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(-) Description

Title :  CRYSTAL STRUCTURE OF CATECHOL 2,3-DIOXYGENASE
 
Authors :  H. J. Cho, K. J. Kim, B. S. Kang
Date :  23 Jun 09  (Deposition) - 01 Sep 10  (Release) - 10 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C,D  (4x)
Biol. Unit 2:  A,B  (4x)
Keywords :  Aromatic Hydrocarbons Catabolism, Iron, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. J. Cho, K. Kim, S. Y. Sohn, H. Y. Cho, K. J. Kim, M. H. Kim, D. Kim, E. Kim, B. S. Kang
Substrate-Binding Mechanism Of A Type I Extradiol Dioxygenase.
J. Biol. Chem. V. 285 34643 2010
PubMed-ID: 20810655  |  Reference-DOI: 10.1074/JBC.M110.130310

(-) Compounds

Molecule 1 - CATECHOL 2,3-DIOXYGENASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PGST-PARALLEL
    Organism Scientific: RHODOCOCCUS SP. DK17
    Organism Taxid: 186196

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (4x):   CD
Biological Unit 2 (4x): AB  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1FE4Ligand/IonFE (III) ION
2GOL3Ligand/IonGLYCEROL
3MBD2Ligand/Ion3-METHYLCATECHOL
4MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2GOL4Ligand/IonGLYCEROL
3MBD4Ligand/Ion3-METHYLCATECHOL
4MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
1FE-1Ligand/IonFE (III) ION
2GOL8Ligand/IonGLYCEROL
3MBD4Ligand/Ion3-METHYLCATECHOL
4MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:149 , HIS A:212 , TYR A:253 , GLU A:263 , HOH A:2078BINDING SITE FOR RESIDUE FE A1301
02AC2SOFTWAREHIS B:149 , HIS B:212 , TYR B:253 , GLU B:263 , MBD B:1301 , HOH B:2064BINDING SITE FOR RESIDUE FE B1300
03AC3SOFTWAREHIS C:149 , HIS C:212 , TYR C:253 , GLU C:263BINDING SITE FOR RESIDUE FE C1300
04AC4SOFTWAREHIS D:149 , HIS D:212 , TYR D:253 , GLU D:263 , MBD D:1303 , HOH D:2062BINDING SITE FOR RESIDUE FE D1301
05AC5SOFTWAREPRO A:111 , ASP A:155 , HOH C:2020 , HOH C:2023 , HOH C:2024BINDING SITE FOR RESIDUE MG A1302
06AC6SOFTWAREGLY A:224 , HIS A:227 , ILE A:241 , GOL A:1304 , ILE B:241 , PHE B:283BINDING SITE FOR RESIDUE GOL A1303
07AC7SOFTWAREILE A:241 , PHE A:283 , GOL A:1303 , GLY B:224 , HIS B:227 , ILE B:241BINDING SITE FOR RESIDUE GOL A1304
08AC8SOFTWAREILE C:241 , PHE C:283 , GLY D:224 , HIS D:227 , ILE D:241BINDING SITE FOR RESIDUE GOL D1302
09AC9SOFTWARETYR B:175 , PHE B:189 , HIS B:197 , HIS B:244 , ASN B:246 , ASP B:247 , TYR B:253 , FE B:1300 , HOH B:2064BINDING SITE FOR RESIDUE MBD B1301
10BC1SOFTWARETYR D:175 , PHE D:189 , HIS D:197 , HIS D:244 , ASN D:246 , TYR D:253 , FE D:1301BINDING SITE FOR RESIDUE MBD D1303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WL9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WL9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WL9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WL9)

(-) Exons   (0, 0)

(no "Exon" information available for 2WL9)

(-) 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:300
 aligned with Q6REQ5_9NOCA | Q6REQ5 from UniProtKB/TrEMBL  Length:305

    Alignment length:300
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300
         Q6REQ5_9NOCA     1 MAKVTELGYLGLSVSNLDAWRDYAAGIMGMQVVDDGEDDRIYLRMDRWHHRIVLHADGSDDLAYIGWRVAGPVELDELAEQLKNAGIPFEVASDADAAERRVLGLVKLHDPGGNPTEIFYGPQVDTSSPFHPGRPMFGKFVTEGQGLGHIIIREDDVEEATRFYRLLGLEGAVEYKFALPNGAVGTPVFMHCNDRHHSLAFGVGPMDKRINHLMIEYTHLDDLGYAHDLVRQQKIDVTLQIGKHSNDEALTFYCANPSGWLWEPGWGSRPAPAQQEHYLRDIFGHDNEVEGYGLDIPLKG 300
               SCOP domains d2wl9a1 A:1-134 automated matches                                                                                                     d2wl9a2 A:135-300 automated matches                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeee..hhhhhhhhhh.....eee......eeeee.......eeee.....eeeeeeee..hhhhhhhhhhhhhhh....ee.hhhhhhhh.eeeeeeee.....eeeeeeee..........................eeee...hhhhhhhhhhhhh.eeee...ee.....ee..eeee.......eee........eeeeeeee.hhhhhhhhhhhhhhh...eeeeeee......eeeeee.....eeeeee................ee................ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2wl9 A   1 MAKVTELGYLGLSVSNLDAWRDYAAGIMGMQVVDDGEDDRIYLRMDRWHHRIVLHADGSDDLAYIGWRVAGPVELDELAEQLKNAGIPFEVASDADAAERRVLGLVKLHDPGGNPTEIFYGPQVDTSSPFHPGRPMFGKFVTEGQGLGHIIIREDDVEEATRFYRLLGLEGAVEYKFALPNGAVGTPVFMHCNDRHHSLAFGVGPMDKRINHLMIEYTHLDDLGYAHDLVRQQKIDVTLQIGKHSNDEALTFYCANPSGWLWEPGWGSRPAPAQQEHYLRDIFGHDNEVEGYGLDIPLKG 300
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300


Chain B from PDB  Type:PROTEIN  Length:293
 aligned with Q6REQ5_9NOCA | Q6REQ5 from UniProtKB/TrEMBL  Length:305

    Alignment length:298
                                    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        
         Q6REQ5_9NOCA     2 AKVTELGYLGLSVSNLDAWRDYAAGIMGMQVVDDGEDDRIYLRMDRWHHRIVLHADGSDDLAYIGWRVAGPVELDELAEQLKNAGIPFEVASDADAAERRVLGLVKLHDPGGNPTEIFYGPQVDTSSPFHPGRPMFGKFVTEGQGLGHIIIREDDVEEATRFYRLLGLEGAVEYKFALPNGAVGTPVFMHCNDRHHSLAFGVGPMDKRINHLMIEYTHLDDLGYAHDLVRQQKIDVTLQIGKHSNDEALTFYCANPSGWLWEPGWGSRPAPAQQEHYLRDIFGHDNEVEGYGLDIPLK 299
               SCOP domains d2wl9b1 B:2-134 automated matches                                                                                                    d2wl9b2 B:135-299 automated matches                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeeee.hhhhhhhhhh.....eee......eeeee.......eeeee....eeeeeeee..hhhhhhhhhhhhhhh....ee.hhhhhhhhh..eeeeee.....eeeeee............................eeee...hhhhhhhhhhhhh.eeee.....-----....eeee.......eee........eeeeeeee.hhhhhhhhhhhhhhh...eeeeeee......eeeeee.....eeeeee................ee............... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wl9 B   2 AKVTELGYLGLSVSNLDAWRDYAAGIMGMQVVDDGEDDRIYLRMDRWHHRIVLHADGSDDLAYIGWRVAGPVELDELAEQLKNAGIPFEVASDADAAERRVLGLVKLHDPGGNPTEIFYGPQVDTSSPFHPGRPMFGKFVTEGQGLGHIIIREDDVEEATRFYRLLGLEGAVEYKFA-----VGTPVFMHCNDRHHSLAFGVGPMDKRINHLMIEYTHLDDLGYAHDLVRQQKIDVTLQIGKHSNDEALTFYCANPSGWLWEPGWGSRPAPAQQEHYLRDIFGHDNEVEGYGLDIPLK 299
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171      |  -  |    191       201       211       221       231       241       251       261       271       281       291        
                                                                                                                                                                                                          178   184                                                                                                                   


Chain C from PDB  Type:PROTEIN  Length:299
 aligned with Q6REQ5_9NOCA | Q6REQ5 from UniProtKB/TrEMBL  Length:305

    Alignment length:299
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290         
         Q6REQ5_9NOCA     1 MAKVTELGYLGLSVSNLDAWRDYAAGIMGMQVVDDGEDDRIYLRMDRWHHRIVLHADGSDDLAYIGWRVAGPVELDELAEQLKNAGIPFEVASDADAAERRVLGLVKLHDPGGNPTEIFYGPQVDTSSPFHPGRPMFGKFVTEGQGLGHIIIREDDVEEATRFYRLLGLEGAVEYKFALPNGAVGTPVFMHCNDRHHSLAFGVGPMDKRINHLMIEYTHLDDLGYAHDLVRQQKIDVTLQIGKHSNDEALTFYCANPSGWLWEPGWGSRPAPAQQEHYLRDIFGHDNEVEGYGLDIPLK 299
               SCOP domains d2wl9c1 C:1-134 automated matches                                                                                                     d2wl9c2 C:135-299 automated matches                                                                                                                                   SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeee.hhhhhhhhhh.....eee......eeeee.......eeeee....eeeeeeee..hhhhhhhhhhhhhhh....ee.hhhhhhhhh..eeeeee.....eeeeee............................eeee...hhhhhhhhhhhhh.eeee...ee.....ee..eeee.......eee........eeeeeeee.hhhhhhhhhhhhhhh...eeeeeee......eeeeee.....eeeeee................ee............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wl9 C   1 MAKVTELGYLGLSVSNLDAWRDYAAGIMGMQVVDDGEDDRIYLRMDRWHHRIVLHADGSDDLAYIGWRVAGPVELDELAEQLKNAGIPFEVASDADAAERRVLGLVKLHDPGGNPTEIFYGPQVDTSSPFHPGRPMFGKFVTEGQGLGHIIIREDDVEEATRFYRLLGLEGAVEYKFALPNGAVGTPVFMHCNDRHHSLAFGVGPMDKRINHLMIEYTHLDDLGYAHDLVRQQKIDVTLQIGKHSNDEALTFYCANPSGWLWEPGWGSRPAPAQQEHYLRDIFGHDNEVEGYGLDIPLK 299
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290         


Chain D from PDB  Type:PROTEIN  Length:294
 aligned with Q6REQ5_9NOCA | Q6REQ5 from UniProtKB/TrEMBL  Length:305

    Alignment length:299
                                    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         
         Q6REQ5_9NOCA     2 AKVTELGYLGLSVSNLDAWRDYAAGIMGMQVVDDGEDDRIYLRMDRWHHRIVLHADGSDDLAYIGWRVAGPVELDELAEQLKNAGIPFEVASDADAAERRVLGLVKLHDPGGNPTEIFYGPQVDTSSPFHPGRPMFGKFVTEGQGLGHIIIREDDVEEATRFYRLLGLEGAVEYKFALPNGAVGTPVFMHCNDRHHSLAFGVGPMDKRINHLMIEYTHLDDLGYAHDLVRQQKIDVTLQIGKHSNDEALTFYCANPSGWLWEPGWGSRPAPAQQEHYLRDIFGHDNEVEGYGLDIPLKG 300
               SCOP domains d2wl9d1 D:2-134 automated matches                                                                                                    d2wl9d2 D:135-300 automated matches                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------Glyoxalase-2wl9D01 D:146-263                                                                                          ------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------Glyoxalase-2wl9D02 D:146-263                                                                                          ------------------------------------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------------------------------Glyoxalase-2wl9D03 D:146-263                                                                                          ------------------------------------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------------------------------Glyoxalase-2wl9D04 D:146-263                                                                                          ------------------------------------- Pfam domains (4)
         Sec.struct. author ....eeeeeeeee.hhhhhhhhhh.....eee......eeeee.......eeeee....eeeeeeee..hhhhhhhhhhhhhhhh...ee.hhhhhhhh...eeeeee.....eeeeee............................eeee...hhhhhhhhhhhhh.eeee....-----.....eeee.......eee........eeeeeeee.hhhhhhhhhhhhhhh...eeeeeee......eeeeee.....eeeeee................ee................ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wl9 D   2 AKVTELGYLGLSVSNLDAWRDYAAGIMGMQVVDDGEDDRIYLRMDRWHHRIVLHADGSDDLAYIGWRVAGPVELDELAEQLKNAGIPFEVASDADAAERRVLGLVKLHDPGGNPTEIFYGPQVDTSSPFHPGRPMFGKFVTEGQGLGHIIIREDDVEEATRFYRLLGLEGAVEYKF-----AVGTPVFMHCNDRHHSLAFGVGPMDKRINHLMIEYTHLDDLGYAHDLVRQQKIDVTLQIGKHSNDEALTFYCANPSGWLWEPGWGSRPAPAQQEHYLRDIFGHDNEVEGYGLDIPLKG 300
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171     |   - |     191       201       211       221       231       241       251       261       271       281       291         
                                                                                                                                                                                                         177   183
   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  (1, 8)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2WL9)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Glyoxalase (58)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q6REQ5_9NOCA | Q6REQ5)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    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:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    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.
    GO:0042178    xenobiotic catabolic process    The chemical reactions and pathways resulting in the breakdown of a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide.

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 Related Entries

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        Q6REQ5_9NOCA | Q6REQ5: 2wl3

(-) Related Entries Specified in the PDB File

2wl3 CRYSTAL STRUCTURE OF CATECHOL 2,3- DIOXYGENASE