Database accession: MF7000764
Name: Catechol 1,2-dioxygenase (Pseudomonas arvilla C-1)
PDB ID: 2azq
Experimental method: X-ray (2.65 Å)
Assembly: Homodimer
Source organism: Pseudomonas putida
Primary publication of the structure:
Earhart CA, Vetting MW, Gosu R, Michaud-Soret I, Que L, Ohlendorf DH
Structure of catechol 1,2-dioxygenase from Pseudomonas arvilla.
(2005) Biochem. Biophys. Res. Commun. 338: 198-205
PMID: 16171781
Abstract:
Catechol 1,2-dioxygenase was first studied by Hayaishi and colleagues in 1950. In 1967, catechol 1,2-dioxygenase from Pseudomonas arvilla C-1 (PaCTD) was chosen as a model system for the catecholic intradiol dioxygenases due to its activity, stability and expression level. Here we report the 2.65 A structure of the betabeta isozyme of PaCTD. The structure supports the hypothesis first made by Vetting and Ohlendorf [The 1.8A crystal structure of catechol 1,2-dioxygenase reveals a novel hydrophobic helical zipper as a subunit linker, Struct. Fold. Des. 8 (2000) 429-440.] that the catechol 1,2-dioxygenases are lipid binding proteins. The 5 amino-terminal helices involved in dimerization and forming the lipid binding site are shown to be plastic in their positions and orientations. The sequence differences between the alpha and beta polypeptides are located at the part of the monomers distant from dimerization surface and thus permit the formation of the 3 isozymes (alphaalpha, alphabeta, and betabeta) of PaCTD. The reported inactivation by sulfhydryl-modifying reagents is explained by the structure. The 10-residue Helix F (residues 203-212) is proposed to be central in communicating between the lipid binding site and the active site.
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
ferric iron binding ferric iron binding
Biological process:
beta-ketoadipate pathway beta-ketoadipate pathway
catechol-containing compound catabolic process catechol-containing compound catabolic process
Cellular component: not assigned
Structural annotations of the participating protein chains.Entry contents: 2 distinct polypeptide molecules
Chains: A, A-2
Notes: All chains according to the most probable oligomerization state stored in PDBe were considered.
Number of unique protein segments: 1
Name: catechol 1,2-dioxygenase
Source organism: Pseudomonas putida
Length: 311 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMTVKISHTADIQAFFNQVAGLDHAEGKPRFKQIILRVLQDTARLIEDLEITEDEFWHAVDYLNRLGGRNEAGLLAAGLGIEHFLDLLQDAKDAEAGLGGGTPRTIEGPLYVAGAPLAQGEVRMDDGTDPGVVMFLQGQVFDANGKPLAGATVDLWHANTQGTYSYFDSTQSEFNLRRRIITDAEGRYRARSIVPSGYGCDPQGPTQECLDLLGRHGQRPAHVHFFISAPGHRHLTTQINFAGDKYLWDDFAYATRDGLIGELRFVEDAAAARDRGVQGERFAELSFDFRLQGAQSPDAEERSHRPRALQEG
UniProtKB AC: Q51433 (positions: 3-311)
Coverage: 99%
Name: catechol 1,2-dioxygenase
Source organism: Pseudomonas putida
Length: 311 residues
Sequence:Sequence according to the corresponding UniProt protein segmentMTVKISHTADIQAFFNQVAGLDHAEGKPRFKQIILRVLQDTARLIEDLEITEDEFWHAVDYLNRLGGRNEAGLLAAGLGIEHFLDLLQDAKDAEAGLGGGTPRTIEGPLYVAGAPLAQGEVRMDDGTDPGVVMFLQGQVFDANGKPLAGATVDLWHANTQGTYSYFDSTQSEFNLRRRIITDAEGRYRARSIVPSGYGCDPQGPTQECLDLLGRHGQRPAHVHFFISAPGHRHLTTQINFAGDKYLWDDFAYATRDGLIGELRFVEDAAAARDRGVQGERFAELSFDFRLQGAQSPDAEERSHRPRALQEG
UniProtKB AC: Q51433 (positions: 3-311)
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 A-2:
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)
Download this entry's JSON file (.json)
