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(-) Description

Title :  CRYSTAL STRUCTURE OF DSZB C27S MUTANT IN COMPLEX WITH 2'-HYDROXYBIPHENYL-2-SULFINIC ACID
 
Authors :  W. C. Lee, T. Ohshiro, T. Matsubara, Y. Izumi, M. Tanokura
Date :  08 Feb 06  (Deposition) - 01 Aug 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Alpha-Beta, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. C. Lee, T. Ohshiro, T. Matsubara, Y. Izumi, M. Tanokura
Crystal Structure And Desulfurization Mechanism Of 2'-Hydroxybiphenyl-2-Sulfinic Acid Desulfinase.
J. Biol. Chem. V. 281 32534 2006
PubMed-ID: 16891315  |  Reference-DOI: 10.1074/JBC.M602974200

(-) Compounds

Molecule 1 - DIBENZOTHIOPHENE DESULFURIZATION ENZYME B
    Chains: A, B
    EC Number: 3.13.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DSZB
    Mutation: YES
    Organism Scientific: RHODOCOCCUS SP.
    Organism Taxid: 54064
    Strain: IGTS8

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2MG1Ligand/IonMAGNESIUM ION
3OBP2Ligand/Ion2'-HYDROXY-1,1'-BIPHENYL-2-SULFINIC ACID
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MG-1Ligand/IonMAGNESIUM ION
3OBP1Ligand/Ion2'-HYDROXY-1,1'-BIPHENYL-2-SULFINIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2MG-1Ligand/IonMAGNESIUM ION
3OBP1Ligand/Ion2'-HYDROXY-1,1'-BIPHENYL-2-SULFINIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:162 , HIS A:166 , ASP A:246 , ARG A:248 , ASN A:249BINDING SITE FOR RESIDUE ACT A 1368
2AC2SOFTWAREHIS B:162 , HIS B:166 , ASP B:246 , ARG B:248 , ASN B:249BINDING SITE FOR RESIDUE ACT B 1369
3AC3SOFTWAREHOH B:2528 , HOH B:2529 , HOH B:2530 , HOH B:2553BINDING SITE FOR RESIDUE MG B 1001
4AC4SOFTWARESER A:27 , PRO A:28 , HIS A:60 , PHE A:61 , ARG A:70 , GLY A:73 , PRO A:76 , TRP A:155 , GLY A:183 , HOH A:392 , HOH A:593BINDING SITE FOR RESIDUE OBP A 1366
5AC5SOFTWARESER B:27 , PRO B:28 , HIS B:60 , PHE B:61 , ARG B:70 , GLY B:73 , PRO B:76 , TRP B:155 , GLY B:183 , HOH B:2372 , HOH B:2469BINDING SITE FOR RESIDUE OBP B 2366

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DE3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DE3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DE3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DE3)

(-) Exons   (0, 0)

(no "Exon" information available for 2DE3)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:344
 aligned with SOXB_RHOSG | P54997 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:344
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359    
           SOXB_RHOSG    20 DTLTYSNCPVPNALLTASESGFLDAAGIELDVLSGQQGTVHFTYDQPAYTRFGGEIPPLLSEGLRAPGRTRLLGITPLLGRQGFFVRDDSPITAAADLAGRRIGVSASAIRILRGQLGDYLELDPWRQTLVALGSWEARALLHTLEHGELGVDDVELVPISSPGVDVPAEQLEESATVKGADLFPDVARGQAAVLASGDVDALYSWLPWAGELQATGARPVVDLGLDERNAYASVWTVSSGLVRQRPGLVQRLVDAAVDAGLWARDHSDAVTSLHAANLGVSTGAVGQGFGADFQQRLVPRLDHDALALLERTQQFLLTNNLLQEPVALDQWAAPEFLNNSLNR 363
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhh..eeee.hhhhhhhhhhh....eeeee.hhhhhhhhhh.....eeeeeeeee...eeeeee......hhhhhh..eeeehhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhheeee........hhhhhhhh...hhhhhh.hhhhhhhhhhhh....eeeeehhhhhhhhhh.eee..hhhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2de3 A  20 DTLTYSNSPVPNALLTASESGFLDAAGIELDVLSGQQGTVHFTYDQPAYTRFGGEIPPLLSEGLRAPGRTRLLGITPLLGRQGFFVRDDSPITAAADLAGRRIGVSASAIRILRGQLGDYLELDPWRQTLVALGSWEARALLHTLEHGELGVDDVELVPISSPGVDVPAEQLEESATVKGADLFPDVARGQAAVLASGDVDALYSWLPWAGELQATGARPVVDLGLDERNAYASVWTVSSGLVRQRPGLVQRLVDAAVDAGLWARDHSDAVTSLHAANLGVSTGAVGQGFGADFQQRLVPRLDHDALALLERTQQFLLTNNLLQEPVALDQWAAPEFLNNSLNR 363
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359    


Chain B from PDB  Type:PROTEIN  Length:347
 aligned with SOXB_RHOSG | P54997 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:347
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       
           SOXB_RHOSG    18 IRDTLTYSNCPVPNALLTASESGFLDAAGIELDVLSGQQGTVHFTYDQPAYTRFGGEIPPLLSEGLRAPGRTRLLGITPLLGRQGFFVRDDSPITAAADLAGRRIGVSASAIRILRGQLGDYLELDPWRQTLVALGSWEARALLHTLEHGELGVDDVELVPISSPGVDVPAEQLEESATVKGADLFPDVARGQAAVLASGDVDALYSWLPWAGELQATGARPVVDLGLDERNAYASVWTVSSGLVRQRPGLVQRLVDAAVDAGLWARDHSDAVTSLHAANLGVSTGAVGQGFGADFQQRLVPRLDHDALALLERTQQFLLTNNLLQEPVALDQWAAPEFLNNSLNRH 364
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhhhhhh.eeeee.hhhhhhhhhhh....eeeee.hhhhhhhhhh.....eeeeeeeee...eeeee.......hhhhhh..eeeehhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhheeee........hhhhhhhh...hhhhhh.hhhhhhhhhhhhh...eeeeehhhhhhhhh...ee..hhhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.hhhhhhhhhh.hhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2de3 B  18 IRDTLTYSNSPVPNALLTASESGFLDAAGIELDVLSGQQGTVHFTYDQPAYTRFGGEIPPLLSEGLRAPGRTRLLGITPLLGRQGFFVRDDSPITAAADLAGRRIGVSASAIRILRGQLGDYLELDPWRQTLVALGSWEARALLHTLEHGELGVDDVELVPISSPGVDVPAEQLEESATVKGADLFPDVARGQAAVLASGDVDALYSWLPWAGELQATGARPVVDLGLDERNAYASVWTVSSGLVRQRPGLVQRLVDAAVDAGLWARDHSDAVTSLHAANLGVSTGAVGQGFGADFQQRLVPRLDHDALALLERTQQFLLTNNLLQEPVALDQWAAPEFLNNSLNRH 364
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2DE3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DE3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DE3)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SOXB_RHOSG | P54997)
molecular function
    GO:0018740    2'-hydroxybiphenyl-2-sulfinate desulfinase activity    Catalysis of the reaction: 2'-hydroxybiphenyl-2-sulfinate + H(2)O = biphenyl-2-ol + sulfite.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004497    monooxygenase activity    Catalysis of the incorporation of one atom from molecular oxygen into a compound and the reduction of the other atom of oxygen to water.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0018896    dibenzothiophene catabolic process    The chemical reactions and pathways resulting in the breakdown of dibenzothiophene, a substance composed of two benzene rings linked by one sulfide bond and one carbon-carbon bond.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SOXB_RHOSG | P54997: 2de2 2de4

(-) Related Entries Specified in the PDB File

2de2 2de4