL (blue) have the same domain arrangement as a PurM dimer. lgPurL has two additional domains as compared with smPurL. The N-terminal domain homologous to the PurS protein is colored green and the C-terminal glutaminase domain is colored red. B: Stereo ribbon diagram of a superposition of smPurL (gray) and residues 183-960 of lgPurL from S. typhimurium (blue). The lgPurL N-terminal domain of unknown function and the C-terminal glutaminase domain are colored green and red, respectively. These extra domains of lgPurL correspond to the PurS (TM1244) and PurQ (TM1245) proteins in T. maritima. The structures were aligned using the DALI server.
Figure 3.
Figure 3. A: Stereo diagram of a close-up of the putative active site of TM1246 superimposed on the lgPurL structure shown in ribbon representation. The sulfate ions are from the lgPurL structure. The start and end regions of the glycine-rich loop in both the structures are labeled in red. B: Stereo diagram of a close-up of the lgPurL ADP-binding site superimposed on the smPurL structure shown in ribbon representation. The ADP moiety and Mg^2+ ions are from the lgPurL structure. In A and B, residues are numbered according to TM1246 structure (PDB 1vk3) and the equivalent residues of lgPurL (PDB 1t3t) are shown in parentheses.
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2006, 63, 1106-1111) 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.  
16865708 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, and I.A.Wilson (2006).
Crystal structure of phosphoribosylformyl-glycinamidine synthase II, PurS subunit (TM1244) from Thermotoga maritima at 1.90 A resolution.
  Proteins, 65, 249-254.
PDB code: 1vq3
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.