Database accession: MF7000769
Name: 4-chlorocatechol dioxygenase with 3,5-dichlorocatechol (Rhodococcus opacus 1CP)
PDB ID: 3o32
Experimental method: X-ray (2.85 Å)
Assembly: Homodimer
Source organism: Rhodococcus opacus
Primary publication of the structure:
Ferraroni M, Kolomytseva M, Scozzafava A, Golovleva L, Briganti F
X-ray structures of 4-chlorocatechol 1,2-dioxygenase adducts with substituted catechols: new perspectives in the molecular basis of intradiol ring cleaving dioxygenases specificity.
(2013) J. Struct. Biol. 181: 274-82
PMID: 23261399
Abstract:
The crystallographic structures of 4-chlorocatechol 1,2-dioxygenase (4-CCD) complexes with 3,5-dichlorocatechol, protocatechuate (3,4-dihydroxybenzoate), hydroxyquinol (benzen-1,2,4-triol) and pyrogallol (benzen-1,2,3-triol), which act as substrates or inhibitors of the enzyme, have been determined and analyzed. 4-CCD from the Gram-positive bacterium Rhodococcus opacus 1CP is a Fe(III) ion containing enzyme specialized in the aerobic biodegradation of chlorocatechols. The structures of the 4-CCD complexes show that the catechols bind the catalytic iron ion in a bidentate mode displacing Tyr169 and the benzoate ion (found in the native enzyme structure) from the metal coordination sphere, as found in other adducts of intradiol dioxygenases with substrates. The analysis of the present structures allowed to identify the residues selectively involved in recognition of the diverse substrates. Furthermore the structural comparison with the corresponding complexes of catechol 1,2-dioxygenase from the same Rhodococcus strain (Rho-1,2-CTD) highlights significant differences in the binding of the tested catechols to the active site of the enzyme, particularly in the orientation of the aromatic ring substituents. As an example the 3-substituted catechols are bound with the substituent oriented towards the external part of the 4-CCD active site cavity, whereas in the Rho-1,2-CTD complexes the 3-substituents were placed in the internal position. The present crystallographic study shed light on the mechanism that allows substrate recognition inside this class of high specific enzymes involved in the biodegradation of recalcitrant pollutants.
Annotations from the GeneOntology database. Only terms that fit at least two of the interacting proteins are shown. Molecular function:
catechol 1,2-dioxygenase activity catechol 1,2-dioxygenase activity
chlorocatechol 1,2-dioxygenase activity chlorocatechol 1,2-dioxygenase activity
ferric iron binding ferric iron binding
Biological process:
aromatic compound catabolic process obsolete aromatic compound catabolic process
catechol-containing compound metabolic process catechol-containing compound metabolic process
Cellular component: not assigned
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, B
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: Chlorocatechol 1,2-dioxygenase
Source organism: Rhodococcus opacus
Length: 257 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMANTRVIELFDEFTDLIRDFIVRHEITTPEYETIMQYMISVGEAGEWPLWLDAFFETTVDSVSYGKGNWTSSAIQGPFFKEGAPLLTGKPATLPMRADEPGDRMRFTGSVRDTSGTPITGAVIDVWHSTNDGNYSFFSPALPDQYLLRGRVVPAEDGSIEFHSIRPVPYEIPKAGPTGQLMNSYLGRHSWRPAHIHIRITADGYRPLITQLYFEGDPYLDSDSCSAVKSELVLPVNKIDIDGETWQLVDFNFILQHN
UniProtKB AC: O67987 (positions: 2-257)
Coverage: 99%
Name: Chlorocatechol 1,2-dioxygenase
Source organism: Rhodococcus opacus
Length: 257 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMANTRVIELFDEFTDLIRDFIVRHEITTPEYETIMQYMISVGEAGEWPLWLDAFFETTVDSVSYGKGNWTSSAIQGPFFKEGAPLLTGKPATLPMRADEPGDRMRFTGSVRDTSGTPITGAVIDVWHSTNDGNYSFFSPALPDQYLLRGRVVPAEDGSIEFHSIRPVPYEIPKAGPTGQLMNSYLGRHSWRPAHIHIRITADGYRPLITQLYFEGDPYLDSDSCSAVKSELVLPVNKIDIDGETWQLVDFNFILQHN
UniProtKB AC: O67987 (positions: 3-257)
Coverage: 99%
Evidence demonstrating that the participating proteins are unstructured prior to the interaction and their folding is coupled to binding. Representative domain in related structures: Dioxygenase
Evidence level: Indirect evidence
Evidence coverage: Only some parts of the structure participates in mutual synergistic folding.
Complex Evidence:
A 'helical zipper', consisting of five N-terminal helices and one extending from the catalytic domain from each subunit forms the dimer interafce, termed linker domain. Helices 4 and 5 lie against the catalytic domain, and helix 4 even donates some residues to the active-site cavity (PMID:10801478).
Chain A:
N/A
Chain B:
N/A
Surface and contacts features:
Structures from the PDB that contain the same number of proteins, and the proteins from the two structures show a sufficient degree of pairwise similarity, i.e. they belong to the same UniRef90 cluster (the full proteins exhibit at least 90% sequence identity) and convey roughly the same region to their respective interactions (the two regions from the two proteins share a minimum of 70% overlap). Download the CIF file (.cif)
Download this entry's XML file (.xml)
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