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The Open Protein Structure Annotation Network
PDB Keyword
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2oc5

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

    Title Crystal structure of hypothetical protein (NP_895059.1) from Prochlorococcus marinus MIT9313 at 1.68 A resolution. To be published
    Site JCSG
    PDB Id 2oc5 Target Id
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    Molecular Characteristics
    Source
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    Alias Ids
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    TPS1554,NP_895059.1, 1.20.1260.10, BIG_457, 92409
    Molecular Weight
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    Da.
    Residues
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    Isoelectric Point
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    Sequence
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      BLAST   FFAS

    Structure Determination
    Method XRAY
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    Chains 1
    Resolution (Å)
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    Rfree
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    Matthews' coefficent 3.16 Rfactor 0.164
    Waters
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    Solvent Content 61.10

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    Ligand Information
    Ligands
    Metals

    Jmol

     
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    Google Scholar output for 2oc5
    1. Microbial biosynthesis of alkanes
    A Schirmer, MA Rude, X Li, E Popova - Science, 2010 - sciencemag.org
     
    2. Detection of formate, rather than carbon monoxide, as the stoichiometric coproduct in conversion of fatty aldehydes to alkanes by a cyanobacterial aldehyde
    DM Warui, N Li, H Nrgaard, C Krebs - Journal of the , 2011 - ACS Publications
     
    3. Metal use in ribonucleotide reductase R2, di-iron, di-manganese and heterodinuclearan intricate bioinorganic workaround to use different metals for the same
    M Hgbom - Metallomics, 2011 - xlink.rsc.org
     
    4. Cyanobacterial alkane biosynthesis further expands the catalytic repertoire of the ferritin-like [] di-iron-carboxylate'proteins
    C Krebs, JM Bollinger Jr, SJ Booker - Current Opinion in Chemical Biology, 2011 - Elsevier
     
    5. Structural insights into the metal binding properties of hypothetical protein MJ0754 from Methanococcus jannaschii
    EH Lee, HS Kim, HY Kim, YH Jeon - Proteins: Structure, , 2011 - Wiley Online Library
     
    6. Characterization of cyanobacterial fatty aldehyde deformylase and biodegradation of hydrocarbons by S. oneidensis MR-1
    D Golwala - 2012 - conservancy.umn.edu
     
    7. Functional, structural and evolutionary analyses of the ferritin-like superfamily of proteins
    RB Cooley - 2011 - scholarsarchive.library.oregonstate.
     

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    Protein Summary

    The PMT1231 gene from Prochlorococcus marinus mit9313 encodes the protein NP_895059 of unknown function belonging to DUF3066 (PF11266) that adopts a ferritin-like fold inside the PMT1231-like SCOP family, and shows some remote homology to rubrerythin (PF02915, P-value 9.6E-07 over residues 42-162). Blast identifies an annotated ferritin-like diiron carboxylate protein (YP_001224377) with 75% seq. id to NP_895059.

    The most similar structure to 2oc5, according to DALI, is a phenyl acetic acid catabolic protein (PDB id:

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    , PF05138 with HHPred P-value 3.1E-36 over residues 2-223, DALI Z-score 19.8 with rmsd 2.5 Å over 197 residues, sequence identity 17%). Also structural similarity is observed (Dali Z-scr=17) with the ribonucleotide reductase
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    .

     

    Of note, all of the above families (and many more) are linked by remote homology. FFAS shows alignment over the entire domain with the following scores:

     

    -87.700 PF03232.6; Q1HQL9_AEDAE/23-193; Ubiquinone biosynthesis protein COQ7
      -32.500 PF02915.10; O26850_METTH/9-145; Rubrerythrin
      -27.800 PF09968.2; A6LNR3_THEM4/28-188; Uncharacterized protein domain (DUF2202)
    -24.600 PF09537.3; A3U8G4_9FLAO/15-125; Domain of unknown function (DUF2383)
    -23.300 PF01786.10; A2QXC9_ASPNC/43-270; Alternative oxidase
    -20.900 PF04305.7; A3JS81_9RHOB/12-264; Protein of unknown function (DUF455)
    -19.300 PF05067.5; Q9KAU6_BACHD/1-281; Manganese containing catalase
    -19.000 PF11266.1; Q8DJB4_THEEB/11-229; Protein of unknown function (DUF3066)
      -16.700 PF05974.5; A4WGM2_ENT38/5-158; Domain of unknown function (DUF892)
    -16.700 PF10118.2; A7HUG2_PARL1/22-272; Predicted metal-dependent hydrolase
    -15.800 PF11583.1; A6V348_PSEA7/1-295; P-aminobenzoate N-oxygenase AurF
    -15.700 PF03405.7; STAD_SPIOL/69-397; Fatty acid desaturase
    -12.400 PF11553.1; Q2BD39_9BACI/1-155; Protein of unknown function (DUF3231)
      -12.000 PF00210.17; Q7NGR9_GLOVI/17-162; Ferritin-like domain
      -11.100 PF03070.9; PQQCL_CHLPN/5-222; TENA/THI-4/PQQC family
    -11.000 PF05138.5; Q5P3I7_AZOSE/1-255; Phenylacetic acid catabolic protein
    -10.700 PF06175.4; Q8CX43_SHEON/3-250; tRNA-(MS[2]IO[6]A)-hydroxylase (MiaE)
    -10.600 PF11251.1; A2TV44_9FLAO/15-246; Protein of unknown function (DUF3050)

     

    FFAS highlights conservation of several His and Glu residues, likely involved in catalysis. Might be interesting to also look at evolution of this family.

     

     

    To do: look at UNL in 3EZ0 entry - is it a phenylacetate?

              follow up family (structure/function/homology) relations to identify this UNL

    Ligand Summary



    References

    Reviews

    References

     

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