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4  structures 628  species 2  interactions 789  sequences 8  architectures

Family: DmpG_comm (PF07836)

Summary: DmpG-like communication domain

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This is the Wikipedia entry entitled "DmpG-like communication domain". More...

DmpG-like communication domain Edit Wikipedia article

DmpG-like communication domain
PDB 1nvm EBI.jpg
crystal structure of a bifunctional aldolase-dehydrogenase : sequestering a reactive and volatile intermediate
Identifiers
Symbol DmpG_comm
Pfam PF07836
InterPro IPR012425
SCOP 1nvm
SUPERFAMILY 1nvm

In molecular biology, the DmpG-like communication domain is a protein domain found towards the C-terminal region of various aldolase enzymes. It consists of five alpha-helices, four of which form an antiparallel helical bundle that plugs the C terminus of the N-terminal TIM barrel domain.[1] The communication domain is thought to play an important role in the heterodimerisation of the enzyme.[1]

This domain heterodimerises with acetaldehyde dehydrogenases to form a bifunctional aldolase-dehydrogenase.[1]

References[edit]

  1. ^ a b c Manjasetty BA, Powlowski J, Vrielink A (June 2003). "Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate". Proc. Natl. Acad. Sci. U.S.A. 100 (12): 6992–7. doi:10.1073/pnas.1236794100. PMC 165818. PMID 12764229. 

This article incorporates text from the public domain Pfam and InterPro IPR012425

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

This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.

DmpG-like communication domain Provide feedback

This domain is found towards the C-terminal region of various aldolase enzymes. It consists of five alpha-helices, four of which form an antiparallel helical bundle that plugs the C-terminus of the N-terminal TIM barrel domain [1]. The communication domain is thought to play an important role in the heterodimerisation of the enzyme [1].

Literature references

  1. Manjasetty BA, Powlowski J, Vrielink A; , Proc Natl Acad Sci U S A 2003;100:6992-6997.: Crystal structure of a bifunctional aldolase-dehydrogenase: sequestering a reactive and volatile intermediate. PUBMED:12764229 EPMC:12764229


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR012425

This domain is found towards the C-terminal region of various aldolase enzymes. It consists of five alpha-helices, four of which form an antiparallel helical bundle that plugs the C terminus of the N-terminal TIM barrel domain [PUBMED:12764229]. The communication domain is thought to play an important role in the heterodimerisation of the enzyme [PUBMED:12764229].

Members of this entry heterodimerise with members of INTERPRO to form a bifunctional aldolase-dehydrogenase [PUBMED:12764229].

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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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
(37)
Full
(789)
Representative proteomes NCBI
(566)
Meta
(103)
RP15
(45)
RP35
(122)
RP55
(167)
RP75
(196)
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Format an alignment

  Seed
(37)
Full
(789)
Representative proteomes NCBI
(566)
Meta
(103)
RP15
(45)
RP35
(122)
RP55
(167)
RP75
(196)
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
(37)
Full
(789)
Representative proteomes NCBI
(566)
Meta
(103)
RP15
(45)
RP35
(122)
RP55
(167)
RP75
(196)
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.

HMM logo

HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

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_1675 (release 14.0)
Previous IDs: none
Type: Domain
Author: Fenech M
Number in seed: 37
Number in full: 789
Average length of the domain: 65.60 aa
Average identity of full alignment: 60 %
Average coverage of the sequence by the domain: 19.32 %

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 21.0 21.0
Trusted cut-off 21.1 24.1
Noise cut-off 19.5 20.5
Model length: 66
Family (HMM) version: 6
Download: download the raw HMM for this family

Species distribution

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Interactions

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

HMGL-like AcetDehyd-dimer

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 DmpG_comm domain has been found. There are 4 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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