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The Open Protein Structure Annotation Network
PDB Keyword
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3pfo

    Title Crystal structure of a putative acetylornithine deacetylase (RPA2325) from RHODOPSEUDOMONAS PALUSTRIS CGA009 at 1.90 A resolution. To be published
    Site JCSG
    PDB Id 3pfo Target Id 403456
    Molecular Characteristics
    Source Rhodopseudomonas palustris cga009
    Alias Ids TPS30776,NP_947670.1, 3.40.630.10, 325378 Molecular Weight 46915.29 Da.
    Residues 432 Isoelectric Point 4.99
    Sequence matetltksdaitqslraavdrnfndqvaflqrmvqfrsvrgeeapqqewlaqqfadrgykvdtfslad vdiashpkaapmdtidpagsmqvvatadsdgkgrslilqghidvvpegpvdlwsdppyeakvrdgwmig rgaqdmkggvsamifaldairtagyapdarvhvqtvteeestgngalstlmrgyradaclipeptghtl traqvgavwfrlrvrgtpvhvaysetgtsailsamhlirafeeytkelnaqavrdpwfgqvknpikfnv giikggdwasstaawceldcrlglltgdtpqeamrgiekcladaqatdsflsenpaelvwsgfqadpav cepggvaedvltaahkaafnapldarlstavndtryysvdygipalcygpygqgphafderidleslrk ttlsialfvaewcglrkl
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.90 Rfree 0.2042
    Matthews' coefficent 2.34 Rfactor 0.1714
    Waters 701 Solvent Content 47.37

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3pfo
    1. Application of DEN refinement and automated model building to a difficult case of molecular-replacement phasing: the structure of a putative succinyl-diaminopimelate
    AT Brunger, D Das, AM Deacon, J Grant - Section D: Biological , 2012 - scripts.iucr.org
     
    2. Mutational and structural analysis of LN-carbamoylase: new insights into a peptidase M20/M25/M40 family member.
    S Martnez-Rodrguez, A Garca-Pino - Journal of , 2012 - Am Soc Microbiol
     

    Protein Summary

    The protein NP_947670.1 is annotated as acetylornithine deacetylase. NP_947670.1 belongs to PFAM PF01546 Peptidase_M20 (residue 106-425), and PFAM PF07687 M20_dimer (residue 209-325). 

    PF01546 family includes a range of zinc metallopeptidases belonging to several families in the peptidase classification [1]. Family M20 are Glutamate carboxypeptidases. Peptidase family M25 contains X-His dipeptidases.

    PF07687 family consists of a domain containing of 4 beta strands and two alpha helices which make up the dimerisation surface of members of the M20 family of peptidases.

     

    The monomer structure is shown below. The protein binds two Zinc ions, shown in magenta sphere rendition.

    MJ3193C.png

     

    The dimerization of the protein is facilitated by the PF07687 domain, shown below.

    MJ3193C_dimer.png

     

    Top 10 DALI Structural Homologs
    N PDB Z-score RMSD LALI NRES %ID Description (JCSG structures highlighted in red)
    1 3dlj 35.7 2.7 387 467 17 Beta-ala-his Dipeptidase
    2 2zof 35.3 2.6 395 478 18 Cytosolic Non-specific Dipeptidase
    3 2zog 35.2 2.6 395 478 18 Cytosolic Non-specific Dipeptidase
    4 3isz 34.9 6.9 354 369 20 Succinyl-diaminopimelate Desuccinylase
    5 1vgy 34.9 5.0 356 375 19 Succinyl-diaminopimelate Desuccinylase
    6 3ic1 34.7 6.6 358 370 20 Succinyl-diaminopimelate Desuccinylase
    7 1cg2 34.7 5.2 370 389 20 Carboxypeptidase G2
    8 3gb0 34.6 4.2 357 373 18 Peptidase T
    9 2rb7 34.6 3.0 339 360 19 Peptidase, M20/m25/m40 Family
    10 2f8h 33.8 3.0 336 360 22 Aectylcitrulline Deacetylase

     

     

    References:

    1. Rawlings ND, Barrett AJ; , Meth Enzymol 1995;248:183-228.: Evolutionary families of metallopeptidases. PUBMED:7674922

    Ligand Summary

    Reviews

    References

     

    No references found.

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    Files (2)

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     MJ3193C.png
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    149.95 kB19:51, 28 Oct 2010abhinavkActions
     MJ3193C_dimer.png
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    134.4 kB19:51, 28 Oct 2010abhinavkActions
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