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387  structures 1090  species 2  interactions 2905  sequences 16  architectures

Family: Dioxygenase_C (PF00775)

Summary: Dioxygenase

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This is the Wikipedia entry entitled "Dioxygenase". More...

Dioxygenase Edit Wikipedia article

Dioxygenase
PDB 1eob EBI.jpg
crystal structure of acinetobacter sp. adp1 protocatechuate 3,4-dioxygenase in complex with 3,4-dihydroxybenzoate
Identifiers
Symbol Dioxygenase_C
Pfam PF00775
Pfam clan CL0287
InterPro IPR000627
PROSITE PDOC00079
SCOP 2pcd
SUPERFAMILY 2pcd
Catechol dioxygenase N terminus
PDB 1s9a EBI.jpg
crystal structure of 4-chlorocatechol 1,2-dioxygenase from rhodococcus opacus 1cp
Identifiers
Symbol Dioxygenase_N
Pfam PF04444
InterPro IPR007535
SCOP 1dlm
SUPERFAMILY 1dlm

In molecular biology, a dioxygenase is an enzyme which catalyses the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds. The substrates of ring-cleavage dioxygenases can be classified into two groups according to the mode of scission of the aromatic ring. Intradiol enzymes use a non-haem Fe(III) to cleave the aromatic ring between two hydroxyl groups (ortho-cleavage), whereas extradiol enzymes use a non-haem Fe(II) to cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage).[1] These two subfamilies differ in sequence, structural fold, iron ligands, and the orientation of second sphere active site amino acid residues.

Enzymes that belong to the intradiol family include catechol 1,2-dioxygenase (1,2-CTD) EC 1.13.11.1; protocatechuate 3,4-dioxygenase (3,4-PCD) EC 1.13.11.3 and chlorocatechol 1,2-dioxygenase EC 1.13.11.1[2]

Enzymes that belong to the extradiol class II family include catechol 2,3-dioxygenase (2,3-CTD) EC 1.13.11.2 and biphenyl-2,3-diol 1,2-dioxygenase (BphC) EC 1.13.11.39.

References[edit]

  1. ^ Broderick JB (1999). "Catechol dioxygenases". Essays Biochem. 34: 173–89. PMID 10730195. 
  2. ^ Ferraroni M, Solyanikova IP, Kolomytseva MP, Scozzafava A, Golovleva L, Briganti F (June 2004). "Crystal structure of 4-chlorocatechol 1,2-dioxygenase from the chlorophenol-utilizing gram-positive Rhodococcus opacus 1CP". J. Biol. Chem. 279 (26): 27646–55. doi:10.1074/jbc.M401692200. PMID 15060064. 

This article incorporates text from the public domain Pfam and InterPro IPR000627

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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Dioxygenase Provide feedback

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Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000627

This entry represents the C-terminal domain common to several intradiol ring-cleavage dioxygenases. Dioxygenases catalyse the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms. Cleavage of aromatic rings is one of the most important functions of dioxygenases, which play key roles in the degradation of aromatic compounds. The substrates of ring-cleavage dioxygenases can be classified into two groups according to the mode of scission of the aromatic ring. Intradiol enzymes use a non-haem Fe(III) to cleave the aromatic ring between two hydroxyl groups (ortho-cleavage), whereas extradiol enzymes (INTERPRO) use a non-haem Fe(II) to cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon (meta-cleavage) [PUBMED:10730195]. These two subfamilies differ in sequence, structural fold, iron ligands, and the orientation of second sphere active site amino acid residues.

Enzymes that belong to the intradiol family include catechol 1,2-dioxygenase (1,2-CTD) (EC); protocatechuate 3,4-dioxygenase (3,4-PCD) (EC); and chlorocatechol 1,2-dioxygenase (EC) [PUBMED:15060064].

Gene Ontology

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Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan Transthyretin (CL0287), which contains the following 13 members:

CarboxypepD_reg Cna_B Dioxygenase_C DUF1416 DUF2012 DUF2606 DUF3823 DUF4480 FctA fn3_3 PEGA phage_tail_N Transthyretin

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(20)
Full
(2905)
Representative proteomes NCBI
(2726)
Meta
(434)
RP15
(252)
RP35
(577)
RP55
(855)
RP75
(1080)
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Format an alignment

  Seed
(20)
Full
(2905)
Representative proteomes NCBI
(2726)
Meta
(434)
RP15
(252)
RP35
(577)
RP55
(855)
RP75
(1080)
Alignment:
Format:
Order:
Sequence:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(20)
Full
(2905)
Representative proteomes NCBI
(2726)
Meta
(434)
RP15
(252)
RP35
(577)
RP55
(855)
RP75
(1080)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

Pfam alignments:

HMM logo

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Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

Note: You can also download the data file for the tree.

Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: Pfam-B_1018 (release 2.1)
Previous IDs: Dioxygenase;
Type: Domain
Author: Bateman A
Number in seed: 20
Number in full: 2905
Average length of the domain: 159.70 aa
Average identity of full alignment: 27 %
Average coverage of the sequence by the domain: 65.12 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 24.2 24.2
Trusted cut-off 24.2 24.2
Noise cut-off 24.1 24.1
Model length: 183
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

Dioxygenase_N Dioxygenase_C

Structures

For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Dioxygenase_C domain has been found. There are 387 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein seqence.

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