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37  structures 1172  species 1  interaction 1439  sequences 12  architectures

Family: CYTH (PF01928)

Summary: CYTH domain

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CYTH domain Provide feedback

These sequences are functionally identified as members of the adenylate cyclase family, which catalyses the conversion of ATP to 3',5'-cyclic AMP and pyrophosphate. Six distinct non-homologous classes of AC have been identified. The structure of three classes of adenylyl cyclases have been solved [3].

Literature references

  1. Sismeiro O, Trotot P, Biville F, Vivares C, Danchin A; , J Bacteriol 1998;180:3339-3344.: Aeromonas hydrophila adenylyl cyclase 2: a new class of adenylyl cyclases with thermophilic properties and sequence similarities to proteins from hyperthermophilic archaebacteria. PUBMED:9642185 EPMC:9642185

  2. Iyer LM, Aravind L; , BMC Genomics 2002;3:33-33.: The catalytic domains of thiamine triphosphatase and CyaB-like adenylyl cyclase define a novel superfamily of domains that bind organic phosphates. PUBMED:12456267 EPMC:12456267

  3. Gallagher DT, Smith NN, Kim SK, Heroux A, Robinson H, Reddy PT; , J Mol Biol. 2006;362:114-122.: Structure of the class IV adenylyl cyclase reveals a novel fold. PUBMED:16905149 EPMC:16905149

  4. Smith N, Kim SK, Reddy PT, Gallagher DT; , Acta Crystallograph Sect F Struct Biol Cryst Commun. 2006;62:200-204.: Crystallization of the class IV adenylyl cyclase from Yersinia pestis. PUBMED:16511301 EPMC:16511301


This tab holds annotation information from the InterPro database.

InterPro entry IPR023577

The entry represents the CYTH domain.

The CyaB like adenylyl cyclase and the mammalian thiamine triphosphatases (ThTPases) define a superfamily of catalytic domains called the CYTH (CyaB, thiamine triphosphatase) domain that is present in all three superkingdoms of life. CYTH domains are likely to be domains specialised to bind nucleotides and other organic phosphates [PUBMED:12456267].

The catalytic core of the CYTH domain is predicted to contain an alpha+beta scaffold with 6 conserved beta-strands and 6 conserved alpha-helices. The CYTH domains contains several nearly universally conserved charged residues that are likely to form the active site. The most prominent of these are an EXEXK motif associated with strand-1 of the domain, two basic residues in helix-2, a K at the end of strand 3, an E in strand 4, a basic residue in helix-4, a D at the end of strand 5 and two acidic residues (typically glutamates) in strand 6. The presence of around 6 conserved acidic positions in the majority of the CYTH domains suggests that it coordinates two divalent metal ions. Both CyaB and ThTPase have been shown to require Mg(2+) ions for their nucleotide cyclase and phosphatase activities. The four conserved basic residues in the CYTH domain are most probably involved in the binding of acidic phosphate moieties of their substrates. The conservation of these two sets of residues in the majority of CYTH domains suggests that most members of this group are likely to possess an activity dependent on two metal ions, with a preference for nucleotides or related phosphate-moiety -bearing substrates. The proposed biochemical activity, and the arrangement of predicted strands in the primary structure of the CYTH domain imply that they may adopt a barrel or sandwich- like configuration, with metal ions and the substrates bound in the central cavity [PUBMED:12456267].

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 CYTH (CL0273), which has the following description:

CyaB like adenylyl cyclase and the mammalian thiamine triphosphatases define a novel superfamily of catalytic domains called the CYTH domain that is present in all three superkingdoms of life. The catalytic core of these enzymes contain a novel alpha beta scaffold with 6 conserved acidic residues and 4 basic residues [1].

The clan contains the following 2 members:

CYTH mRNA_triPase

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, 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
(51)
Full
(1439)
Representative proteomes UniProt
(7291)
NCBI
(10983)
Meta
(240)
RP15
(393)
RP35
(1062)
RP55
(1644)
RP75
(2313)
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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
(51)
Full
(1439)
Representative proteomes UniProt
(7291)
NCBI
(10983)
Meta
(240)
RP15
(393)
RP35
(1062)
RP55
(1644)
RP75
(2313)
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
(51)
Full
(1439)
Representative proteomes UniProt
(7291)
NCBI
(10983)
Meta
(240)
RP15
(393)
RP35
(1062)
RP55
(1644)
RP75
(2313)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   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.

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: Aravind L
Previous IDs: Adenylate_cyc_2;
Type: Domain
Author: Aravind L
Number in seed: 51
Number in full: 1439
Average length of the domain: 170.70 aa
Average identity of full alignment: 17 %
Average coverage of the sequence by the domain: 60.96 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 11927849 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 23.2 23.2
Trusted cut-off 23.5 23.2
Noise cut-off 23.1 23.1
Model length: 179
Family (HMM) version: 18
Download: download the raw HMM for this family

Species distribution

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Archea Archea Eukaryota Eukaryota
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Viroids Viroids Unclassified sequence Unclassified sequence

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Interactions

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

CYTH

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 CYTH domain has been found. There are 37 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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