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The Open Protein Structure Annotation Network
PDB Keyword
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3ky8

    Table of contents
    1. 1. Protein Summary
    2. 2.
      1. 2.1. Ligand Summary

    Title Crystal structure of Putative riboflavin biosynthesis protein (YP_001092907.1) from SHEWANELLA SP. PV-4 at 2.12 A resolution. To be published
    Site JCSG
    PDB Id 3ky8 Target Id 394242
    Molecular Characteristics
    Source Shewanella sp. pv-4
    Alias Ids TPS29509,YP_001092907.1, _0023.002889_, 326351 Molecular Weight 19836.83 Da.
    Residues 178 Isoelectric Point 4.70
    Sequence manivfiatsldgyiadkrgkldwlhsvpnpnnvdtgfvalmervdglvmgrntldmvlsfdcdwpysk pvfvlsntmtevpqgyedkvflvkgklvdiiadlnakgfnelyidggvtiqnflkedlidemvitrfpi llgggvplfgelesslsfnviksevvldsltqttyhrkra
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.12 Rfree 0.231
    Matthews' coefficent 2.30 Rfactor 0.181
    Waters 199 Solvent Content 46.60

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3ky8
    1. Characterisation of an oxidoreductase from the Arylamine N_acetyltransferase operon in Mycobacterium smegmatis
    D Evangelopoulos, N Cronin, T Daviter, E Sim - FEBS , 2011 - Wiley Online Library
     

    Protein Summary

    Pfam update: RibD_C (PF01872) family

    394242 from Shewanella sp. pv-4 encodes a protein which belongs to Pfam; PF01872; RibD_C; thought to be involved in riboflavin biosynthesis.

    There are two protomers (A and B chains; biological dimer) found in the asu.

    asu.png

    Figure 1. Two protomers in asu.

     


     

    The PDB hits of structural homologs by DALI are:

        No:  Chain   Z    rmsd lali nres  %id PDB  Description
    1: 1cz3-B 19.5 2.1 160 168 21 PDB MOLECULE: DIHYDROFOLATE REDUCTASE; 2: 1d1g-B 19.4 2.2 159 165 21 PDB MOLECULE: DIHYDROFOLATE REDUCTASE; 3: 1cz3-A 19.3 2.2 159 164 21 PDB MOLECULE: DIHYDROFOLATE REDUCTASE; 4: 1d1g-A 19.2 2.2 159 165 21 PDB MOLECULE: DIHYDROFOLATE REDUCTASE; 5: 2gd9-B 18.0 2.3 153 171 25 PDB MOLECULE: HYPOTHETICAL PROTEIN YYAP; 6: 2azn-F 17.8 2.3 166 219 16 PDB MOLECULE: PUTATIVE 5-AMINO-6-(5-PHOSPHORIBOSYLAMINO)URACIL 7: 2azn-C 17.8 2.2 165 219 16 PDB MOLECULE: PUTATIVE 5-AMINO-6-(5-PHOSPHORIBOSYLAMINO)URACIL 8: 2azn-B 17.8 2.2 165 219 16 PDB MOLECULE: PUTATIVE 5-AMINO-6-(5-PHOSPHORIBOSYLAMINO)URACIL 9: 2azn-A 17.7 2.3 165 219 16 PDB MOLECULE: PUTATIVE 5-AMINO-6-(5-PHOSPHORIBOSYLAMINO)URACIL 10: 2azn-E 17.7 2.3 166 219 16 PDB MOLECULE: PUTATIVE 5-AMINO-6-(5-PHOSPHORIBOSYLAMINO)URACIL 11: 2azn-D 17.7 2.3 165 219 16 PDB MOLECULE: PUTATIVE 5-AMINO-6-(5-PHOSPHORIBOSYLAMINO)URACIL 12: 2gd9-A 17.2 2.3 152 177 25 PDB MOLECULE: HYPOTHETICAL PROTEIN YYAP; 13: 3ex8-B 17.1 2.5 168 359 17 PDB MOLECULE: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBD; 14: 2d5n-D 17.1 2.4 168 360 18 PDB MOLECULE: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBD; 15: 2d5n-C 17.1 2.5 169 359 18 PDB MOLECULE: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBD; 16: 2b3z-D 17.0 2.4 165 360 18 PDB MOLECULE: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBD; 17: 2hxv-A 17.0 2.5 164 349 18 PDB MOLECULE: DIAMINOHYDROXYPHOSPHORIBOSYLAMINOPYRIMIDINE 18: 3ex8-D 17.0 2.5 168 360 17 PDB MOLECULE: RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBD; 19: 3dl6-B 16.3 2.5 156 510 17 PDB MOLECULE: DIHYDROFOLATE REDUCTASE, DHFR; 20: 2oip-B 16.2 2.4 156 516 15 PDB MOLECULE: CHAIN A, CRYSTAL STRUCTURE OF DHFR; 21: 3dl5-A 16.2 2.5 154 509 17 PDB MOLECULE: DIHYDROFOLATE REDUCTASE, DHFR; 22: 3dl5-D 16.2 2.6 156 509 17 PDB MOLECULE: DIHYDROFOLATE REDUCTASE, DHFR; 23: 3dl6-A 16.2 2.6 155 507 17 PDB MOLECULE: DIHYDROFOLATE REDUCTASE, DHFR; 24: 3dl5-B 16.2 2.6 156 510 17 PDB MOLECULE: DIHYDROFOLATE REDUCTASE, DHFR; 25: 1vdr-A 16.2 2.5 152 157 16 PDB MOLECULE: DIHYDROFOLATE REDUCTASE;

     

    Superposition of the 394242 with 1d1g shows that their active site resides are conserved. Interestingly, there are two UNLs bound in the each protomer of 394242. UNL1 &3 are modelled at the MTX site of 1d1g, and UNL2 &4 are modelled at the NDP binding site of 1d1g.

    super_omit.png

     Figure 3. Superposition of 394242 (green) with 1d1g (gray). 1sigma omit maps of UNLs are shown.

                    From top to bottom: UNL1 &2 (left), UNL3 &4 (right).


    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (3)

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     asu.png
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    279.64 kB03:14, 16 Sep 2009gyewonActions
     super_omit.png
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    273.59 kB04:13, 2 Oct 2009gyewonActions
     tetramer.png
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    261.35 kB03:14, 16 Sep 2009gyewonActions
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