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6  structures 324  species 1  interaction 375  sequences 1  architecture

Family: DDR (PF08841)

Summary: Diol dehydratase reactivase ATPase-like domain

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Diol dehydratase reactivase ATPase-like domain Provide feedback

Diol dehydratase (DDH, EC:4.2.1.28) and its isofunctional homologue glycerol dehydratase (GDH, EC.4.2.1.30) are enzymes which catalyse the conversion of glycerol 1,2-propanediol, and 1,2-ethanediol to aldehydes [1]. These reactions require coenzyme B12. Cleavage of the Co-C bond of coenzyme B12 by substrates or coenzyme analogues results in inactivation during which coenzyme B12 remains tightly bound to the apoenzyme. This family comprises of the large subunit of the diol dehydratase and glycerol dehydratase reactivating factors whose function is to reactivate the holoenzyme by exchange of a damaged cofactor for intact coenzyme.

Literature references

  1. Daniel R, Bobik TA, Gottschalk G; , FEMS Microbiol Rev. 1998;22:553-566.: Biochemistry of coenzyme B12-dependent glycerol and diol dehydratases and organization of the encoding genes. PUBMED:9990728 EPMC:9990728

  2. Shibata N, Mori K, Hieda N, Higuchi Y, Yamanishi M, Toraya T; , Structure. 2005;13:1745-1754.: Release of a damaged cofactor from a coenzyme B12-dependent enzyme: X-ray structures of diol dehydratase-reactivating factor. PUBMED:16338403 EPMC:16338403


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR009191

Diol dehydratase (propanediol dehydratase) and glycerol dehydratase undergo concomitant, irreversible inactivation by glycerol during catalysis [PUBMED:889846, PUBMED:321014]. This inactivation is mechanism-based and involves cleavage of the Co-C bond of the cobalamin cofactor, coenzyme B12 (AdoCbl), forming 5 -deoxyadenosine and a modified coenzyme [PUBMED:889846]. Irreversible inactivation of the enzyme results from tight binding to the modified, inactive cobalamin [PUBMED:889846, PUBMED:321014].

The glycerol-inactivated enzyme undergoes rapid reactivation in the presence of free AdoCbl, ATP, and Mg 2+ (or Mn 2+ ) [PUBMED:6752354]. Reactivation is mediated by a complex of two proteins: a large subunit (DdrA/PduG) and a small subunit (DdrB/PduH, INTERPRO) [PUBMED:9362119, PUBMED:9405397].

The two subunits of the reactivating factor for glycerol dehydratase have been shown to form a tight complex that serves to reactivate the glycerol-inactivated holoenzyme, as well as O2-inactivated holoenzyme in vitro [PUBMED:9920879]. It is believed that this reactivating factor replaces an enzyme-bound, adenine-lacking inactive cobalamin with a free, adenine-containing active cobalamin [PUBMED:9920879].

PduG and PduH, part of the propanediol utilization pdu operon, are believed to have a similar function in the reactivation of propanediol dehydratase. PduG was also proposed, on the basis of genetic tests, to be a cobalamin adenosyltransferase involved in the conversion of inactive cobalamin (B12) to AdoCbl [PUBMED:9023178]. However, this function has since been shown to belong to another protein, PduO (INTERPRO, INTERPRO) [PUBMED:11160088].

Please see INTERPRO, INTERPRO, INTERPRO for more details on the propanediol utilization pathway and pdu operon, as well as on the glycerol breakdown pathway.

Domain organisation

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Alignments

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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
(12)
Full
(375)
Representative proteomes NCBI
(285)
Meta
(7)
RP15
(14)
RP35
(21)
RP55
(30)
RP75
(39)
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(12)
Full
(375)
Representative proteomes NCBI
(285)
Meta
(7)
RP15
(14)
RP35
(21)
RP55
(30)
RP75
(39)
Alignment:
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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
(12)
Full
(375)
Representative proteomes NCBI
(285)
Meta
(7)
RP15
(14)
RP35
(21)
RP55
(30)
RP75
(39)
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:

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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.

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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: pdb_2d0o
Previous IDs: none
Type: Family
Author: Mistry J
Number in seed: 12
Number in full: 375
Average length of the domain: 314.90 aa
Average identity of full alignment: 70 %
Average coverage of the sequence by the domain: 55.80 %

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 24.6 24.6
Trusted cut-off 24.6 24.7
Noise cut-off 24.5 24.4
Model length: 332
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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Interactions

There is 1 interaction for this family. More...

DDR

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 DDR domain has been found. There are 6 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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