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The Open Protein Structure Annotation Network
PDB Keyword
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3fgv

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

    Title Crystal structure of protein of unknown function with ferredoxin-like fold (YP_167536.1) from SILICIBACTER POMEROYI DSS-3 at 1.30 A resolution. To be published
    Site JCSG
    PDB Id 3fgv Target Id 391426
    Molecular Characteristics
    Source Silicibacter pomeroyi dss-3
    Alias Ids TPS20247,YP_167536.1, 3.30.70.900, 336136 Molecular Weight 12149.07 Da.
    Residues 105 Isoelectric Point 4.50
    Sequence mtesdrdqeasmrevvivkstpqrgkfnafaelvgklvsetrdfpgclgaylmlaperneqvvmhiwet pdaleayltwradrgdfleineyleveqdfktyqla
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.30 Rfree 0.150
    Matthews' coefficent 2.52 Rfactor 0.130
    Waters 302 Solvent Content 51.17

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3fgv
    1. Ligands in PSI structures
    A Kumar, HJ Chiu, HL Axelrod, A Morse - Section F: Structural , 2010 - scripts.iucr.org
     
    2. Crystal structure and catalytic mechanism of 4-methylmuconolactone methylisomerase
    M Marn, DW Heinz, DH Pieper, BU Klink - Journal of Biological Chemistry, 2009 - ASBMB
     

    Protein Summary

    Gene SPO2313 from Silicibacter pomeroyi dss-3 encodes the YP_167536 protein that belongs to the antibiotic biosynthesis monooxygenase (ABM) group ( PF03992). The ABM domain is found in monooxygenases involved in the biosynthesis of several antibiotics by Streptomyces species. Its gene occurrence as a repeat in Streptomyces coelicolor SCO1909 (Q9X9W3) is suggestive that they may function as multimers.

    SCOP classifies 3fgv in the alpha+beta class, dimeric alpha+beta barrel superfamily, PA3566-like family. DALI top hits are with 1y0h, 2omo (Zscr=14), 2gff, 3e8o, 2fb0 (Zscr=13). SSM search using 3fgv as query scores with proteins annotated as antibiotic biosynthesis monooxygenases as shown in table below.


    SSM Structure Alignment Results

    N

     Scoring 

     Rmsd 

    %seq

    Target (PDB entry)

     Q 

     P 

     Z 

    Match

    %sse

    Nres

    Title

    1

    0.71

    5.2

    6.7

    1.55

    14

    2omo:E

    100

    95

    PUTATIVE ANTIBIOTIC BIOSYNTHESIS MONOOXYGENASE FROM NITROSOMONAS EUROPAEA

    2

    0.69

    5.4

    6.7

    1.56

    18

    1y0h:B

    100

    98

    STRUCTURE OF RV0793 FROM MYCOBACTERIUM TUBERCULOSIS

    3

    0.68

    5.3

    6.7

    1.58

    18

    1y0h:B

    100

    98

    STRUCTURE OF RV0793 FROM MYCOBACTERIUM TUBERCULOSIS

    4

    0.67

    4.7

    6.3

    1.51

    15

    2omo:E

    100

    95

    PUTATIVE ANTIBIOTIC BIOSYNTHESIS MONOOXYGENASE FROM NITROSOMONAS EUROPAEA

    5

    0.67

    5.2

    6.4

    1.46

    12

    2fb0:A

    86

    94

    CRYSTAL STRUCTURE OF CONSERVED PROTEIN OF UNKNOWN FUNCTION FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 2.10 A RESOLUTION, POSSIBLE OXIDOREDUCTASE

    6

    0.66

    4.7

    6.3

    1.48

    15

    2omo:G

    100

    99

    PUTATIVE ANTIBIOTIC BIOSYNTHESIS MONOOXYGENASE FROM NITROSOMONAS EUROPAEA

    7

    0.66

    4.7

    6.3

    1.50

    15

    2omo:G

    100

    99

    PUTATIVE ANTIBIOTIC BIOSYNTHESIS MONOOXYGENASE FROM NITROSOMONAS EUROPAEA

    8

    0.66

    4.9

    6.4

    1.45

    12

    2fb0:A

    100

    94

    CRYSTAL STRUCTURE OF CONSERVED PROTEIN OF UNKNOWN FUNCTION FROM BACTEROIDES THETAIOTAOMICRON VPI-5482 AT 2.10 A RESOLUTION, POSSIBLE OXIDOREDUCTASE

    9

    0.64

    4.4

    6.1

    1.82

    10

    2gff:A

    100

    97

    CRYSTAL STRUCTURE OF YERSINIA PESTIS LSRG

    10

    0.64

    3.9

    5.7

    1.60

    14

    3bm7:A

    75

    106

    CRYSTAL STRUCTURE OF PROTEIN OF UNKNOWN FUNCTION WITH FERREDOXIN-LIKE FOLD (NP_420935.1) FROM CAULOBACTER CRESCENTUS AT 1.35 A RESOLUTION

    11

    0.64

    4.9

    6.5

    1.52

    15

    2omo:D

    100

    104

    PUTATIVE ANTIBIOTIC BIOSYNTHESIS MONOOXYGENASE FROM NITROSOMONAS EUROPAEA

    12

    0.64

    3.9

    5.8

    1.62

    14

    3bm7:A

    75

    106

    CRYSTAL STRUCTURE OF PROTEIN OF UNKNOWN FUNCTION WITH FERREDOXIN-LIKE FOLD (NP_420935.1) FROM CAULOBACTER CRESCENTUS AT 1.35 A RESOLUTION

    13

    0.64

    4.9

    6.5

    1.53

    15

    2omo:D

    100

    104

    PUTATIVE ANTIBIOTIC BIOSYNTHESIS MONOOXYGENASE FROM NITROSOMONAS EUROPAEA

    14

    0.63

    4.3

    6.1

    1.87

    10

    2gff:A

    100

    97

    CRYSTAL STRUCTURE OF YERSINIA PESTIS LSRG

    15

    0.63

    4.9

    6.5

    1.52

    15

    2omo:A

    100

    105

    PUTATIVE ANTIBIOTIC BIOSYNTHESIS MONOOXYGENASE FROM NITROSOMONAS EUROPAEA

    16

    0.63

    4.1

    5.9

    1.81

    20

    1x7v:C

    100

    99

    CRYSTAL STRUCTURE OF PA3566 FROM PSEUDOMONAS AERUGINOSA

    17

    0.63

    4.7

    6.3

    1.72

    14

    2omo:C

    100

    104

    PUTATIVE ANTIBIOTIC BIOSYNTHESIS MONOOXYGENASE FROM NITROSOMONAS EUROPAEA

    18

    0.63

    4.9

    6.5

    1.53

    15

    2omo:A

    100

    105

    PUTATIVE ANTIBIOTIC BIOSYNTHESIS MONOOXYGENASE FROM NITROSOMONAS EUROPAEA

    19

    0.63

    4.7

    6.4

    1.79

    11

    3e8o:A

    88

    102

    CRYSTAL STRUCTURE OF PROTEIN OF UNKNOWN FUNCTION WITH FERREDOXIN-LIKE FOLD (NP_295823.1) FROM DEINOCOCCUS RADIODURANS AT 1.40 A RESOLUTION

    20

    0.63

    4.1

    5.9

    1.82

    20

    1x7v:C

    100

    99

    CRYSTAL STRUCTURE OF PA3566 FROM PSEUDOMONAS AERUGINOSA

     

    A superposition of some of these proteins are shown below with 3fgv (green), 1x7v (cyan), 1y0h (magenta), 2fb0 (yellow), 2gff (pink), 2omo (grey), 2pd1 (blue), 3bm7 (orange), 3e8o (lime).

    all.png

    3fgv crystallizes as a dimer (shown below) forming a tight interface.

    dimer (1).png

    Each 3fgv monomer consists of a sheet flanked by helices. The two sheets come together to form the dimer. In the core of each 3fgv monomer is the putative active site.

     

     

    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
     

    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page

    Files (2)

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     all.png
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    150.27 kB16:55, 21 Oct 2008abhinavkActions
     dimer (1).png
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    60.34 kB18:38, 28 Oct 2008abhinavkActions
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