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The Open Protein Structure Annotation Network
PDB Keyword
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4mud

    Title Crystal structure of a ring oxydation complex/ phenylacetic acid degradation-like protein (SSO1313) from Sulfolobus solfataricus P2 at 2.43 A resolution. To be published
    Site JCSG
    PDB Id 4mud Target Id 377813
    Molecular Characteristics
    Source Sulfolobus solfataricus p2
    Alias Ids TPS7005,NP_342759.1, 1.20.1260.10, 335796 Molecular Weight 27278.94 Da.
    Residues 234 Isoelectric Point 5.58
    Sequence mqklrsvkevpqdltntlvniielradfelamveqyspwlvnaptvdsrlfvaklvsdelnhgwqlvrl leefkvkdvierisnarlgihklevsnlplfnwedviaftflvdgaglyqlkilkdcsfeplstlassm ikeeeshiffsqnelrnyqnknrmqgainfwfpravemlhmtwslnethlrdlnisdltkndlingyik ttneelkkcgynevnydkalhynvvlk
      BLAST   FFAS

    Structure Determination
    Method XRAY Chains 4
    Resolution (Å) 2.43 Rfree 0.2034
    Matthews' coefficent 2.19 Rfactor 0.1809
    Waters 172 Solvent Content 43.73

    Ligand Information
    Ligands
    Metals

    Jmol

     

    Protein Summary

     

    FM11532A/137616 (SULFOLOBUS SOLFATARICUS)

     

    Ffass scrore of 75.8 for a  Phenylacetic acid degradation protein paaC

    gives a high probability for that type of enzyme.  Journal: (2011) J.Biol.Chem. 286: 10735-10743 describes its function, which according to the abstract:

    The utilization of phenylacetic acid (PA) in Escherichia coli occurs through a hybrid pathway that shows features of both aerobic and anaerobic metabolism. Oxygenation of the aromatic ring is performed by a multisubunit phenylacetyl-coenzyme A oxygenase complex that shares remote homology of two subunits to well studied bacterial multicomponent monooxygenases and was postulated to form a new bacterial multicomponent monooxygenase subfamily. We expressed the subunits PaaA, B, C, D, and E of the PA-CoA oxygenase and showed that PaaABC, PaaAC, and PaaBC form stable subcomplexes that can be purified. In vitro reconstitution of the oxygenase subunits showed that each of the PaaA, B, C, and E subunits are necessary for catalysis, whereas PaaD is not essential. We have determined the crystal structure of the PaaAC complex in a ligand-free form and with several CoA derivatives. We conclude that PaaAC forms a catalytic core with a monooxygenase fold with PaaA being the catalytic α subunit and PaaC, the structural β subunit. PaaAC forms heterotetramers that are organized very differently from other known multisubunit monooxygenases and lacks their conservative network of hydrogen bonds between the di-iron center and protein surface, suggesting different association with the reductase and different mechanisms of electron transport. The PaaA structure shows adaptation of the common access route to the active site for binding a CoA-bound substrate. The enzyme-substrate complex shows the orientation of the aromatic ring, which is poised for oxygenation at the ortho-position, in accordance with the expected chemistry. The PA-CoA oxygenase complex serves as a paradigm for the new subfamily multicomponent monooxygenases comprising several hundred homologs.

    It's a pur helical structure with conserved residues of the active pocket

    as compared with 3PVR Phenylacetyl-CoA monooxygenase. Profunc results:

     

    Sequence motifs with InterPro

    4 motifs matched in scan against PROSITE, PRINTS, PFam-A, TIGRFAM, PROFILES and PRODOM motifs

     

    Type

    Motif

    Name

    1.

    Gene3D

    G3DSA:1.20.1260.10

    no description

    2.

    HMMPfam

    PF05138

    PaaA_PaaC

    3.

    HMMPanther

    PTHR30458

    PHENYLACETIC ACID DEGRADATION PROTEIN PAA

    4.

    superfamily

    SSF47240

    Ferritin-like

     

    Sequence search vs existing PDB entries. Chains A, B, C, D

    25 matching sequences found by FASTA search

     

    PDB code

    E-value

    %-tage id

    Overlap

    Name

    1.

    3pvr(A)

    4.4e-08

    24.771

    218

    The phenylacetyl-coa monooxygenase paaac subcomplex with ben

    2.

    3pvt(A)

    4.4e-08

    24.771

    218

    The phenylacetyl-coa monooxygenase paaac subcomplex with 3- hydroxybutanoyl-coa

    3.

    3pvy(A)

    4.4e-08

    24.771

    218

    The phenylacetyl-coa monooxygenase paaac subcomplex with coe

    4.

    3pw1(A)

    4.4e-08

    24.771

    218

    The phenylacetyl-coa monooxygenase paaac subcomplex with phe coa

    5.

    3pw8(C)

    4.3e-08

    24.771

    218

    The phenylacetyl-coa monooxygenase paaac subcomplex with ace

     

    BLAST search vs Uniprot. Chains A, B, C, D

    50 matching sequences found by BLAST search

     

    Ref. no.

    E-value

    %-tage id

    Overlap

    Name

    1.

    Q97YL0_SULSO

     

    100.000

    222

    Q97YL0 Ring oxydation complex/ phenylacetic acid degradation

    2.

    F0NJU0_SULIH

     

    71.622

    222

    F0NJU0 Phenylacetic acid catabolic family protein OS=Sulfolobus

    3.

    Q97WU5_SULSO

     

    71.622

    222

    Q97WU5 Ring oxydation complex/ phenylacetic acid degradation

    4.

    Q4J805_SULAC

     

    43.396

    212

    Q4J805 Phenylacetic acid catabolic protein OS=Sulfolobus

    5.

    Q4J804_SULAC

     

    35.841

    226

    Q4J804 Phenylacetic acid catabolic protein OS=Sulfolobus

     

     

    Matching folds. Chains A, B, C, D

    5324 significant structural matches

     

    Q-score

    Rmsd

    No. SSE

    Z-score

    PDB

    Name

    1.

    0.486

    1.90Å

    8

    7.6

    1otk

    Structural genomics, protein paac

    2.

    0.477

    1.87Å

    8

    7.7

    3pwq

    The phenylacetyl-coa monooxygenase paaac subcomplex

    3.

    0.472

    1.66Å

    7

    8.9

    3pvt

    The phenylacetyl-coa monooxygenase paaac subcomplex with 3- hydroxybutanoyl-coa

    4.

    0.469

    1.68Å

    8

    9.0

    3pw1

    The phenylacetyl-coa monooxygenase paaac subcomplex with phe coa

    5.

    0.469

    1.68Å

    7

    8.8

    3pvr

    The phenylacetyl-coa monooxygenase paaac subcomplex with ben

     

     

     

    Enzyme active site templates.

    1 significant hit out of 584 enzyme active site templates.

     

    Score

    Template

    PDB

    Name

    1.

    180.555

    PSA00001

    8tln

    Structural comparison suggests that thermolysin and related neutral proteases undergo hinge-bending motion during catalysis
    Metalloproteinase M4

     

     

    File:C:/Users/Herb/AppData/Local/Temp/msoclip1/01/clip_image001.gif

    Ligand-binding templates.

    20 significant hits out of 94055 ligand-binding templates.

     

    Score

    Template

    PDB

    Name

    1.

    399.438

    _MNb0013

    1bcf

    The structure of a unique, two-fold symmetric, haem-binding
    Het Group MN

    2.

    398.305

    _MNb0014

    1bfr

    Iron storage and electron transport
    Het Group MN

    3.

    383.422

    _MNb0423

    2ind

    Mn(ii) reconstituted toluene/o-xylene monooxygenase hydroxylase x-ray crystal structure
    Het Group MN

    4.

    332.781

    _FEb0187

    2itb

    Crystal structure of a putative tRNA-(ms(2)io(6)a)-hydroxyla (pp_2188) from pseudomonas putida kt2440 at 2.05 a resoluti
    Het Group FE

    5.

    313.844

    _ZNb1340

    2clu

    Recombinant human h ferritin, k86q and e107d mutant
    Het Group ZN

     

    Reverse template comparison vs structures in PDB.

    20 significant hits out of 444 auto-generated templates.

     

    Score

    Template

    PDB

    Name

    1.

    415.594

    TMP00353

    3pvt

    The phenylacetyl-coa monooxygenase paaac subcomplex with 3- hydroxybutanoyl-coa

    2.

    327.031

    TMP00444

    2itb

    Crystal structure of a putative tRNA-(ms(2)io(6)a)-hydroxyla (pp_2188) from pseudomonas putida kt2440 at 2.05 a resoluti

    3.

    306.656

    TMP00186

    1otk

    Structural genomics, protein paac

    4.

    322.875

    TMP00373

    2vzb

    A dodecameric thioferritin in the bacterial domain, characte of the bacterioferritin-related protein from bacteroides fr

    5.

    303.812

    TMP00168

    3r2k

    1.55a resolution structure of as-isolated ftna from pseudomo aeruginosa (ph 7.5)

    DALI results:

        No:  Chain   Z    rmsd lali nres  %id PDB  Description

       1:  3pw8-D 23.6  2.0  215   301   21 PDB  MOLECULE: PHENYLACETIC ACID DEGRADATION PROTEIN PAAC;    

      17:  3pf7-A 21.5  1.9  217   477   23 PDB  MOLECULE: BENZOYL-COA OXYGENASE COMPONENT B;          

      37:  3pm5-C 21.2  1.9  217   475   23 PDB  MOLECULE: BENZOYL-COA OXYGENASE COMPONENT B;                         

     221:  3dhg-D 15.6  2.7  213   492   17 PDB  MOLECULE: TOLUENE 4-MONOOXYGENASE HYDROXYLASE ALPHA SUBUNIT         

     366:  3q3m-F 14.2  2.3  172   305   16 PDB  MOLECULE: TOLUENE-4-MONOOXYGENASE SYSTEM PROTEIN A;                  

     846:  2vxx-C 11.6  3.0  147   173   12 PDB  MOLECULE: STARVATION INDUCED DNA BINDING PROTEIN;                  

     848:  3uof-C 11.6  2.8  133   159   13 PDB  MOLECULE: BACTERIOFERRITIN;                 

     No 1: Query=mol1A Sbjct=3pw8D Z-score=23.6

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    DSSP  ------------LLLLlLLLL-LLHHHHHHHHHHHHHHHHHHHHHHHHHLLHHHHLLLHH

    Query ------------XQKLrSVKE-VPQDLTNTLVNIIELRADFELAXVEQYSPWLVNAPTVD   47

    ident                        |     ||   |   |  |         |   ||| 

    Sbjct tqeerfeqriaqETAI-EPQDwMPDAYRKTLIRQIGQHAHSEIVGMLPEGNWITRAPTLR   59

    DSSP  lhhhhhhhhhhhLLLL-LLLLlLLHHHHHHHHHHHHHHHHHHHHLHHHHHLLLLLLLLHH

     

     

    DSSP  HHHHHHHHHHHHHHHHHHHHHHHHLLLLH--HHHHHHHHLllllLLLLHHHLLLLLHHHH

    Query SRLFVAKLVSDELNHGWQLVRLLEEFKVK--DVIERISNArlgiHKLEVSNLPLFNWEDV  105

     

    FIG1.bmp

     

     

    FIG2.bmp

    Ligand Summary

    Reviews

    References

     

    No references found.

    Tag page
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    Files (2)

    FileSizeDateAttached by 
     FIG1.bmp
    No description
    458.91 kB21:36, 16 Aug 2013haxelrodActions
     FIG2.bmp
    No description
    310.55 kB21:36, 16 Aug 2013haxelrodActions
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