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(-) Description

Title :  CRYSTAL STRUCTURE OF HOMOPROTOCATECHUATE 2,3-DIOXYGENASE FROM ARTHROBACTER GLOBIFORMIS (NATIVE, NON-CRYO)
 
Authors :  M. W. Vetting, J. D. Lipscomb, L. P. Wackett, L. Que Jr. , D. H. Ohlendorf
Date :  19 May 00  (Deposition) - 10 Jun 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:155 , HIS A:214 , GLU A:267 , HOH A:945 , HOH A:946 , HOH A:947BINDING SITE FOR RESIDUE MN A 500
2AC2SOFTWAREHIS B:155 , HIS B:214 , GLU B:267 , HOH B:948 , HOH B:949 , HOH B:950BINDING SITE FOR RESIDUE MN B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F1R)

(-) 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 1F1R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1F1R)

(-) Exons   (0, 0)

(no "Exon" information available for 1F1R)

(-) 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:321
 aligned with Q44048_ARTGO | Q44048 from UniProtKB/TrEMBL  Length:343

    Alignment length:321
                                                                                                                                                                                                                                                                           243                                                                               
                                                                                                                                                                                                                                                                         242 |                                                                               
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242 |     251       261       271       281       291       301       311       321 
         Q44048_ARTGO     3 NFVPTPSVPAPDIVRCAYMEIVVTDLAKSREFYVDVLGLHVTEEDENTIYLRSLEEFIHHNLVLRQGPIAAVAAFAYRVKSPAEVDAAEAYYKELGCRTERRKEGFTKGIGDSVRVEDPLGFPYEFFYETEHVERLTQRYDLYSAGELVRLDHFNQVTPDVPRGRAYLEDLGFRVSEDIKDSDGVTYAAWMHRKQTVHDTALTGGNGPRMHHVAFATHEKHNIIQICDKMRPCASATGSN-GPRPAPVSNAFYLYILDPDGHRIEIYTQDYYTGDPDNPTITWDVHDNQRRDWWGNPVVPSWYTEASLVLDLDGNPQPVIV 322
               SCOP domains d1f1ra1 A:3-147 Homoprotocatechuate 2,3-dioxygenase                                                                                              d1f1ra2 A:148-323 Homoprotocatechuate 2,3-dioxygenase                                                                                                                            SCOP domains
               CATH domains -1f1rA01 A:4-151 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                     1f1rA02 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..hhhhh.......hhhhhhh.ee............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f1r A   3 NFVPTPSVPAPDIVRCAYMEIVVTDLAKSREFYVDVLGLHVTEEDENTIYLRSLEEFIHHNLVLRQGPIAAVAAFAYRVKSPAEVDAAEAYYKELGCRTERRKEGFTKGIGDSVRVEDPLGFPYEFFYETEHVERLTQRYDLYSAGELVRLDHFNQVTPDVPRGRAYLEDLGFRVSEDIKDSDGVTYAAWMHRKQTVHDTALTGGNGPRMHHVAFATHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDGHRIEIYTQDYYTGDPDNPTITWDVHDNQRRDWWGNPVVPSWYTEASLVLDLDGNPQPVIV 323
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322 


Chain B from PDB  Type:PROTEIN  Length:321
 aligned with Q44048_ARTGO | Q44048 from UniProtKB/TrEMBL  Length:343

    Alignment length:321
                                                                                                                                                                                                                                                                           243                                                                               
                                                                                                                                                                                                                                                                         242 |                                                                               
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242 |     251       261       271       281       291       301       311       321 
         Q44048_ARTGO     3 NFVPTPSVPAPDIVRCAYMEIVVTDLAKSREFYVDVLGLHVTEEDENTIYLRSLEEFIHHNLVLRQGPIAAVAAFAYRVKSPAEVDAAEAYYKELGCRTERRKEGFTKGIGDSVRVEDPLGFPYEFFYETEHVERLTQRYDLYSAGELVRLDHFNQVTPDVPRGRAYLEDLGFRVSEDIKDSDGVTYAAWMHRKQTVHDTALTGGNGPRMHHVAFATHEKHNIIQICDKMRPCASATGSN-GPRPAPVSNAFYLYILDPDGHRIEIYTQDYYTGDPDNPTITWDVHDNQRRDWWGNPVVPSWYTEASLVLDLDGNPQPVIV 322
               SCOP domains d1f1rb1 B:3-147 Homoprotocatechuate 2,3-dioxygenase                                                                                              d1f1rb2 B:148-323 Homoprotocatechuate 2,3-dioxygenase                                                                                                                            SCOP domains
               CATH domains -1f1rB01 B:4-151 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                     1f1rB02 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..hhhhhhhhhhhhhh...eeee..........eeeee.....eeeee......................eeeeeeeee.hhhhhhhhhhhh..eeeeeee.....eeeeeee.......eeeee....eeeeeeee..hhhhhhhhhhhhhhh.hhh.eeeeeee......eeeeee.....eeeeee............eeee..hhhhh........hhhhhh.ee............. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1f1r B   3 NFVPTPSVPAPDIVRCAYMEIVVTDLAKSREFYVDVLGLHVTEEDENTIYLRSLEEFIHHNLVLRQGPIAAVAAFAYRVKSPAEVDAAEAYYKELGCRTERRKEGFTKGIGDSVRVEDPLGFPYEFFYETEHVERLTQRYDLYSAGELVRLDHFNQVTPDVPRGRAYLEDLGFRVSEDIKDSDGVTYAAWMHRKQTVHDTALTGGNGPRMHHVAFATHEKHNIIQICDKMGALRISDRIERGPGRHGVSNAFYLYILDPDGHRIEIYTQDYYTGDPDNPTITWDVHDNQRRDWWGNPVVPSWYTEASLVLDLDGNPQPVIV 323
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322
   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 1F1R)

(-) 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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  1f1r
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 Related Entries

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

UniProtKB/TrEMBL
        Q44048_ARTGO | Q44048: 1f1u 1f1v

(-) Related Entries Specified in the PDB File

1f1u SAME PROTEIN, SAME SOURCE, NATIVE, LOW TEMPERATURE
1f1v SAME PROTEIN, SAME SOURCE, COMPLEXED WITH 3,4- DIHYDROXYPHENYLACETATE
1f1x SAME PROTEIN FROM BREVIBACTERIUM FUSCUM, C-TERMINAL REMOVED WITH TRYPSIN
1f1y SAME PROTEIN FROM BREVIBACTERIUM FUSCUM, C-TERMINAL NOT REMOVED WITH TRYPSIN