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PDBsum entry 1vlp

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protein ligands metals Protein-protein interface(s) links
Transferase PDB id
1vlp
Jmol
Contents
Protein chains
418 a.a. *
Ligands
PO4 ×4
MES
EDO ×3
Metals
_CL ×3
Waters ×1272
* Residue conservation analysis
PDB id:
1vlp
Name: Transferase
Title: Crystal structure of a putative nicotinate phosphoribosyltra (yor209c, npt1) from saccharomyces cerevisiae at 1.75 a res
Structure: Nicotinate phosphoribosyltransferase. Chain: a, b, c, d. Synonym: naprtase. Engineered: yes
Source: Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: npt1, yor209c. Expressed in: escherichia coli. Expression_system_taxid: 562.
Resolution:
1.75Å     R-factor:   0.172     R-free:   0.210
Authors: Joint Center For Structural Genomics (Jcsg)
Key ref:
J.S.Chappie et al. (2005). The structure of a eukaryotic nicotinic acid phosphoribosyltransferase reveals structural heterogeneity among type II PRTases. Structure, 13, 1385-1396. PubMed id: 16154095 DOI: 10.1016/j.str.2005.05.016
Date:
06-Aug-04     Release date:   24-Aug-04    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P39683  (NPT1_YEAST) -  Nicotinate phosphoribosyltransferase
Seq:
Struc:
429 a.a.
418 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.6.3.4.21  - Nicotinate phosphoribosyltransferase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Nicotinate + 5-phospho-alpha-D-ribose 1-diphosphate + ATP + H2O = beta- nicotinate D-ribonucleotide + diphosphate + ADP + phosphate
Nicotinate
+
5-phospho-alpha-D-ribose 1-diphosphate
Bound ligand (Het Group name = PO4)
matches with 55.56% similarity
+ ATP
+ H(2)O
= beta- nicotinate D-ribonucleotide
+ diphosphate
+ ADP
+ phosphate
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   2 terms 
  Biological process     replicative cell aging   7 terms 
  Biochemical function     protein binding     5 terms  

 

 
    reference    
 
 
DOI no: 10.1016/j.str.2005.05.016 Structure 13:1385-1396 (2005)
PubMed id: 16154095  
 
 
The structure of a eukaryotic nicotinic acid phosphoribosyltransferase reveals structural heterogeneity among type II PRTases.
J.S.Chappie, J.M.Cànaves, G.W.Han, C.L.Rife, Q.Xu, R.C.Stevens.
 
  ABSTRACT  
 
Nicotinamide adenine dinucleotide (NAD) is an essential cofactor for cellular redox reactions and can act as an important substrate in numerous biological processes. As a result, nature has evolved multiple biosynthetic pathways to meet this high chemical demand. In Saccharomyces cerevisiae, the NAD salvage pathway relies on the activity of nicotinic acid phosphoribosyltransferase (NAPRTase), a member of the phosphoribosyltransferase (PRTase) superfamily. Here, we report the structure of a eukaryotic (yeast) NAPRTase at 1.75 A resolution (locus name: YOR209C, gene name: NPT1). The structure reveals a two-domain fold that resembles the architecture of quinolinic acid phosphoribosyltransferases (QAPRTases), but with completely different dispositions that provide evidence for structural heterogeneity among the Type II PRTases. The identification of a third domain in NAPRTases provides a structural basis and possible mechanism for the functional modulation of this family of enzymes by ATP.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. ATP Binding in yNAPRTase
(A) View of the predicted ATP binding site from a SiteEngine search. Loop residues of domain C (shown in magenta) help position the adenosine ring, allowing the phosphates to extend into the barrel cavity to interact with the autophosphorylatable H232 (orange), as well as L269 and D296 (green). AMP is modeled into the binding pocket. The bound phosphate ligand (presumably indicating the PRPP binding site) is shown. Domains are colored as in Figure 1.
(B) Superposition of the four molecules of yNAPRTase in the asymmetric unit (colored cyan, orange, green, and white) reveals the inherent flexibility of the domain C loop. This segment occupies two distinct conformations in the crystal (signified by a black arrow), one of which is present in molecules A and B, the other being found in molecules C and D.
Figure 6.
Figure 6.
 
  The above figures are reprinted by permission from Cell Press: Structure (2005, 13, 1385-1396) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
  20838591 H.Lin, A.L.Kwan, and S.K.Dutcher (2010).
Synthesizing and salvaging NAD: lessons learned from Chlamydomonas reinhardtii.
  PLoS Genet, 6, 0.  
20047307 Z.Bello, B.Stitt, and C.Grubmeyer (2010).
Interactions at the 2 and 5 positions of 5-phosphoribosyl pyrophosphate are essential in Salmonella typhimurium quinolinate phosphoribosyltransferase.
  Biochemistry, 49, 1377-1387.  
20047306 Z.Bello, and C.Grubmeyer (2010).
Roles for cationic residues at the quinolinic acid binding site of quinolinate phosphoribosyltransferase.
  Biochemistry, 49, 1388-1395.  
19721089 F.Gazzaniga, R.Stebbins, S.Z.Chang, M.A.McPeek, and C.Brenner (2009).
Microbial NAD metabolism: lessons from comparative genomics.
  Microbiol Mol Biol Rev, 73, 529.  
19201765 S.N.Hashida, H.Takahashi, and H.Uchimiya (2009).
The role of NAD biosynthesis in plant development and stress responses.
  Ann Bot (Lond), 103, 819-824.  
18490451 H.I.Boshoff, X.Xu, K.Tahlan, C.S.Dowd, K.Pethe, L.R.Camacho, T.H.Park, C.S.Yun, D.Schnappinger, S.Ehrt, K.J.Williams, and C.E.Barry (2008).
Biosynthesis and recycling of nicotinamide cofactors in mycobacterium tuberculosis. An essential role for NAD in nonreplicating bacilli.
  J Biol Chem, 283, 19329-19341.  
16826227 A.Mattevi (2006).
A close look at NAD biosynthesis.
  Nat Struct Mol Biol, 13, 563-564.  
16783377 J.A.Khan, X.Tao, and L.Tong (2006).
Molecular basis for the inhibition of human NMPRTase, a novel target for anticancer agents.
  Nat Struct Mol Biol, 13, 582-588.
PDB codes: 2gvg 2gvj 2gvl
16959969 P.O.Hassa, S.S.Haenni, M.Elser, and M.O.Hottiger (2006).
Nuclear ADP-ribosylation reactions in mammalian cells: where are we today and where are we going?
  Microbiol Mol Biol Rev, 70, 789-829.  
16783373 T.Wang, X.Zhang, P.Bheda, J.R.Revollo, S.Imai, and C.Wolberger (2006).
Structure of Nampt/PBEF/visfatin, a mammalian NAD+ biosynthetic enzyme.
  Nat Struct Mol Biol, 13, 661-662.
PDB codes: 2h3b 2h3d
16154080 C.Brenner (2005).
Evolution of NAD biosynthetic enzymes.
  Structure, 13, 1239-1240.  
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.