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(-) Description

Title :  CRYSTAL STRUCTURE OF CATECHOL 2,3-DIOXYGENASE
 
Authors :  H. J. Cho, K. J. Kim, B. S. Kang
Date :  21 Jun 09  (Deposition) - 01 Sep 10  (Release) - 10 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  C,D  (4x)
Biol. Unit 2:  A,B  (4x)
Keywords :  Aromatic Hydrocarbons Catabolism, Akbc, 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: B834
    Expression System Taxid: 562
    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, 39)

Asymmetric Unit (4, 39)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2FE4Ligand/IonFE (III) ION
3GOL5Ligand/IonGLYCEROL
4MSE29Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 64)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FE-1Ligand/IonFE (III) ION
3GOL8Ligand/IonGLYCEROL
4MSE56Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 72)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FE-1Ligand/IonFE (III) ION
3GOL12Ligand/IonGLYCEROL
4MSE60Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:149 , HIS A:212 , TYR A:253 , GLU A:263 , HOH A:2046 , HOH A:2072BINDING SITE FOR RESIDUE FE A1289
02AC2SOFTWAREPRO A:111 , ASP A:155 , HOH A:2048 , HOH C:2016 , HOH C:2017BINDING SITE FOR RESIDUE CA A1290
03AC3SOFTWAREHIS A:227 , ARG A:231 , VAL A:237 , GLN A:240 , ILE A:241 , GLU A:288BINDING SITE FOR RESIDUE GOL A1291
04AC4SOFTWAREASP A:94BINDING SITE FOR RESIDUE GOL A1292
05AC5SOFTWAREHIS B:149 , HIS B:212 , TYR B:253 , GLU B:263 , HOH B:2059BINDING SITE FOR RESIDUE FE B1288
06AC6SOFTWAREASP B:94 , ALA B:97 , VAL B:102 , LEU B:103 , LYS B:176BINDING SITE FOR RESIDUE GOL B1289
07AC7SOFTWAREHIS C:149 , HIS C:212 , TYR C:253 , GLU C:263 , HOH C:2048BINDING SITE FOR RESIDUE FE C1286
08AC8SOFTWARELYS C:176 , VAL C:184BINDING SITE FOR RESIDUE GOL C1287
09AC9SOFTWAREHIS D:149 , HIS D:212 , TYR D:253 , GLU D:263BINDING SITE FOR RESIDUE FE D1287
10BC1SOFTWAREASP D:94 , VAL D:102 , LYS D:176BINDING SITE FOR RESIDUE GOL D1288

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WL3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WL3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WL3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WL3)

(-) Exons   (0, 0)

(no "Exon" information available for 2WL3)

(-) 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:287
 aligned with Q6REQ5_9NOCA | Q6REQ5 from UniProtKB/TrEMBL  Length:305

    Alignment length:287
                                    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       
         Q6REQ5_9NOCA     2 AKVTELGYLGLSVSNLDAWRDYAAGIMGMQVVDDGEDDRIYLRMDRWHHRIVLHADGSDDLAYIGWRVAGPVELDELAEQLKNAGIPFEVASDADAAERRVLGLVKLHDPGGNPTEIFYGPQVDTSSPFHPGRPMFGKFVTEGQGLGHIIIREDDVEEATRFYRLLGLEGAVEYKFALPNGAVGTPVFMHCNDRHHSLAFGVGPMDKRINHLMIEYTHLDDLGYAHDLVRQQKIDVTLQIGKHSNDEALTFYCANPSGWLWEPGWGSRPAPAQQEHYLRDIFGHDNE 288
               SCOP domains d2wl3a1 A:2-134 automated matches                                                                                                    d2wl3a2 A:135-288 automated matches                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee..hhhhhhhhhh..............eeee........eeee.....eeeeeeee..hhhhhhhhhhhhhhh....ee.hhhhhhhh...eeeeee.....eeeeee............................eeee...hhhhhhhhhhhhh...ee..............eee........eee........eeeee....hhhhhhhhhhhhhhh...eeeeeee......eeeeee.....ee..ee................ee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wl3 A   2 AKVTELGYLGLSVSNLDAWRDYAAGImGmQVVDDGEDDRIYLRmDRWHHRIVLHADGSDDLAYIGWRVAGPVELDELAEQLKNAGIPFEVASDADAAERRVLGLVKLHDPGGNPTEIFYGPQVDTSSPFHPGRPmFGKFVTEGQGLGHIIIREDDVEEATRFYRLLGLEGAVEYKFALPNGAVGTPVFmHCNDRHHSLAFGVGPmDKRINHLmIEYTHLDDLGYAHDLVRQQKIDVTLQIGKHSNDEALTFYCANPSGWLWEPGWGSRPAPAQQEHYLRDIFGHDNE 288
                                    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       
                                                     28-MSE           45-MSE                                                                                    136-MSE                                               190-MSE         206-MSE 214-MSE                                                                      
                                                       30-MSE                                                                                                                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:287
 aligned with Q6REQ5_9NOCA | Q6REQ5 from UniProtKB/TrEMBL  Length:305

    Alignment length:287
                                    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       
         Q6REQ5_9NOCA     1 MAKVTELGYLGLSVSNLDAWRDYAAGIMGMQVVDDGEDDRIYLRMDRWHHRIVLHADGSDDLAYIGWRVAGPVELDELAEQLKNAGIPFEVASDADAAERRVLGLVKLHDPGGNPTEIFYGPQVDTSSPFHPGRPMFGKFVTEGQGLGHIIIREDDVEEATRFYRLLGLEGAVEYKFALPNGAVGTPVFMHCNDRHHSLAFGVGPMDKRINHLMIEYTHLDDLGYAHDLVRQQKIDVTLQIGKHSNDEALTFYCANPSGWLWEPGWGSRPAPAQQEHYLRDIFGHDN 287
               SCOP domains d2wl3b1 B:1-134 automated matches                                                                                                     d2wl3b2 B:135-287 automated matches                                                                                                                       SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeee..hhhhhhhhhh..............eeee........eeee.....eeeeeeee..hhhhhhhhhhhhhhhh...ee.hhhhhhhh...eeeeee.....eeeeee............................eeee...hhhhhhhhhhhhh...ee...ee.hhh.ee..eee........eee........eeeee....hhhhhhhhhhhhhhh...eeeeeee......eeeeee.....ee..ee................ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wl3 B   1 mAKVTELGYLGLSVSNLDAWRDYAAGImGmQVVDDGEDDRIYLRmDRWHHRIVLHADGSDDLAYIGWRVAGPVELDELAEQLKNAGIPFEVASDADAAERRVLGLVKLHDPGGNPTEIFYGPQVDTSSPFHPGRPmFGKFVTEGQGLGHIIIREDDVEEATRFYRLLGLEGAVEYKFALPNGAVGTPVFmHCNDRHHSLAFGVGPmDKRINHLmIEYTHLDDLGYAHDLVRQQKIDVTLQIGKHSNDEALTFYCANPSGWLWEPGWGSRPAPAQQEHYLRDIFGHDN 287
                            |       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       
                            1-MSE                     28-MSE           45-MSE                                                                                    136-MSE                                               190-MSE         206-MSE 214-MSE                                                                     
                                                        30-MSE                                                                                                                                                                                                                                                             


Chain C from PDB  Type:PROTEIN  Length:284
 aligned with Q6REQ5_9NOCA | Q6REQ5 from UniProtKB/TrEMBL  Length:305

    Alignment length:284
                                    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    
         Q6REQ5_9NOCA     2 AKVTELGYLGLSVSNLDAWRDYAAGIMGMQVVDDGEDDRIYLRMDRWHHRIVLHADGSDDLAYIGWRVAGPVELDELAEQLKNAGIPFEVASDADAAERRVLGLVKLHDPGGNPTEIFYGPQVDTSSPFHPGRPMFGKFVTEGQGLGHIIIREDDVEEATRFYRLLGLEGAVEYKFALPNGAVGTPVFMHCNDRHHSLAFGVGPMDKRINHLMIEYTHLDDLGYAHDLVRQQKIDVTLQIGKHSNDEALTFYCANPSGWLWEPGWGSRPAPAQQEHYLRDIFGH 285
               SCOP domains d2wl3c1 C:2-134 automated matches                                                                                                    d2wl3c2 C:135-285 automated matches                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee..hhhhhhhhhh..............eeee........eeee.....eeeeeeee..hhhhhhhhhhhhhh.....ee.hhhhhhhhh..eeeeee.....eeeeee............................eeee...hhhhhhhhhhhhh...ee...ee.....ee..eee........eee........eeeee....hhhhhhhhhhhhhhh.....eeeee......eeeeee.....ee..ee................eee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wl3 C   2 AKVTELGYLGLSVSNLDAWRDYAAGImGmQVVDDGEDDRIYLRmDRWHHRIVLHADGSDDLAYIGWRVAGPVELDELAEQLKNAGIPFEVASDADAAERRVLGLVKLHDPGGNPTEIFYGPQVDTSSPFHPGRPmFGKFVTEGQGLGHIIIREDDVEEATRFYRLLGLEGAVEYKFALPNGAVGTPVFmHCNDRHHSLAFGVGPmDKRINHLmIEYTHLDDLGYAHDLVRQQKIDVTLQIGKHSNDEALTFYCANPSGWLWEPGWGSRPAPAQQEHYLRDIFGH 285
                                    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    
                                                     28-MSE           45-MSE                                                                                    136-MSE                                               190-MSE         206-MSE 214-MSE                                                                   
                                                       30-MSE                                                                                                                                                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:280
 aligned with Q6REQ5_9NOCA | Q6REQ5 from UniProtKB/TrEMBL  Length:305

    Alignment length:285
                                    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     
         Q6REQ5_9NOCA     2 AKVTELGYLGLSVSNLDAWRDYAAGIMGMQVVDDGEDDRIYLRMDRWHHRIVLHADGSDDLAYIGWRVAGPVELDELAEQLKNAGIPFEVASDADAAERRVLGLVKLHDPGGNPTEIFYGPQVDTSSPFHPGRPMFGKFVTEGQGLGHIIIREDDVEEATRFYRLLGLEGAVEYKFALPNGAVGTPVFMHCNDRHHSLAFGVGPMDKRINHLMIEYTHLDDLGYAHDLVRQQKIDVTLQIGKHSNDEALTFYCANPSGWLWEPGWGSRPAPAQQEHYLRDIFGHD 286
               SCOP domains d2wl3d1 D:2-134 automated matches                                                                                                    d2wl3d2 D:135-286 automated matches                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------------------------------------------------------------------------------------------------------------Glyoxalase-2wl3D01 D:146-263                                                                                          ----------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------------------------------------------------------------------------------------------Glyoxalase-2wl3D02 D:146-263                                                                                          ----------------------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------------------------------------------------------------------------------------------Glyoxalase-2wl3D03 D:146-263                                                                                          ----------------------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------------------------------------------------------------------------------------------Glyoxalase-2wl3D04 D:146-263                                                                                          ----------------------- Pfam domains (4)
         Sec.struct. author ....eeeeeeee..hhhhhhhhhh..............eeee........eeee.....eeeeeeee..hhhhhhhhhhhhhhhh...ee.hhhhhhhhh..eeeeee.....eeeeee............................eeee...hhhhhhhhhhhhh...ee....-----.....eee........eee........eeeee....hhhhhhhhhhhhhhh...eeeeeee......eeeeee.....ee..ee................ee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wl3 D   2 AKVTELGYLGLSVSNLDAWRDYAAGImGmQVVDDGEDDRIYLRmDRWHHRIVLHADGSDDLAYIGWRVAGPVELDELAEQLKNAGIPFEVASDADAAERRVLGLVKLHDPGGNPTEIFYGPQVDTSSPFHPGRPmFGKFVTEGQGLGHIIIREDDVEEATRFYRLLGLEGAVEYKF-----AVGTPVFmHCNDRHHSLAFGVGPmDKRINHLmIEYTHLDDLGYAHDLVRQQKIDVTLQIGKHSNDEALTFYCANPSGWLWEPGWGSRPAPAQQEHYLRDIFGHD 286
                                    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     
                                                     28-MSE           45-MSE                                                                                    136-MSE                                  177   183      |             206-MSE 214-MSE                                                                    
                                                       30-MSE                                                                                                                                                         190-MSE
   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 2WL3)

(-) 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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        Q6REQ5_9NOCA | Q6REQ5: 2wl9

(-) Related Entries Specified in the PDB File

2wl9 CRYSTAL STRUCTURE OF CATECHOL 2,3- DIOXYGENASE