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The Open Protein Structure Annotation Network
PDB Keyword
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3f9s

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

    Title Crystal structure of putative polyketide cyclase (AFE_2539) from ACIDITHIOBACILLUS FERROOXIDANS NCIB8455 at 1.76 A resolution. To be published
    Site JCSG
    PDB Id 3f9s Target Id 391571
    Molecular Characteristics
    Source Acidithiobacillus ferrooxidans atcc 23270
    Alias Ids TPS14633,AFE_2539, 3.10.450.50, 88968 Molecular Weight 16275.49 Da.
    Residues 145 Isoelectric Point 5.58
    Sequence msisskakeiltqftrevwsegnieasdkyiapkytvlhdpgdpwegreldvagykervktlraafpdq cfdiqglfadgdavvmtwlwtathkedipgfpstgkqikmsgatvyyfdgnrltghwqitdrlgvyqql rqaaaga
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 2
    Resolution (Å) 1.76 Rfree 0.208
    Matthews' coefficent 2.10 Rfactor 0.170
    Waters 290 Solvent Content 41.30

    Ligand Information
    Ligands
    Metals

    Jmol

     
    Google Scholar output for 3f9s
    1. Fold space unlimited
    MJ Sippl - Current opinion in structural biology, 2009 - Elsevier
     

    Protein Summary

    The Lferr_0659 gene from Acidithiobacillus ferrooxidans atcc 23270 encodes the protein YP_002219118 annotated as NTF-2 like protein. It belongs to PFAM PF07366 which is a family of SnoaL-Like Polyketide Cyclases. A search of structural homologs of 3f9s confirms this assignment (see table below). Dali top hits are with SnoaL -like polyketide cyclase 3ehc (Z-scr=16), and ester cyclases 1sjw and 2f99 (Z-scr=16).

    SSM Structural Homologs

    N

    Scoring 

     

    Rmsd 

     

    Nalgn

     

    %seq

     

    Query

     

    Target (PDB entry)

     

     Q 

     

     P 

     

     Z 

     

    Ch

     

    Nres

     

    %sse

     

    Match

     

    %sse

     

    Nres

     

    Title

     

    1

    0.55

     

    5.8

     

    7.1

     

    1.65

     

    113

     

    15

     

    A

     

    143

     

    89

     

    3ehc

     

    89

     

    125

     

    Crystal Structure Of Snoal-Like Polyketide Cyclase (17741376) From Agrobacterium Tumefaciens Str. C58 (Dupont) At 2.12 A Resolution

     

    2

    0.54

     

    4.7

     

    6.4

     

    1.85

     

    119

     

    18

     

    A

     

    143

     

    100

     

    2gey

     

    90

     

    133

     

    Crystal Structure Of Aclr A Putative Hydroxylase From Streptomyces Galilaeus

     

    3

    0.53

     

    6.2

     

    7.3

     

    1.82

     

    120

     

    18

     

    B

     

    140

     

    89

     

    1sjw

     

    89

     

    142

     

    Structure Of Polyketide Cyclase Snoal

     

    4

    0.53

     

    5.9

     

    7.1

     

    1.90

     

    121

     

    16

     

    B

     

    140

     

    89

     

    2f99

     

    89

     

    140

     

    Crystal Structure Of The Polyketide Cyclase Aknh With Bound Substrate And Product Analogue: Implications For Catalytic Mechanism And Product Stereoselectivity.

     

     

    A superposition of these structures on 3f9s (green) is shown below with 1sjw (cyan), 2f99 (magenta), 2gey (yellow), 3ehc (pink).

    all.png

    Other holmologs solved by JCSG include 3cu3, 3cnx, 2rfr, 3b8l, 2rgq, 3d9r, 2r4i, 3b7c, 3dxo, 3e99, 3en8, 3er7, 3ecf, 3ec9, 3ebt, 3ejv, 3dmc, 3ef8, 2rcd, 2owp.

    The protein crystallizes as a dimer in the structure and most likely represents its solution oligomeric state.

    MG5552I_dimer.png

    Each monomer is barrel shaped and consists of a sheet and helices.

     

    A glycerol molecule has been modeled in the putative active site of each monomer (see below).  The nature of density suggests that a substrate could be bound here. However, glycerol is the best possible assignment so far in the absence of the identity of the substrate. A comparison to some homologous structures from JCSG (399744 and 391191) supports the assignment of this region as the putative active site.

    MG5552I_gol.png

     

     

    References:

    • 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

    Ligand Summary

    Reviews

    References

     

    No references found.

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