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The Open Protein Structure Annotation Network
PDB Keyword
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3f8h

    Title Crystal structure of putative polyketide cyclase (YP_611791.1) from SILICIBACTER SP. TM1040 at 2.00 A resolution. To be published
    Site JCSG
    PDB Id 3f8h Target Id 391384
    Molecular Characteristics
    Source Silicibacter sp. tm1040
    Alias Ids TPS20227,YP_611791.1, 3.10.450.50, 336145 Molecular Weight 14573.45 Da.
    Residues 131 Isoelectric Point 4.79
    Sequence mndtiaryfdafnagdtdgmlaclsedvahhvnegnirvgkekfaafcahmshcykeeltdmvifatpd atraaaeytvngtylatdeglpearqqsyklpagsffdlrdglitrvttyynlsdwikqvsa
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 2.00 Rfree 0.213
    Matthews' coefficent 2.87 Rfactor 0.167
    Waters 272 Solvent Content 57.09

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

    Gene TM1040_3560 from Silicibacter sp. tm1040 encodes the YP_611791 protein from the SnoaL-like polyketide cyclase family (PF07366). Genome context analysis predicts (score 0.96) a functional link of this target with its genomic neighbor TM1040_3558 annotated as nitrilase/cyanide hydratase and apolipoprotein N-acetyltransferase.

    3f8h classifies in the alpha+beta class, NTF2-like superfamily, SnoaL-like polyketide cyclase family (?). DALI returns as top hits putative polyketide cyclases like PDB:3i0y (Z=21), PDB:3f7x (Z=21), PDB:3kkg (Z=16), PDB:3ebt (Z=15), PDB:2f98 (Z=15), PDB:3d9r (Z=15). 

    SSM Structure Alignment Results
    N  Scoring   Rmsd  Nalgn Ng %seq Query Target (PDB entry)
     Q   P   Z  %sse Match %sse Nres Title
    1 0.58 7.9 8.3 1.62 116 4 20 100 3ebt:A 91 131 CRYSTAL STRUCTURE OF NTF2-LIKE PROTEIN OF UNKNOWN FUNCTION (YP_110153.1) FROM BURKHOLDERIA PSEUDOMALLEI K96243 AT 1.30 A RESOLUTION
    2 0.56 5.3 6.9 1.73 120 5 18 80 2f98:D 89 140 CRYSTAL STRUCTURE OF THE POLYKETIDE CYCLASE AKNH WITH BOUND SUBSTRATE AND PRODUCT ANALOGUE: IMPLICATIONS FOR CATALYTIC MECHANISM AND PRODUCT STEREOSELECTIVITY.
    3 0.56 5.3 6.9 1.68 119 5 18 80 2f99:C 89 140 CRYSTAL STRUCTURE OF THE POLYKETIDE CYCLASE AKNH WITH BOUND SUBSTRATE AND PRODUCT ANALOGUE: IMPLICATIONS FOR CATALYTIC MECHANISM AND PRODUCT STEREOSELECTIVITY.
    4 0.55 4.0 5.9 2.05 118 7 18 70 3ehc:D 78 125 CRYSTAL STRUCTURE OF SNOAL-LIKE POLYKETIDE CYCLASE (17741376) FROM AGROBACTERIUM TUMEFACIENS STR. C58 (DUPONT) AT 2.12 A RESOLUTION
    5 0.55 4.0 5.9 1.95 117 8 18 70 3ehc:A 78 127 CRYSTAL STRUCTURE OF SNOAL-LIKE POLYKETIDE CYCLASE (17741376) FROM AGROBACTERIUM TUMEFACIENS STR. C58 (DUPONT) AT 2.12 A RESOLUTION
    6 0.55 4.0 5.8 1.96 117 8 18 70 3ehc:C 78 127 CRYSTAL STRUCTURE OF SNOAL-LIKE POLYKETIDE CYCLASE (17741376) FROM AGROBACTERIUM TUMEFACIENS STR. C58 (DUPONT) AT 2.12 A RESOLUTION
    7 0.55 5.9 7.1 1.59 112 5 16 80 3d9r:D 100 130 CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE-LIKE PROTEIN (YP_049581.1) FROM ERWINIA CAROTOVORA ATROSEPTICA SCRI1043 AT 2.40 A RESOLUTION
    8 0.55 5.4 6.9 1.75 120 6 18 80 2f98:C 89 143 CRYSTAL STRUCTURE OF THE POLYKETIDE CYCLASE AKNH WITH BOUND SUBSTRATE AND PRODUCT ANALOGUE: IMPLICATIONS FOR CATALYTIC MECHANISM AND PRODUCT STEREOSELECTIVITY.
    9 0.55 5.4 7.0 1.77 120 5 17 80 1sjw:A 89 142 STRUCTURE OF POLYKETIDE CYCLASE SNOAL
    10 0.55 3.8 5.8 2.16 123 6 16 100 2gey:B 100 133 CRYSTAL STRUCTURE OF ACLR A PUTATIVE HYDROXYLASE FROM STREPTOMYCES GALILAEUS
    11 0.54 5.3 6.9 1.72 118 4 18 80 2f99:B 89 141 CRYSTAL STRUCTURE OF THE POLYKETIDE CYCLASE AKNH WITH BOUND SUBSTRATE AND PRODUCT ANALOGUE: IMPLICATIONS FOR CATALYTIC MECHANISM AND PRODUCT STEREOSELECTIVITY.
    12 0.54 4.3 5.9 1.72 109 5 18 70 1k41:B 88 121 CRYSTAL STRUCTURE OF KSI Y57S MUTANT
    13 0.54 4.2 6.4 1.86 112 6 19 70 1c7h:A 100 123 CRYSTAL STRUCTURE OF A MUTANT R75A IN KETOSTEROID ISOMERASE FROM PSEDOMONAS PUTIDA BIOTYPE B
    14 0.53 5.5 7.0 1.72 117 5 18 80 2f98:A 89 141 CRYSTAL STRUCTURE OF THE POLYKETIDE CYCLASE AKNH WITH BOUND SUBSTRATE AND PRODUCT ANALOGUE: IMPLICATIONS FOR CATALYTIC MECHANISM AND PRODUCT STEREOSELECTIVITY.
    15 0.53 5.2 6.8 1.78 118 5 18 80 2f99:A 89 141 CRYSTAL STRUCTURE OF THE POLYKETIDE CYCLASE AKNH WITH BOUND SUBSTRATE AND PRODUCT ANALOGUE: IMPLICATIONS FOR CATALYTIC MECHANISM AND PRODUCT STEREOSELECTIVITY.
    16 0.53 5.8 7.1 1.59 111 5 16 80 3d9r:A 100 132 CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE-LIKE PROTEIN (YP_049581.1) FROM ERWINIA CAROTOVORA ATROSEPTICA SCRI1043 AT 2.40 A RESOLUTION
    17 0.53 5.4 6.9 1.74 117 5 18 80 2f98:B 89 141 CRYSTAL STRUCTURE OF THE POLYKETIDE CYCLASE AKNH WITH BOUND SUBSTRATE AND PRODUCT ANALOGUE: IMPLICATIONS FOR CATALYTIC MECHANISM AND PRODUCT STEREOSELECTIVITY.
    18 0.53 3.6 5.7 2.21 122 7 16 100 2gey:D 100 133 CRYSTAL STRUCTURE OF ACLR A PUTATIVE HYDROXYLASE FROM STREPTOMYCES GALILAEUS
    19 0.53 5.4 7.0 1.69 113 5 16 80 3d9r:C 100 134 CRYSTAL STRUCTURE OF KETOSTEROID ISOMERASE-LIKE PROTEIN (YP_049581.1) FROM ERWINIA CAROTOVORA ATROSEPTICA SCRI1043 AT 2.40 A RESOLUTION
    20 0.53 5.2 6.8 1.83 119 4 17 80 2f99:D 89 143 CRYSTAL STRUCTURE OF THE POLYKETIDE CYCLASE AKNH WITH BOUND SUBSTRATE AND PRODUCT ANALOGUE: IMPLICATIONS FOR CATALYTIC MECHANISM AND PRODUCT STEREOSELECTIVITY.

     

    The protein crystallizes as a dimer in the 3f8h structure which may represent its solution state, too. 3f8h structure is shown below which consists of a six stranded beta sheet flanked by helices.

    MG14561D_dimer.png

    One calcium ion (magenta sphere above) is observed in the crystal structure that interacts with both chains of the dimer, but coming from symmetry related molecule. Thus, it may not be of functional significance and may simply help facilitate crystal packing in the unit cell. Residues ASP 16 and ASP 18 along with three water molecules interact with the ion, as shown below.

    MG14561D_CA.png

     

     

    Structural superposition of 3f8h (green) with 2f98 (magenta), 3d9r (yellow), 3ebt (pink), and 3ehc (grey) is displayed below.

    all.png
     

     

    Ligand Summary

    References:

    1. Sultana A, Kallio P, Jansson A, Wang JS, Niemi J, Mantsala P, Schneider G; , EMBO J 2004;23:1911-1921.: Structure of the polyketide cyclase SnoaL reveals a novel mechanism for enzymatic aldol condensation.  PUBMED:15071504
       

    Reviews

    References

     

    No references found.

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