.
The Open Protein Structure Annotation Network
PDB Keyword
.

3fj2

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

    Title Crystal structure of Monooxygenase-like Protein (NP_471648.1) from LISTERIA INNOCUA at 1.85 A resolution. To be published
    Site JCSG
    PDB Id 3fj2 Target Id 390900
    Molecular Characteristics
    Source Listeria innocua clip11262
    Alias Ids TPS20166,NP_471648.1, 3.30.70.900, 85300 Molecular Weight 19632.38 Da.
    Residues 167 Isoelectric Point 5.97
    Sequence mkkvfittgtehylrqlmenyigenvtllqnfsqsllyqestgeklfqegkeyrvlqssgslkgfgivv feyiqlrdeeipiflqmyqhaslhfsetpglqstkltkamntnqflivsfwdsevffqewkktplhkei tsimkknntqvgfshediyhypefshdak
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 1
    Resolution (Å) 1.85 Rfree 0.186
    Matthews' coefficent 3.69 Rfactor 0.167
    Waters 184 Solvent Content 66.65

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3fj2
    1. Structure of the signal transduction protein TRAP (target of RNAIII-activating protein)
    K Henrick, M Hirshberg - Acta Crystallographica Section F: Structural , 2012 - scripts.iucr.org
     

    Protein Summary

    Gene lin2316 from Listeria innocua encodes the NP_471648 protein that belongs to the ABM (antibiotic biosynthesis monooxygenase) family (PF03992). This domain is found in monooxygenases involved in the biosynthesis of several antibiotics by Streptomyces species.

    3fj2 structure contains a monomer in the asymmetric unit, which is suggested as a likely biological molecule.

     

    monomer_97408.png

    Fig. 1: 3fj2 monomer structure.

    3fj2 is structurally similar to proteins from the dimeric alpha + beta barrel superfamily, PG130-like family from SCOP.  Dali hits mostly hypothetical or uncharacterized proteins [2pgc, TOPSAN page (3.2 A rmsd, 153 Ca aligned, 11% id, Z=13), 2omo, TOPSAN page (3.0A rmsd, 94 Ca aligned, 12% id; Z=10), 1y0h, TOPSAN page (2.9A rmsd, 94 Ca aligned, 10% id; Z=10), 3dtz, TOPSAN page (3.0A rmsd, 138 Ca aligned, 7% id, Z=9.7))]. The only characterized one is the sulfur oxygenase reductase (SOR) [2cb2 (3.0A rmsd, 149 Ca aligned, 11% id, Z=10.5)].

    However, comparision of the presumable active site residues of the above targets - 2pgc, 2omo and 3dtz-  does not show any clear clue of the conservation. Superposition of 3fj2 with the SOR structure (2cb2) shows that the conserved cysteins (Cys31, Cys101, Cys104) of SOR are not conserved or missing in the 3fj2 structure. Besides that, the iron catalytic site of SOR is not observed in the 3fj2 structure, either.

     

    super_2cb2 (1).png 

    Fig. 2 Superposition of 3fj2 (green) with 2cb2 monomer (cyan). Fe atom of 2cb2 is shown as sphere (dark orange). Three conserved Cys residues of 2cb2 are shown as stick [Cys 31-orange (refined as cysteine persulfide, Css 31), Cys101-red and Cys104-magenta). 

     

    The most significant DALI and NCBI Blast hit of 3fj2 against PDB is JCSG target 3fez with Z score=303, E value =2e-83, and Dali Z-score=30. Since the putative active site residues (Tyr53, Tyr72, Asp155, Glu154, Glu71, Asp54, Lys107) are identical between 3fj2 and 3fez, it is proposed that the function of both proteins is similar.

    super_3fez.png

    Fig. 3.  Superposition of 3fj2 (green) with 3fez monomer (yellow) (0.8A rmsd, 166 Ca aligned, 89% id). The predicted active site residues of both 3fj2 and 3fez are shown as stick (red).

     

    References:

    Yeats C, Bentley S, Bateman A; , BMC Microbiol 2003;3:3-3.: New Knowledge from Old: In silico discovery of novel protein domains in Streptomyces coelicolor. PUBMED:12625841

    Urich, T.,  Gomes, C.M.,  Kletzin, A.,  Frazao, C. (2006) X-ray Structure of a self-compartmentalizing sulfur cycle metalloenzyme. Science 311: 996-1000

    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page
    • No tags
    You must login to post a comment.
    All content on this site is licensed under a Creative Commons Attribution 3.0 License
    Powered by MindTouch