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3pm9

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

    Title Crystal structure of a Putative dehydrogenase (RPA1076) from Rhodopseudomonas palustris CGA009 at 2.57 A resolution. To be published
    Site JCSG
    PDB Id 3pm9 Target Id 403484
    Molecular Characteristics
    Source Rhodopseudomonas palustris cga009
    Alias Ids TPS30777,NP_946427.1, _0045.001334_, 325349 Molecular Weight 50785.22 Da.
    Residues 475 Isoelectric Point 5.29
    Sequence mnivsqlspvtlspeliarftaivgdkhaltdpleleayiteernlyrghsplvlrpgsteevvaickl anearvalvpqggntglvggqtphngevvislkrmdkireidtssntitveagailqrvqekaaevdrl fplslgaqgsctiggnlstnaggtaalayglardmalgvevvladgrvmnllsklkkdntgydlrdlfi gaegtlgiitaatlklfpkpravetafvglqspddalkllgiaqgeaagnltsfeliaetpldfsvrha nnrdplearypwyvlielssprddaraalesilergfedgivvdaaiansvqqqqafwklreeispaqk peggsikhdisvpvaavpqfieqanaavvalipgarpvpfghlgdgnihynvsqpvgadkaeflarwhd vsqvvfevvlrlggsisaehgigvmkrdelaevkdktaielmrsikalldphgimnpgkvv
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 6
    Resolution (Å) 2.57 Rfree 0.2266
    Matthews' coefficent 3.75 Rfactor 0.1931
    Waters 919 Solvent Content 67.19

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3pm9
    1. Crystallization and preliminary X-ray analysis of a dye-linked D-lactate dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix
    T Shibahara, T Satomura, R Kawakami - Section F: Structural , 2011 - scripts.iucr.org
     

    Protein Summary

    Pfam Update: This sequence has two domains on it: FAD_binding_4 (PF01565) from 51-190 and FAD-oxidase_C (PF02913) from 226-474. Both of these are well-characterised families.

     

    Target ID 403484 from the photosynthetic bacterium Rhodopseudomonas palustris is comprised of two Pfam sequence domains. The N-terminal domain (residues 51-190) belongs to the FAD_binding_4 (PF01565) Pfam family. Residues 226-474 belongs to the FAD-oxidase_C (PF02913) Pfam family. Many structures have been determined for both Pfam families. Shown below is a ribbons representation of the structure of target ID 403484 color coded with the N-terminal end in blue and the C-terminal end in red. An FAD cofactor (shown in magenta) is bound to each monomer.

    monomer.png

     A DALI search reveals that target ID 403484 has structural similairity to the following entries listed in the table below. The entries shown are some of the top scoring DALI hits, there are several more not listed.

     

    PDB ID
    Description
    DALI Z Score
    rmsd (Ang)
    length of alignment
    number of residues in related structure
    % sequence ID
    Citation
    1f0x CRYSTAL STRUCTURE OF D-LACTATE DEHYDROGENASE, A PERIPHERAL MEMBRANE RESPIRATORY ENZYME. 32.9 2.6 419 502 19

    Dym, O. et al. (2000) [Ref]

    1wve p-Cresol Methylhydroxylase: Alteration of the Structure of the Flavoprotein Subunit upon its Binding to the Cytochrome Subunit 30.5 3.0 435 515 18 Cunane et. al (2005) [Ref]
    1diq CRYSTAL STRUCTURE OF P-CRESOL METHYLHYDROXYLASE WITH SUBSTRATE BOUND 30.4 3.0 435 515 18 Cunane, L.M. et al. (2000) [Ref]
     2uuv ALKYLDIHYDROXYACETONEPHOSPHATE SYNTHASE IN P1  30.0  2.9  415  523  20  Razeto, A. et al. (2000) [Ref]
     1qlu  STRUCTURE OF THE H422A MUTANT VANILLYL-ALCOHOL OXIDASE IN COMPLEX WITH ISOEUGENOL  27.6  3.2  432  550  17  Fraaije, M.W. et al. (1999)  [Ref]
     1w10  NATIVE CYTOKININ DEHYDROGENASE  27.5  3.2  399  479  16  Malito, E. et al. (2004) [Ref]

     

     

    Shown below is a positiong of the substrate binding site adjacent to the FAD cofactor of vanillyl-alcohol oxidase (PDB ID 1qlu) onto the putative active site of target ID 403484. PDB ID is colored in cyan and targetid 1qlu is colored in green. The bound substrate of vanillyl alcohol oxidase is 2-METHOXY-4-VINYL-PHENOL. In the structure of target ID 403484, unidentified electron density was observed adjacent to the FAD cofactor at the putative active site. This electron density was modeled as an unknown ligand (UNL) and is shown by red spheres.

     

    1qlu_active_site_superposition.png

     

     

     Shown below is a close-up representation of the structure of target ID 403484. Electron density contoured at 1sigma for the FAD cofactor and UNL ligand (red spheres) is shown in cyan.

     

    active_site_density.bmp

     

     

     

     

     

     

     

    Ligand Summary

    Reviews

    References

     

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