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The Open Protein Structure Annotation Network
PDB Keyword
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1vlp

    Table of contents
    1. 1. Protein Summary
    2. 2. Ligand Summary
    3. 3. References

    Title The structure of a eukaryotic nicotinic acid phosphoribosyltransferase reveals structural heterogeneity among type II PRTases. Structure 13 1385-1396 2005
    Site JCSG
    PDB Id 1vlp Target Id 354135
    Molecular Characteristics
    Source Saccharomyces cerevisiae
    Alias Ids TPS1322,YOR209C Molecular Weight 49144.67 Da.
    Residues 430 Isoelectric Point 6.44
    Sequence msepvikslldtdmykitmhaavftnfpdvtvtykytnrssqltfnkeainwlkeqfsylgnlrfteee ieylkqeipylpsayikyisssnyklhpeeqisftseeiegkpthyklkilvsgswkdtilyeipllsl iseayfkfvdidwdyenqleqaekkaetlfdngirfsefgtrrrrslkaqdlimqgimkavngnpdrnk slllgtsnilfakkygvkpigtvahewvmgvasisedylhanknamdcwintfgaknaglaltdtfgtd dflksfrppysdayvgvrqdsgdpveytkkishhyhdvlklpkfskiicysdslnvekaityshaaken gmlatfgigtnftndfrkksepqvkseplnivikllevngnhaikisdnlgknmgdpatvkrvkeelgy terswsgdneahrwtz
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 1.75 Rfree 0.20962
    Matthews' coefficent 2.32 Rfactor 0.16964
    Waters 1272 Solvent Content 46.90

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1vlp
    1. FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6
    J Kosinski, MJ Gajda, IA Cymerman - PROTEINS: , 2005 - Wiley Online Library
     
    2. Domain definition and target classification for CASP6
    M Tress, CH Tai, G Wang, I Ezkurdia - PROTEINS: , 2005 - Wiley Online Library
     
    3. Fast and accurate algorithms for protein side-chain packing
    J Xu, B Berger - Journal of the ACM (JACM), 2006 - dl.acm.org
     
    4. The structure of a eukaryotic nicotinic acid phosphoribosyltransferase reveals structural heterogeneity among type II PRTases
    JS Chappie, JM C_naves, GW Han, CL Rife, Q Xu - Structure, 2005 - Elsevier
     
    5. A phosphoenzyme mimic, overlapping catalytic sites and reaction coordinate motion for human NAMPT
    ES Burgos, MC Ho, SC Almo - Proceedings of the , 2009 - National Acad Sciences
     
    6. Prediction of protein domain boundaries from statistics of appearance of amino acid residues
    OV Galzitskaya, NV Dovidchenko, MY Lobanov - Molecular Biology, 2006 - Springer
     
    7. Protein structure prediction based on the sliced lattice model
    CC Wang, CB Yang, HY Ann - 2008 Conference on , 2005 - etd.lib.nsysu.edu.tw
     
    8. Investigating diproline segments in proteins: Occurrences, conformation and classification
    I Saha, N Shamala - Biopolymers, 2012 - Wiley Online Library
     
    9. Prediction of Protein Backbone Based on the Sliced Lattice Model
    CC Wang, CB Yang, HY Ann, HY Chang - 2008 - csie.npu.edu.tw
     
    10. Protein Structure Prediction Using a Profile-Profile Comparison Method: FORTE
    _____ - ____, 2006 - J-STAGE
     
    11. Characterization of human nicotinate phosphoribosyltransferase: Kinetic studies, structure prediction and functional analysis by site-directed mutagenesis
    L Galassi, M Di Stefano, L Brunetti, G Orsomando - Biochimie, 2011 - Elsevier
     

    Protein Summary

    The NPT1 (YOR209C) gene from Saccharomyces cerevisiae encodes the NP_014852 protein, a nicotinate phosphoribosyltransferase (NAPRTase), and member of the phosphoribosyltransferase (PRTase) superfamily PF04095 EC 2.4.2.11 COG1488.  

    The 1vlp folds into a two-domain structure that resembles the architecture of quinolinic acid phosphoribosyltransferases (QAPRTases), however with different arrangement [Ref]. SCOP classifies the N-terminal domain in alpha+beta class, alpha/beta hammerhead fold, nicotinate PRTase N-terminal domain like superfamily; the C-terminal domain in the alpha/beta class, TIM barrel fold, nicotinate PRTase C-terminal domain like superfamily. The closest structure according to DALI is the transferase 2im5 (Z=54). Several crystal structures of its homologues from other organisms have been solved: 1YIR(Z=50), Pseudomonas aeruginosa; 1YBE (Z=46), Agrobacterium tumefaciens.

    This enzyme catalyzes the formation of NAMN and PPi from 5-phosphoribosy -1-pyrophosphate (PRPP) and nicotinic acid.  This is the first and the rate limiting step in the NAD salvage pathway. This salvage pathway recycles NAD degradation products.  

    Ligand Summary



    References

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