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(-) Description

Title :  CRYSTAL STRUCTURE OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM BREVIBACTERIUM FUSCUM
 
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) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Dioxygenase, Extradiol, Iron, 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. Ohlendorf
Crystallographic Comparison Of Manganese- And Iron-Dependent 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, C, D
    EC Number: 1.13.11.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: BREVIBACTERIUM FUSCUM
    Organism Taxid: 47914
    Synonym: 3,4-DIHYDROXYPHENYLACETATE 2,3-DIOXYGENASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1FEL4Ligand/IonHYDRATED FE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:155 , ASN A:157 , TRP A:192 , HIS A:200 , HIS A:214 , TYR A:257 , GLU A:267 , HOH A:1320BINDING SITE FOR RESIDUE FEL A 500
2AC2SOFTWAREHIS B:155 , ASN B:157 , TRP B:192 , HIS B:200 , HIS B:214 , TYR B:257 , GLU B:267 , HOH B:1568 , HOH B:1675BINDING SITE FOR RESIDUE FEL B 500
3AC3SOFTWAREHIS C:155 , ASN C:157 , TRP C:192 , HIS C:200 , HIS C:214 , TYR C:257 , GLU C:267 , HOH C:1450BINDING SITE FOR RESIDUE FEL C 500
4AC4SOFTWAREHIS D:155 , ASN D:157 , TRP D:192 , HIS D:200 , HIS D:214 , TYR D:257 , GLU D:267BINDING SITE FOR RESIDUE FEL D 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F1X)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological 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
5Gly C:209 -Pro C:210
6Gly C:244 -Pro C:245
7Gly D:209 -Pro D:210
8Gly D:244 -Pro D:245

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F1X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1F1X)

(-) Exons   (0, 0)

(no "Exon" information available for 1F1X)

(-) 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:319
 aligned with Q45135_9MICO | Q45135 from UniProtKB/TrEMBL  Length:365

    Alignment length:319
                                    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         
         Q45135_9MICO     4 EIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVHDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEII 322
               SCOP domains d1f1xa1 A:4-147 Homoprotocatechuate 2,3-dioxygenase                                                                                             d1f1xa2 A:148-322 Homoprotocatechuate 2,3-dioxygenase                                                                                                                           SCOP domains
               CATH domains 1f1xA01 A:4-138 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                        -----------1f1xA02 A:150-311 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                                 ----------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeeeee.hhhhhhhhhh.....eeeee...eeeee.........eeeee....eeeeeeeee..hhhhhhhhhhhhhh...eeee..........eeeee.....eeeee......................eeeeeeeee.hhhhhhhhhhhhh.eeeeeee.....eeeeeee.......eeeee....eeeeeeee..hhhhhhhhhhhhhhh.hhh.eeeeeee......eeeeee.....eeeeee............eeee..hhhhh........hhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f1x A   4 EIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVHDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEII 322
                                    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         


Chain B from PDB  Type:PROTEIN  Length:319
 aligned with Q45135_9MICO | Q45135 from UniProtKB/TrEMBL  Length:365

    Alignment length:319
                                    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         
         Q45135_9MICO     4 EIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVHDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEII 322
               SCOP domains d1f1xb1 B:4-147 Homoprotocatechuate 2,3-dioxygenase                                                                                             d1f1xb2 B:148-322 Homoprotocatechuate 2,3-dioxygenase                                                                                                                           SCOP domains
               CATH domains 1f1xB01 B:4-138 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                        -----------1f1xB02 B:150-311 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                                 ----------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeeeee.hhhhhhhhhh.....eeeee...eeeee.........eeeee....eeeeeeeee..hhhhhhhhhhhhhh...eeee..........eeeee.....eeeee......................eeeeeeeee.hhhhhhhhhhhh..eeeeeee.....eeeeeee.......eeeee....eeeeeeee..hhhhhhhhhhhhhhh.hhh.eeeeeee......eeeeee.....eeeeee............eeee..hhhhh.......hhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f1x B   4 EIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVHDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEII 322
                                    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         


Chain C from PDB  Type:PROTEIN  Length:319
 aligned with Q45135_9MICO | Q45135 from UniProtKB/TrEMBL  Length:365

    Alignment length:319
                                    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         
         Q45135_9MICO     4 EIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVHDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEII 322
               SCOP domains d1f1xc1 C:4-147 Homoprotocatechuate 2,3-dioxygenase                                                                                             d1f1xc2 C:148-322 Homoprotocatechuate 2,3-dioxygenase                                                                                                                           SCOP domains
               CATH domains 1f1xC01 C:4-138 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                        -----------1f1xC02 C:150-311 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                                 ----------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeeeeee.hhhhhhhhhh.....eeeee...eeeee.........eeeee....eeeeeeeee..hhhhhhhhhhhhhh...eeee..........eeeee.....eeeee......................eeeeeeeee.hhhhhhhhhhhh..eeeeeee.....eeeeeee.......eeeee....eeeeeeee..hhhhhhhhhhhhhhh.hhh.eeeeeee......eeeeee.....eeeeee............eeee..hhhhh.......hhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f1x C   4 EIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVHDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEII 322
                                    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         


Chain D from PDB  Type:PROTEIN  Length:319
 aligned with Q45135_9MICO | Q45135 from UniProtKB/TrEMBL  Length:365

    Alignment length:319
                                    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         
         Q45135_9MICO     4 EIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVHDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEII 322
               SCOP domains d1f1xd1 D:4-147 Homoprotocatechuate 2,3-dioxygenase                                                                                             d1f1xd2 D:148-322 Homoprotocatechuate 2,3-dioxygenase                                                                                                                           SCOP domains
               CATH domains 1f1xD01 D:4-138 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                        -----------1f1xD02 D:150-311 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..hhhhh.......hhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f1x D   4 EIPKPVAPAPDILRCAYAELVVTDLAKSRNFYVDVLGLHVSYEDENQIYLRSFEEFIHHNLVLTKGPVAALKAMAFRVRTPEDVDKAEAYYQELGCRTERRKDGFVKGIGDALRVEDPLGFPYEFFFETTHVERLHMRYDLYSAGELVRLDHFNQVTPDVPRGRKYLEDLGFRVTEDIQDDEGTTYAAWMHRKGTVHDTALTGGNGPRLHHVAFSTHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDNHRIEIYTQDYYTGDPDNPTITWNVHDNQRRDWWGNPVVPSWYTEASKVLDLDGNVQEII 322
                                    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
   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, 8)

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

(-) CATH Domains  (1, 8)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F1X)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q45135_9MICO | Q45135)
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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  1f1x
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  Q45135_9MICO | Q45135
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  1.13.11.15
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 Related Entries

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

UniProtKB/TrEMBL
        Q45135_9MICO | Q45135: 1q0c 1q0o 2ig9 2iga 3bza 3ecj 3eck 3ojj 3ojk 3ojn 3ojt 4ghc 4ghd 4ghe 4ghf 4ghg 4ghh 4z6l 4z6m 4z6n 4z6o 4z6p 4z6q 4z6r 4z6s 4z6t 4z6u 4z6v 4z6w 4z6z 5bwg 5bwh 5trx

(-) Related Entries Specified in the PDB File

1f1r SAME PROTEIN, FROM ARTHROBACTER GLOBIFORMIS, REFINED AGAINST A DATA SET COLLECTED AT ROOM TEMPERATURE
1f1u SAME PROTEIN, FROM ARTHROBACTER GLOBIFORMIS, NATIVE, LOW TEMPERATURE
1f1v SAME PROTEIN, FROM ARTHROBACTER GLOBIFORMIS, COMPLEXED WITH 3,4-DIHYDROXYPHENYLACETATE
1f1y SAME PROTEIN, SAME SOURCE, C-TERMINAL NOT REMOVED WITH TRYPSIN