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The Open Protein Structure Annotation Network
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1vrm

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

    Title Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 A resolution. Proteins 64 1083-1090 2006
    Site JCSG
    PDB Id 1vrm Target Id 358474
    Molecular Characteristics
    Source Thermotoga maritima msb8
    Alias Ids TPS1394,TM1553 Molecular Weight 35112.95 Da.
    Residues 313 Isoelectric Point 5.27
    Sequence rtkdqyyelrdfalgtsvrivvssqkinprtiaeailedmkritykfsftdersvvkkindhpnewvev deetyslikaacafaeltdgafdptvgrllelwgftgnyenlrvpsreeieealkhtgyknvlfddknm rvmvkngvkidlggiakgyaldrarqialsfdenatgfveaggdvriigpkfgkypwvigvkdprgddv idyiylksgavatsgdyeryfvvdgvryhhildpstgypargvwsvtiiaedattadalstagfvmagk dwrkvvldfpnmgahllivleggaiersetfklfere
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.58 Rfree 0.191
    Matthews' coefficent 2.37 Rfactor 0.157
    Waters 404 Solvent Content 47.76

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    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 1vrm
    1. Decision-making in structure solution using Bayesian estimates of map quality: the PHENIX AutoSol wizard
    TC Terwilliger, PD Adams, RJ Read - Section D: Biological , 2009 - scripts.iucr.org
     
    2. A Survey of Aspartate-Phenylalanine and Glutamate-Phenylalanine Interactions in the Protein Data Bank: Searching for Anion-Pi Pairs
    V Philip, JB Harris, RM Adams, D Nguyen, J Spiers - Biochemistry, 2011 - ACS Publications
     
    3. Crystal structure of the ApbE protein (TM1553) from Thermotoga maritima at 1.58 resolution
    GW Han, S Sri Krishna - Proteins: Structure, , 2006 - Wiley Online Library
     
    4. Structure and ligand binding of the soluble domain of a Thermotoga maritima membrane protein of unknown function TM1634
    CJ McCleverty, L Columbus, A Kreusch - Protein , 2008 - Wiley Online Library
     
    5. FAD Binding by ApbE Protein from Salmonella enterica: a New Class of FAD-Binding Proteins
    JM Boyd, JA Endrizzi, TL Hamilton - Journal of , 2011 - Am Soc Microbiol
     

    Protein Summary

    The TM1553 gene of Thermotoga maritima encodes the NP_229353 lipoprotein involved in thiamine (vitamin B1) biosynthesis and has been proposed to carry out the conversion of aminoimidazole ribotide (AIR) to 4-amino-5-hydroxymethyl-2-methyl pyrimidine (HMP) [Ref] [Ref]. NP_229353 belongs to the ApbE group (PF02424). Mutagenesis studies have indicated that ApbE is important for Fe-S cluster metabolism [Ref]. The exact role played by ApbE in either of these activities remains unclear [Ref].

    Phylogenetic cooccurrence and genomic neighbourhood (STRING) indicate that functions of TM1553 is interdependent with TM0248 (NA-translocating NADH-quinone reductase, NQR5 subunit), TM0247 (NA-translocating NADH-quinone reductase, NQR4 subunit), TM1555 (hypothetical protein), and TM1767 (methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase).

    SCOP classifies 1vrm in the alpha+beta class, ApbE-like (super)family. DALI top hit (Z=30) is with the thiamine biosynthesis lipoprotein ApbE 2o18. The hypothetical protein 2o34 is a second hit with Z=14.

    Ligand Summary



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