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(-) Description

Title :  ANAEROBIC SUBSTRATE COMPLEX OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM ARTHROBACTER GLOBIFORMIS. (COMPLEX WITH 3,4-DIHYDROXYPHENYLACETATE)
 
Authors :  M. W. Vetting, J. D. Lipscomb, L. P. Wackett, L. Que Jr. , D. H. Ohlendorf
Date :  20 May 00  (Deposition) - 10 Jun 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Dioxygenase, Extradiol, Manganese, Biodegradation, Aromatic, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. W. Vetting, L. P. Wackett, L. Que Jr. , J. D. Lipscomb, D. H. Ohlendor
Crystallographic Comparison Of Manganese- And Iron-Dependen Homoprotocatechuate 2, 3-Dioxygenases.
J. Bacteriol. V. 186 1945 2004
PubMed-ID: 15028678  |  Reference-DOI: 10.1128/JB.186.7.1945-1958.2004
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HOMOPROTOCATECHUATE 2,3-DIOXYGENASE
    Chains: A, B
    EC Number: 1.13.11.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ARTHROBACTER GLOBIFORMIS
    Organism Taxid: 1665
    Strain: CM-2
    Synonym: 3,4-DIHYDROXYPHENYLACETATE 2,3-DIOXYGENASE

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1DHY2Ligand/Ion2-(3,4-DIHYDROXYPHENYL)ACETIC ACID
2MN2Ligand/IonMANGANESE (II) ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1DHY4Ligand/Ion2-(3,4-DIHYDROXYPHENYL)ACETIC ACID
2MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:155 , HIS A:214 , GLU A:267 , HOH A:915 , DHY A:999BINDING SITE FOR RESIDUE MN A 500
2AC2SOFTWAREHIS B:155 , HIS B:214 , GLU B:267 , HOH B:916 , DHY B:999BINDING SITE FOR RESIDUE MN B 500
3AC3SOFTWAREHIS A:155 , TRP A:192 , HIS A:200 , HIS A:214 , ARG A:243 , HIS A:248 , VAL A:250 , SER A:251 , TYR A:257 , GLU A:267 , TYR A:269 , ARG A:293 , TRP A:304 , MN A:500 , HOH A:915BINDING SITE FOR RESIDUE DHY A 999
4AC4SOFTWAREHIS B:155 , TRP B:192 , HIS B:200 , HIS B:214 , ARG B:243 , HIS B:248 , VAL B:250 , SER B:251 , TYR B:257 , GLU B:267 , TYR B:269 , ARG B:293 , TRP B:304 , MN B:500 , HOH B:916BINDING SITE FOR RESIDUE DHY B 999

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F1V)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:209 -Pro A:210
2Gly A:244 -Pro A:245
3Gly B:209 -Pro B:210
4Gly B:244 -Pro B:245

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F1V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1F1V)

(-) Exons   (0, 0)

(no "Exon" information available for 1F1V)

(-) 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:320
 aligned with Q44048_ARTGO | Q44048 from UniProtKB/TrEMBL  Length:343

    Alignment length:320
                                                                                                                                                                                                                                                                          243                                                                               
                                                                                                                                                                                                                                                                        242 |                                                                               
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233        |-|      252       262       272       282       292       302       312       322
         Q44048_ARTGO     4 FVPTPSVPAPDIVRCAYMEIVVTDLAKSREFYVDVLGLHVTEEDENTIYLRSLEEFIHHNLVLRQGPIAAVAAFAYRVKSPAEVDAAEAYYKELGCRTERRKEGFTKGIGDSVRVEDPLGFPYEFFYETEHVERLTQRYDLYSAGELVRLDHFNQVTPDVPRGRAYLEDLGFRVSEDIKDSDGVTYAAWMHRKQTVHDTALTGGNGPRMHHVAFATHEKHNIIQICDKMRPCASATGSN-GPRPAPVSNAFYLYILDPDGHRIEIYTQDYYTGDPDNPTITWDVHDNQRRDWWGNPVVPSWYTEASLVLDLDGNPQPVIV 322
               SCOP domains d1f1va1 A:4-147 Homoprotocatechuate 2,3-dioxygenase                                                                                             d1f1va2 A:148-323 Homoprotocatechuate 2,3-dioxygenase                                                                                                                            SCOP domains
               CATH domains 1f1vA01 A:4-151 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                     1f1vA02 A:152-310 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                              ------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeeeee.hhhhhhhhhh.....eeeee...eeeee.........eeeee....eeeeeeeee.hhhhhhhhhhhhhhh...eeee..........eeeee.....eeeee......................eeeeeeeee.hhhhhhhhhhhh..eeeeeee.....eeeeeee.......eeeee....eeeeeeee..hhhhhhhhhhhhhhh.hhh.eeeeeee......eeeeee.....eeeeee............eeee..............hhhhhhh.ee............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f1v A   4 FVPTPSVPAPDIVRCAYMEIVVTDLAKSREFYVDVLGLHVTEEDENTIYLRSLEEFIHHNLVLRQGPIAAVAAFAYRVKSPAEVDAAEAYYKELGCRTERRKEGFTKGIGDSVRVEDPLGFPYEFFYETEHVERLTQRYDLYSAGELVRLDHFNQVTPDVPRGRAYLEDLGFRVSEDIKDSDGVTYAAWMHRKQTVHDTALTGGNGPRMHHVAFATHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDGHRIEIYTQDYYTGDPDNPTITWDVHDNQRRDWWGNPVVPSWYTEASLVLDLDGNPQPVIV 323
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323


Chain B from PDB  Type:PROTEIN  Length:320
 aligned with Q44048_ARTGO | Q44048 from UniProtKB/TrEMBL  Length:343

    Alignment length:320
                                                                                                                                                                                                                                                                          243                                                                               
                                                                                                                                                                                                                                                                        242 |                                                                               
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233        |-|      252       262       272       282       292       302       312       322
         Q44048_ARTGO     4 FVPTPSVPAPDIVRCAYMEIVVTDLAKSREFYVDVLGLHVTEEDENTIYLRSLEEFIHHNLVLRQGPIAAVAAFAYRVKSPAEVDAAEAYYKELGCRTERRKEGFTKGIGDSVRVEDPLGFPYEFFYETEHVERLTQRYDLYSAGELVRLDHFNQVTPDVPRGRAYLEDLGFRVSEDIKDSDGVTYAAWMHRKQTVHDTALTGGNGPRMHHVAFATHEKHNIIQICDKMRPCASATGSN-GPRPAPVSNAFYLYILDPDGHRIEIYTQDYYTGDPDNPTITWDVHDNQRRDWWGNPVVPSWYTEASLVLDLDGNPQPVIV 322
               SCOP domains d1f1vb1 B:4-147 Homoprotocatechuate 2,3-dioxygenase                                                                                             d1f1vb2 B:148-323 Homoprotocatechuate 2,3-dioxygenase                                                                                                                            SCOP domains
               CATH domains 1f1vB01 B:4-151 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                     1f1vB02 B:152-310 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                              ------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeeeee.hhhhhhhhhh.....eeeee...eeeee.........eeeee....eeeeeeeee.hhhhhhhhhhhhhhh...eeee..........eeeee.....eeeee......................eeeeeeeee.hhhhhhhhhhhh..eeeeeee.....eeeeeee.......eeeee....eeeeeeee..hhhhhhhhhhhhhhh.hhh.eeeeeee......eeeeee.....eeeeee............eeee..............hhhhhhh.ee............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f1v B   4 FVPTPSVPAPDIVRCAYMEIVVTDLAKSREFYVDVLGLHVTEEDENTIYLRSLEEFIHHNLVLRQGPIAAVAAFAYRVKSPAEVDAAEAYYKELGCRTERRKEGFTKGIGDSVRVEDPLGFPYEFFYETEHVERLTQRYDLYSAGELVRLDHFNQVTPDVPRGRAYLEDLGFRVSEDIKDSDGVTYAAWMHRKQTVHDTALTGGNGPRMHHVAFATHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDGHRIEIYTQDYYTGDPDNPTITWDVHDNQRRDWWGNPVVPSWYTEASLVLDLDGNPQPVIV 323
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323
   Legend:   → Mismatch (orange background)
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  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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F1V)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q44048_ARTGO | Q44048)
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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    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
        Q44048_ARTGO | Q44048: 1f1r 1f1u

(-) Related Entries Specified in the PDB File

1f1r NATIVE CRYSTAL, DATA COLLECTION AT ROOM TEMPERATURE.
1f1u NATIVE CRYSTAL, DATA COLLECTION AT CRYOGENIC TEMPERATURE
1f1x SAME PROTEIN FROM BREVIBACTERIUM FUSCUM, C-TERMINAL REMOVED WITH TRYPSIN
1f1y SAME PROTEIN FROM BREVIBACTERIUM FUSCUM, C-TERMINAL NOT REMOVED WITH TRYPSIN