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PDBsum entry 1o4v

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Lyase PDB id
1o4v
Jmol
Contents
Protein chain
169 a.a. *
Ligands
SO4 ×2
Waters ×118
* Residue conservation analysis
PDB id:
1o4v
Name: Lyase
Title: Crystal structure of the catalytic subunit of a phosphoribosylaminoimidazole mutase (tm0446) from thermotog at 1.77 a resolution
Structure: Phosphoribosylaminoimidazole mutase pure. Chain: a. Synonym: air carboxylase, airc. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Gene: pure or tm0446. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Octamer (from PDB file)
Resolution:
1.77Å     R-factor:   0.151     R-free:   0.182
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
R.Schwarzenbacher et al. (2004). Crystal structure of a phosphoribosylaminoimidazole mutase PurE (TM0446) from Thermotoga maritima at 1.77-A resolution. Proteins, 55, 474-478. PubMed id: 15048837 DOI: 10.1002/prot.20023
Date:
11-Jul-03     Release date:   22-Jul-03    
PROCHECK
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 Headers
 References

Protein chain
Pfam   ArchSchema ?
Q9WYS7  (PURE_THEMA) -  N5-carboxyaminoimidazole ribonucleotide mutase
Seq:
Struc:
171 a.a.
169 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.5.4.99.18  - 5-(carboxyamino)imidazole ribonucleotide mutase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: 5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole = 5-amino-1-(5-phospho-D- ribosyl)imidazole-4-carboxylate
5-carboxyamino-1-(5-phospho-D-ribosyl)imidazole
= 5-amino-1-(5-phospho-D- ribosyl)imidazole-4-carboxylate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     purine nucleotide biosynthetic process   2 terms 
  Biochemical function     isomerase activity     2 terms  

 

 
    Added reference    
 
 
DOI no: 10.1002/prot.20023 Proteins 55:474-478 (2004)
PubMed id: 15048837  
 
 
Crystal structure of a phosphoribosylaminoimidazole mutase PurE (TM0446) from Thermotoga maritima at 1.77-A resolution.
R.Schwarzenbacher, L.Jaroszewski, F.von Delft, P.Abdubek, E.Ambing, T.Biorac, L.S.Brinen, J.M.Canaves, J.Cambell, H.J.Chiu, X.Dai, A.M.Deacon, M.DiDonato, M.A.Elsliger, S.Eshagi, R.Floyd, A.Godzik, C.Grittini, S.K.Grzechnik, E.Hampton, C.Karlak, H.E.Klock, E.Koesema, J.S.Kovarik, A.Kreusch, P.Kuhn, S.A.Lesley, I.Levin, D.McMullan, T.M.McPhillips, M.D.Miller, A.Morse, K.Moy, J.Ouyang, R.Page, K.Quijano, A.Robb, G.Spraggon, R.C.Stevens, H.van den Bedem, J.Velasquez, J.Vincent, X.Wang, B.West, G.Wolf, Q.Xu, K.O.Hodgson, J.Wooley, I.A.Wilson.
 
  ABSTRACT  
 
No abstract given.

 
  Selected figure(s)  
 
Figure 1.
Figure 1. Crystal structure of TM0446. (A) Ribbon diagram of Thermotoga maritima TM0446 color coded from N-terminus (blue) to C-terminus (red), showing the domain organization and the location of the active site (arrow). The helices H1-H8 and -strands ( 1- 5) are indicated. (B) Ribbon diagram of the TM0446 octamer with one monomer shown in purple. For comparison, the PurE octamer from E. coli (PDB code: 1D7A) is shown with an aminoimidazole ribonucleotide (AIR) molecule (cpk-mode) bound to the active site. Figures 1A and 1B produced with PYMOL (DeLano Scientific LLC). (C) Diagram showing the secondary structure elements in TM0446 superimposed on its primary sequence. Figure 1C adapted from PDBsum (http://www.biochem.ucl.ac.uk/bsm/pdsum).
Figure 2.
Figure 2. (A) Ribbon diagram of a superposition of TM0446 (cyan) with its structural homologue PurE from E. coli (PDB code: 1D7A; white). For reference, the sulphate in TM0446 and the aminoimidazole ribonucleotide (AIR) molecule bound to PurE from E. coli are depicted in ball and stick. (B) Superposition of the active sites in TM0446 (cyan) and PurE from E. coli (white). The active site residues, the AIR molecule, and the sulphate are shown in ball and stick, with residue numbering indicated for TM0446. Pro105 belongs to the next subunit in the octamer. The atoms are indicated as follows: carbon (cyan: TM0446; gray: PurE), nitrogen (blue), oxygen (red), phosphor (purple), and sulfur (orange). Figures produced with PYMOL (DeLano Scientific LLC).
 
  The above figures are reprinted by permission from John Wiley & Sons, Inc.: Proteins (2004, 55, 474-478) copyright 2004.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
17298082 A.A.Hoskins, M.Morar, T.J.Kappock, I.I.Mathews, J.B.Zaugg, T.E.Barder, P.Peng, A.Okamoto, S.E.Ealick, and J.Stubbe (2007).
N5-CAIR mutase: role of a CO2 binding site and substrate movement in catalysis.
  Biochemistry, 46, 2842-2855.
PDB codes: 2ate 2nsh 2nsj 2nsl
16138311 M.P.Boyle, A.K.Kalliomaa, V.Levdikov, E.Blagova, M.J.Fogg, J.A.Brannigan, K.S.Wilson, and A.J.Wilkinson (2005).
Crystal structure of PurE (BA0288) from Bacillus anthracis at 1.8 A resolution.
  Proteins, 61, 674-676.
PDB codes: 1xmp 1ypf
16211521 R.Page, A.M.Deacon, S.A.Lesley, and R.C.Stevens (2005).
Shotgun crystallization strategy for structural genomics II: crystallization conditions that produce high resolution structures for T. maritima proteins.
  J Struct Funct Genomics, 6, 209-217.  
15388921 E.C.Settembre, J.R.Chittuluru, C.P.Mill, T.J.Kappock, and S.E.Ealick (2004).
Acidophilic adaptations in the structure of Acetobacter aceti N5-carboxyaminoimidazole ribonucleotide mutase (PurE).
  Acta Crystallogr D Biol Crystallogr, 60, 1753-1760.
PDB code: 1u11
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.