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The Open Protein Structure Annotation Network
PDB Keyword
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2rld

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

    Title Crystal structure of uncharacterized protein (NP_809265.1) from Bacteroides thetaiotaomicron VPI-5482 at 1.70 A resolution. To be published
    Site JCSG
    PDB Id 2rld Target Id 380318
    Molecular Characteristics
    Source Bacteroides thetaiotaomicron vpi-5482
    Alias Ids TPS1754,NP_809265.1, PF05635 Molecular Weight 13603.84 Da.
    Residues 116 Isoelectric Point 5.30
    Sequence mredmkdnvvkdkslefavrivnlykflvneqkefvmskqilrsgtsiganireaeqaqsradfinkln ialkeaneteywlellirteyitreqyesinndsteinkllisiikt
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.70 Rfree 0.201
    Matthews' coefficent 2.13 Rfactor 0.163
    Waters 519 Solvent Content 42.25

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 2rld
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     

    Protein Summary

    Gene BT_0352 from Bacteroides thetaiotaomicron vpi-5482 encodes the NP_809265 protein, a member of PFAM 05635 group that consists of bacterial 23S rRNA proteins. Another related seq family is PRK12275 (?). Genome context analysis indicates a possible functional link (string score 0.7) of BT_0352 with its neighbors BT_0353, a ribulose-5-phosphate 4-epimerase, and BT_0354, a Nudix family hydrolase.

    SCOP classifies 2rld in the all alpha class, bromodomain-like fold, IVS-encoded protein-like (super)family. In the 2rld structure, each monomer is a four-helix bundle with a left-handed twist. Five monomers in the ASU form a pentameric ring with H2 and H3 facing inward and H1, H4 at the outside.


    2rld structure (red) is structurally similar to the uncharacterized protein 2gsc (blue, 22% seq id, 104 residues aligned with a 1.5A Ca rmsd, Dali Zscr=16). The packing of the pentamer is less conserved compared to the monomer. It is also similar to the methylesterase inhibitor 1x8z (14% seq id; Z=12).

    >q|final1.pdb:B|PDB:2gsc:E ---
    -mkdNVVKDKSLEFAVRIVNLYKflvneQKEFvm--skQILRSGTSIGANIREAEQAQSRADFINKLNIA
    LKEANETEYWLELLIRTEYITREQYESINNDSTEINKLLISIIKT
     
    >t|PDB:2gsc:E|final1.pdb:B CRYSTAL STRUCTURE OF THE CONSERVED HYPOTHETICAL CY
    pherLDAWRDSMELVEMIYRLTEv---fPDQErygltaQLRRAAVSIPSNIAEGAARRSTPDYSRFLSIA
    RGSLSELDTQVQIAARLGYSRSEDDQSVRRQVDLVFAKLTALMNA

    The following residues between 2rld and 2gsc have small rmsd and same seq id:
    14,16,21,24,40,43,47,48,51,52,54,60,63,68,70,71,77,87,90,94,98,110



    Based on sequence analysis, it is clear that the site of interest is located on the 2nd and 3rd helices. The following residues are highly conserved: 40,45,46,49,50,54,58,60,67,70,74,77,80,81,84,85. All these residues are facing the central channel. It is also noticed that conserved residues from the neighboring monomer in the pentamer are needed to form a continuous site. The predict active site is likely around residue 54 of one monomer and residue 77 of the neigbouring monomer; in other words, one active site might be formed by Helix-2 of monomer A and Helix-3 of monomer B.



    The initial annotation of similar proteins was probably based on the article "Intervening sequence with conserved open reading frame in eubacterial 23S rRNA genes."

     

    Ligand Summary



    References

    Reviews

    References

     

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