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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ANAEROBIC DESB-GALLATE COMPLEX
 
Authors :  K. Sugimoto, M. Senda, D. Kasai, M. Fukuda, E. Masai, T. Senda
Date :  13 Feb 14  (Deposition) - 30 Apr 14  (Release) - 30 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Type Ii Extradiol Dioxygenase, Domain-Swap Dimer, Extradiol Dioxygenase, Fe2+ Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Sugimoto, M. Senda, D. Kasai, M. Fukuda, E. Masai, T. Senda
Molecular Mechanism Of Strict Substrate Specificity Of An Extradiol Dioxygenase, Desb, Derived From Sphingobium Sp. Syk-6
Plos One V. 9 92249 2014
PubMed-ID: 24657997  |  Reference-DOI: 10.1371/JOURNAL.PONE.0092249

(-) Compounds

Molecule 1 - GALLATE DIOXYGENASE
    Chains: A, B
    EC Number: 1.13.11.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Gene: DESB
    Organism Scientific: SPHINGOBIUM
    Organism Taxid: 627192
    Strain: SYK-6

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1FE2Ligand/IonFE (III) ION
2GDE1Ligand/Ion3,4,5-TRIHYDROXYBENZOIC ACID

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:12 , ASN A:57 , HIS A:59 , GLU A:239BINDING SITE FOR RESIDUE FE A 501
2AC2SOFTWAREHIS B:12 , ASN B:57 , HIS B:59 , GLU B:239BINDING SITE FOR RESIDUE FE B 501
3AC3SOFTWAREGLU A:377 , TYR A:391 , TYR A:412 , THR B:13 , PRO B:14 , HIS B:59 , HIS B:124 , HIS B:192 , MET B:266 , THR B:267BINDING SITE FOR RESIDUE GDE B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WR4)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1His A:154 -Pro A:155
2Gly A:189 -Leu A:190
3His B:154 -Pro B:155
4Gly B:189 -Leu B:190

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WR4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WR4)

(-) Exons   (0, 0)

(no "Exon" information available for 3WR4)

(-) 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:407
 aligned with G2IKE5_9SPHN | G2IKE5 from UniProtKB/TrEMBL  Length:418

    Alignment length:412
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411  
         G2IKE5_9SPHN     2 AKIIGGFAVSHTPTIAFAHDANKYDDPVWAPIFQGFEPVKQWLAEQKPDVTFYVYNDHMTSFFEHYSHFALGVGEEYSPADEGGGQRDLPPIKGDPELAKHIAECLVADEFDLAYWQGMGLDHGAFSPLSVLLPHEHGWPCRIVPLQCGVLQHPIPKARRFWNFGRSLRRAIQSYPRDIKVAIAGTGGLSHQVHGERAGFNNTEWDMEFMERLANDPESLLGATVTDLAKKGGWEGAEVVMWLLMRGALSPEVKTLHQSYFLPSMTAIATMLFEDQGDAAPPAESDEALRARAKRELAGVEEIEGTYPFTIDRAVKGFRINHFLHRLIEPDFRKRFVEDPEGLFAESDLTEEEKSLIRNRDWIGMIHYGVIFFMLEKMAAVLGIGNIDVYAAFRGLSVPEFQKTRNAAITYS 413
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..hhhhh....-----...hhhhhh.hhhhhhhhhhh...eeeeeee........eee.eeee...ee..............ee.hhhhhhhhhhhhhhh....eee.....hhhhhhhhh...........eeeeeee........hhhhhhhhhhhhhhhhhh.....eeeeeee...............hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.....................eee............hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh..hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wr4 A   2 AKIIGGFAVSHTPTIAFAHD-----DPVWAPIFQGFEPVKQWLAEQKPDVTFYVYNDHMTSFFEHYSHFALGVGEEYSPADEGGGQRDLPPIKGDPELAKHIAECLVADEFDLAYWQGMGLDHGAFSPLSVLLPHEHGWPCRIVPLQCGVLQHPIPKARRFWNFGRSLRRAIQSYPRDIKVAIAGTGGLSHQVHGERAGFNNTEWDMEFMERLANDPESLLGATVTDLAKKGGWEGAEVVMWLLMRGALSPEVKTLHQSYFLPSMTAIATMLFEDQGDAAPPAESDEALRARAKRELAGVEEIEGTYPFTIDRAVKGFRINHFLHRLIEPDFRKRFVEDPEGLFAESDLTEEEKSLIRNRDWIGMIHYGVIFFMLEKMAAVLGIGNIDVYAAFRGLSVPEFQKTRNAAITYS 413
                                    11        21     |  31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411  
                                              21    27                                                                                                                                                                                                                                                                                                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:405
 aligned with G2IKE5_9SPHN | G2IKE5 from UniProtKB/TrEMBL  Length:418

    Alignment length:405
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401     
         G2IKE5_9SPHN     2 AKIIGGFAVSHTPTIAFAHDANKYDDPVWAPIFQGFEPVKQWLAEQKPDVTFYVYNDHMTSFFEHYSHFALGVGEEYSPADEGGGQRDLPPIKGDPELAKHIAECLVADEFDLAYWQGMGLDHGAFSPLSVLLPHEHGWPCRIVPLQCGVLQHPIPKARRFWNFGRSLRRAIQSYPRDIKVAIAGTGGLSHQVHGERAGFNNTEWDMEFMERLANDPESLLGATVTDLAKKGGWEGAEVVMWLLMRGALSPEVKTLHQSYFLPSMTAIATMLFEDQGDAAPPAESDEALRARAKRELAGVEEIEGTYPFTIDRAVKGFRINHFLHRLIEPDFRKRFVEDPEGLFAESDLTEEEKSLIRNRDWIGMIHYGVIFFMLEKMAAVLGIGNIDVYAAFRGLSVPEFQKTR 406
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh..eeeeee.........eee.eeee...ee..............ee.hhhhhhhhhhhhhhh....eee.....hhhhhhhhhhhh........eeeeeee........hhhhhhhhhhhhhhhhhhh....eeeeeee...............hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeeee......eeeeeeee.........hhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhh..hhhhhhhhhhh.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wr4 B   2 AKIIGGFAVSHTPTIAFAHDANKYDDPVWAPIFQGFEPVKQWLAEQKPDVTFYVYNDHMTSFFEHYSHFALGVGEEYSPADEGGGQRDLPPIKGDPELAKHIAECLVADEFDLAYWQGMGLDHGAFSPLSVLLPHEHGWPCRIVPLQCGVLQHPIPKARRFWNFGRSLRRAIQSYPRDIKVAIAGTGGLSHQVHGERAGFNNTEWDMEFMERLANDPESLLGATVTDLAKKGGWEGAEVVMWLLMRGALSPEVKTLHQSYFLPSMTAIATMLFEDQGDAAPPAESDEALRARAKRELAGVEEIEGTYPFTIDRAVKGFRINHFLHRLIEPDFRKRFVEDPEGLFAESDLTEEEKSLIRNRDWIGMIHYGVIFFMLEKMAAVLGIGNIDVYAAFRGLSVPEFQKTR 406
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401
   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 3WR4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WR4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WR4)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (G2IKE5_9SPHN | G2IKE5)
molecular function
    GO:0051213    dioxygenase activity    Catalysis of an oxidation-reduction (redox) reaction in which both atoms of oxygen from one molecule of O2 are incorporated into the (reduced) product(s) of the reaction. The two atoms of oxygen may be distributed between two different products.
    GO:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0006725    cellular aromatic compound metabolic process    The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
    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/TrEMBL
        G2IKE5_9SPHN | G2IKE5: 3wku 3wpm 3wr3 3wr8 3wr9 3wra 3wrb 3wrc

(-) Related Entries Specified in the PDB File

3vju 3vjv 3vjw 3vjx 3vjy 3wku 3wr3