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PDBsum entry 1o4u

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protein Protein-protein interface(s) links
Transferase PDB id
1o4u
Jmol
Contents
Protein chains
265 a.a. *
Waters ×113
* Residue conservation analysis
PDB id:
1o4u
Name: Transferase
Title: Crystal structure of a nicotinate nucleotide pyrophosphoryla (tm1645) from thermotoga maritima at 2.50 a resolution
Structure: Type ii quinolic acid phosphoribosyltransferase. Chain: a, b. Engineered: yes
Source: Thermotoga maritima. Organism_taxid: 2336. Gene: tm1645. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.50Å     R-factor:   0.216     R-free:   0.272
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
R.Schwarzenbacher et al. (2004). Crystal structure of a type II quinolic acid phosphoribosyltransferase (TM1645) from Thermotoga maritima at 2.50 A resolution. Proteins, 55, 768-771. PubMed id: 15103640 DOI: 10.1002/prot.20029
Date:
09-Jul-03     Release date:   22-Jul-03    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9X1X8  (Q9X1X8_THEMA) -  Nicotinate-nucleotide pyrophosphorylase
Seq:
Struc:
273 a.a.
265 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.4.2.19  - Nicotinate-nucleotide diphosphorylase (carboxylating).
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Beta-nicotinate D-ribonucleotide + diphosphate + CO2 = pyridine-2,3- dicarboxylate + 5-phospho-alpha-D-ribose 1-diphosphate
Beta-nicotinate D-ribonucleotide
+ diphosphate
+ CO(2)
= pyridine-2,3- dicarboxylate
+ 5-phospho-alpha-D-ribose 1-diphosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     pyridine nucleotide biosynthetic process   2 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1002/prot.20029 Proteins 55:768-771 (2004)
PubMed id: 15103640  
 
 
Crystal structure of a type II quinolic acid phosphoribosyltransferase (TM1645) from Thermotoga maritima at 2.50 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 TM1645. (A) Stereo Ribbon diagram of Thermotoga maritima TM1645 color coded from N-terminus (blue) to C-terminus (red) showing the domain organization and the location of the active site (arrow). Helices (H1-H11) and -strands ( 1- 12) are indicated. Figure 1A produced with PYMOL (DeLano Scientific LLC). (B) Diagram showing the secondary structure elements in TM1645 superimposed on its primary sequence. The disordered region (residues 145-152) is shown in a dashed line and the three -sheets (A,B,C) are labeled in red. Figure 1B produced with PDBsum (http://www.biochem.ucl.ac.uk/bsm/pdbsum).
Figure 2.
Figure 2. (A) Ribbon diagram of the TM1645 dimer. (B) Ribbon diagram of a superposition of TM1645 (rainbow) with its structural homologue QAPRTase from Mycobacterium tuberculosis (PDB: 1QPN; white). For reference, the nicotinate mononucleotide (NAMN) from 1QPN is shown in cpk mode. (C) Superposition of the active sites in TM1645 (cyan) and 1QPN (white). The active site residues and the NAMN molecule are shown in ball and stick. Residue names (if different) and numbers for 1QPN are shown in brackets. The atoms are indicated as follows: carbon (TM1645: cyan; 1QPN: white), 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, 768-771) copyright 2004.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
17763926 M.K.Kim, G.B.Kang, W.K.Song, and S.H.Eom (2007).
The role of Phe181 in the hexamerization of Helicobacter pylori quinolinate phosphoribosyltransferase.
  Protein J, 26, 517-521.  
16419067 M.K.Kim, Y.J.Im, J.H.Lee, and S.H.Eom (2006).
Crystal structure of quinolinic acid phosphoribosyltransferase from Helicobacter pylori.
  Proteins, 63, 252-255.
PDB codes: 2b7n 2b7p 2b7q
16154095 J.S.Chappie, J.M.Cànaves, G.W.Han, C.L.Rife, Q.Xu, and R.C.Stevens (2005).
The structure of a eukaryotic nicotinic acid phosphoribosyltransferase reveals structural heterogeneity among type II PRTases.
  Structure, 13, 1385-1396.
PDB code: 1vlp
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.  
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