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26  structures 2995  species 1  interaction 42746  sequences 1972  architectures

Family: GGDEF (PF00990)

Summary: GGDEF domain

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This is the Wikipedia entry entitled "GGDEF domain". More...

GGDEF domain Edit Wikipedia article

GGDEF domain
PDB 1w25 EBI.jpg
response regulator pled in complex with c-digmp
Identifiers
Symbol GGDEF
Pfam PF00990
Pfam clan CL0276
InterPro IPR000160
SCOP 1w25
SUPERFAMILY 1w25
CDD cd01949

In molecular biology, the GGDEF domain is a protein domain which appears to be ubiquitous in bacteria and is often linked to a regulatory domain, such as a phosphorylation receiver or oxygen sensing domain. Its function is to synthesize cyclic di-GMP, which is used as an intracellular signalling molecule in a wide variety of bacteria.[1][2] Enzymatic activity can be strongly influenced by the adjacent domains. Processes regulated by this domain include exopolysaccharide synthesis, biofilm formation, motility and cell differentiation.

Structural studies of PleD from Caulobacter crescentus show that this domain forms a five-stranded beta sheet surrounded by helices, similar to the catalytic core of adenylate cyclase.[3]

References[edit]

  1. ^ Paul R, Weiser S, Amiot NC, Chan C, Schirmer T, Giese B, Jenal U (March 2004). "Cell cycle-dependent dynamic localization of a bacterial response regulator with a novel di-guanylate cyclase output domain". Genes Dev. 18 (6): 715–27. doi:10.1101/gad.289504. PMC 387245. PMID 15075296. 
  2. ^ Ryjenkov DA, Tarutina M, Moskvin OV, Gomelsky M (March 2005). "Cyclic diguanylate is a ubiquitous signaling molecule in bacteria: insights into biochemistry of the GGDEF protein domain". J. Bacteriol. 187 (5): 1792–8. doi:10.1128/JB.187.5.1792-1798.2005. PMC 1064016. PMID 15716451. 
  3. ^ Chan C, Paul R, Samoray D, Amiot NC, Giese B, Jenal U, Schirmer T (December 2004). "Structural basis of activity and allosteric control of diguanylate cyclase". Proc. Natl. Acad. Sci. U.S.A. 101 (49): 17084–9. doi:10.1073/pnas.0406134101. PMC 535365. PMID 15569936. 

This article incorporates text from the public domain Pfam and InterPro IPR000160

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.

GGDEF domain Provide feedback

This domain is found linked to a wide range of non-homologous domains in a variety of bacteria. It has been shown to be homologous to the adenylyl cyclase catalytic domain [1] and has diguanylate cyclase activity [4]. This observation correlates with the functional information available on two GGDEF-containing proteins, namely diguanylate cyclase and phosphodiesterase A of Acetobacter xylinum, both of which regulate the turnover of cyclic diguanosine monophosphate.

Literature references

  1. Pei J, Grishin NV; , Proteins 2001;42:210-216.: GGDEF domain is homologous to adenylyl cyclase. PUBMED:11119645 EPMC:11119645

  2. Galperin MY, Nikolskaya AN, Koonin EV; , FEMS Microbiol Lett 2001;203:11-21.: Novel domains of the prokaryotic two-component signal transduction systems. PUBMED:11557134 EPMC:11557134

  3. Jenal U; , Curr Opin Microbiol 2004;7:185-191.: Cyclic di-guanosine-monophosphate comes of age: a novel secondary messenger involved in modulating cell surface structures in bacteria?. PUBMED:15063857 EPMC:15063857

  4. Paul R, Weiser S, Amiot NC, Chan C, Schirmer T, Giese B, Jenal U; , Genes Dev 2004;18:715-727.: Cell cycle-dependent dynamic localization of a bacterial response regulator with a novel di-guanylate cyclase output domain. PUBMED:15075296 EPMC:15075296

  5. Galperin MY; , Environ Microbiol 2004;6:552-567.: Bacterial signal transduction network in a genomic perspective. PUBMED:15142243 EPMC:15142243

  6. Chan C, Paul R, Samoray D, Amiot NC, Giese B, Jenal U, Schirmer T; , Proc Natl Acad Sci U S A 2004;101:17084-17089.: Structural basis of activity and allosteric control of diguanylate cyclase. PUBMED:15569936 EPMC:15569936


External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000160

This domain appears to be ubiquitous in bacteria and is often linked to a regulatory domain, such as a phosphorylation receiver or oxygen sensing domain. Its function is to synthesize cyclic di-GMP, which is used as an intracellular signalling molecule in a wide variety of bacteria [PUBMED:15075296,PUBMED:15716451]. Enzymatic activity can be strongly influenced by the adjacent domains. Processes regulated by this domain include exopolysaccharide synthesis, biofilm formation, motility and cell differentiation.

Structural studies of PleD from Caulobacter crescentus show that this domain forms a five-stranded beta sheet surrounded by helices, similar to the catalytic core of adenylate cyclase [PUBMED:15569936].

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 Nucleot_cyclase (CL0276), which has the following description:

This superfamily includes adenylyl cyclase and the GGDEF domain [1].

The clan contains the following 3 members:

GGDEF GGDN Guanylate_cyc

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
(49)
Full
(42746)
Representative proteomes NCBI
(36762)
Meta
(3058)
RP15
(3883)
RP35
(8047)
RP55
(10652)
RP75
(12809)
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Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(49)
Full
(42746)
Representative proteomes NCBI
(36762)
Meta
(3058)
RP15
(3883)
RP35
(8047)
RP55
(10652)
RP75
(12809)
Alignment:
Format:
Order:
Sequence:
Gaps:
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Download options

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
(49)
Full
(42746)
Representative proteomes NCBI
(36762)
Meta
(3058)
RP15
(3883)
RP35
(8047)
RP55
(10652)
RP75
(12809)
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

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_112 (release 3.0)
Previous IDs: DUF9;
Type: Domain
Author: Bateman A
Number in seed: 49
Number in full: 42746
Average length of the domain: 153.10 aa
Average identity of full alignment: 28 %
Average coverage of the sequence by the domain: 27.32 %

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 21.0 21.0
Noise cut-off 20.9 20.9
Model length: 161
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Interactions

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

Response_reg

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 GGDEF domain has been found. There are 26 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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