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(-) Description

Title :  CRYSTAL STRUCTURE OF DESULFURIZATION ENZYME DSZB
 
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 :  1.80
Chains :  Asym./Biol. Unit :  A
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
    EC Number: 3.13.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: DSZB
    Organism Scientific: RHODOCOCCUS SP.
    Organism Taxid: 54064
    Strain: IGTS8
    Synonym: 2'-HYDROXYBIPHENYL-2-SULFINATE DESULFINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2GOL7Ligand/IonGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:166 , ASP A:246 , ARG A:248 , ASN A:249BINDING SITE FOR RESIDUE ACT A 421
2AC2SOFTWAREPRO A:28 , GLY A:73 , TRP A:155 , GLY A:183 , TRP A:228 , HOH A:511 , HOH A:525 , HOH A:549BINDING SITE FOR RESIDUE GOL A 501
3AC3SOFTWAREASP A:143 , PRO A:144 , TRP A:145 , HOH A:570 , HOH A:627BINDING SITE FOR RESIDUE GOL A 502
4AC4SOFTWAREGLY A:57 , PRO A:96 , LEU A:97 , LEU A:98 , PHE A:309 , ARG A:316 , HOH A:547 , HOH A:548BINDING SITE FOR RESIDUE GOL A 503
5AC5SOFTWAREGLU A:81 , GLY A:82 , PRO A:86 , PRO A:345 , ASN A:358 , ASN A:362 , HOH A:657 , HOH A:708 , HOH A:763BINDING SITE FOR RESIDUE GOL A 504
6AC6SOFTWARESER A:39 , GLY A:40 , PHE A:41 , ALA A:215 , SER A:216 , TRP A:282 , HOH A:630 , HOH A:649 , HOH A:660 , HOH A:694BINDING SITE FOR RESIDUE GOL A 505
7AC7SOFTWAREASP A:116 , ALA A:118 , ARG A:120 , ASN A:297 , HOH A:599 , HOH A:833BINDING SITE FOR RESIDUE GOL A 506
8AC8SOFTWARETYR A:24 , ASN A:26 , LEU A:34 , SER A:37 , GLU A:38 , VAL A:51 , GLU A:193 , HOH A:832BINDING SITE FOR RESIDUE GOL A 507

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DE2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DE2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DE2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DE2)

(-) Exons   (0, 0)

(no "Exon" information available for 2DE2)

(-) Sequences/Alignments

Asymmetric/Biological 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:347
 aligned with SOXB_RHOSG | P54997 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:347
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       
           SOXB_RHOSG    19 RDTLTYSNCPVPNALLTASESGFLDAAGIELDVLSGQQGTVHFTYDQPAYTRFGGEIPPLLSEGLRAPGRTRLLGITPLLGRQGFFVRDDSPITAAADLAGRRIGVSASAIRILRGQLGDYLELDPWRQTLVALGSWEARALLHTLEHGELGVDDVELVPISSPGVDVPAEQLEESATVKGADLFPDVARGQAAVLASGDVDALYSWLPWAGELQATGARPVVDLGLDERNAYASVWTVSSGLVRQRPGLVQRLVDAAVDAGLWARDHSDAVTSLHAANLGVSTGAVGQGFGADFQQRLVPRLDHDALALLERTQQFLLTNNLLQEPVALDQWAAPEFLNNSLNRHR 365
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....hhhhhhhhhhhhhhh.eeeee.........hhhhh..eeeee.hhhhhhhhhh.....eeeeeeeee...eeeee.......hhhhhh..eeeehhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh...hhhhheeee........hhhhh......hhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhhhhh..ee..hhhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh.hhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhh.hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2de2 A  19 RDTLTYSNCPVPNALLTASESGFLDAAGIELDVLSGQQGTVHFTYDQPAYTRFGGEIPPLLSEGLRAPGRTRLLGITPLLGRQGFFVRDDSPITAAADLAGRRIGVSASAIRILRGQLGDYLELDPWRQTLVALGSWEARALLHTLEHGELGVDDVELVPISSPGVDVPAEQLEESATVKGADLFPDVARGQAAVLASGDVDALYSWLPWAGELQATGARPVVDLGLDERNAYASVWTVSSGLVRQRPGLVQRLVDAAVDAGLWARDHSDAVTSLHAANLGVSTGAVGQGFGADFQQRLVPRLDHDALALLERTQQFLLTNNLLQEPVALDQWAAPEFLNNSLNRHR 365
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358
   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 2DE2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DE2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DE2)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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: 2de3 2de4

(-) Related Entries Specified in the PDB File

2de3 2de4