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3i7d

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

    Title Crystal structure of sugar phosphate isomerase from a cupin superfamily SPO2919 from Silicibacter pomeroyi (YP_168127.1) from SILICIBACTER POMEROYI DSS-3 at 2.30 A resolution. To be published
    Site JCSG
    PDB Id 3i7d Target Id 391429
    Molecular Characteristics
    Source Silicibacter pomeroyi dss-3
    Alias Ids TPS20249,YP_168127.1, 2.60.120.10, 336150 Molecular Weight 17521.59 Da.
    Residues 162 Isoelectric Point 4.64
    Sequence mpkldldsierrigsvypgrlnaamdgrsslrlgdagglsqfgvnlvrlepgaksslrhyhmeqdefvm vtegalvlvddqgehpmvpgdcaafpagdpnghqfvnrtdapatflvvgtrtptetayysdmdmmvkqd asgfaftrkdgspltadqigddne
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.30 Rfree 0.245
    Matthews' coefficent 2.45 Rfactor 0.196
    Waters 179 Solvent Content 49.71

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3i7d
    1. Crystal structures of the apo and GDP_bound forms of a cupin_like protein BbDUF985 from Branchiostoma belcheri tsingtauense
    Y Du, YX He, S Gaowa, X Zhang - Proteins: Structure, , 2010 - Wiley Online Library
     

    Protein Summary

    Pfam update: This protein is now in family PF07883.4 Cupin_ CL0029 along with other structures.

    Gene SPO2919 from Silicibacter pomeroyi dss-3 is annotated ashypothetical protein YP_168127.1. It belongs to Pfam; PF07883; Cupin_2 superfamily. This family is a member of clan Cupin (CL0029), which contains the following 24 members: 3-HAO AraC_binding ARD Asp_Arg_Hydrox Auxin_BP CDO_I Cupin_1 Cupin_2 Cupin_3 Cupin_4 Cupin_5 dTDP_sugar_isom DUF1498 DUF386 Ectoine_synth EutQ FdtA GPI HgmA JmjC MannoseP_isomer Pirin Pirin_C PMI_typeI

     

    SCOP classifies 3I7D in the all-beta class, RmlC-like cupins superfamily, TM1287-like family. The 3I7D structure assembles as a dimer in the crystallographic asymmetric unit. Analysis of the crystallographic packing of 3I7D by PISA server indicates that this dimer is the biologically relevant form.

     

    dimer_105648.png 

    Fig. 1. Biiological dimer of 3I7D

    DALI top hit for 3I7D is TM1459 from Thermotoga Maritima (1vj2, Z=13.9, rmsd 2.0A, 111 Ca aligned, 23% %id), and the 2nd hit is the auxin binding protein (1lr5, Z=13.2, rmsd 2.4A, 122 aligned, 20%id). The superposition of 3I7D with those two are shown in the figure 2.

     

     super_1vj2_1lr5.png

    Fig. 2. Superposition of 3i7d with 1vj2 (light pink) and 1lr5 (light blue) structures.

     

    Putative active site of 3i7d is formed by His59, His61, Glu66 and His102 and contains two acetate ions. 1vj2 from Thermotoga Maritima contains a Mn ion coordinated by four histidines (His52, His54, His58, and His92) [Ref]. In the 1lr5 structure, this position is occupied by a Zn ion coordinated by His57, His59, Glu63 and His106 [Ref].

    Ligand Summary

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    References

     

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    258.97 kB01:49, 19 May 2009gyewonActions
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