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683  structures 7904  species 0  interactions 78333  sequences 1206  architectures

Family: cNMP_binding (PF00027)

Summary: Cyclic nucleotide-binding domain

Pfam includes annotations and additional family information from a range of different sources. These sources can be accessed via the tabs below.

This is the Wikipedia entry entitled "Cyclic nucleotide-binding domain". More...

Cyclic nucleotide-binding domain Edit Wikipedia article

Cyclic nucleotide-binding domain
PDB 1cgp EBI.jpg
Structure of a CAP-DNA complex.[1]
Identifiers
Symbol cNMP_binding
Pfam PF00027
InterPro IPR000595
SMART SM00100
PROSITE PDOC00691
SCOP 1cgp
SUPERFAMILY 1cgp
CDD cd00038

Proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues. The best studied of these proteins is the prokaryotic catabolite gene activator (also known as the cAMP receptor protein) (gene crp) where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure. There are six invariant amino acids in this domain, three of which are glycine residues that are thought to be essential for maintenance of the structural integrity of the beta-barrel. cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain. The cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain. The cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section. Vertebrate cyclic nucleotide-gated ion-channels also contain this domain. Two such cations channels have been fully characterized, one is found in rod cells where it plays a role in visual signal transduction.

Human proteins containing this domain

CNBD1; CNGA1; CNGA2; CNGA3; CNGB1; CNGB3; HCN1; HCN2; HCN3; HCN4; KCNH1; KCNH2; KCNH3; KCNH4; KCNH5; KCNH6; KCNH7; KCNH8; PNPLA6; PNPLA7; PRKAR1A; PRKAR1B; PRKAR2A; PRKAR2B; PRKG1; PRKG2; RAPGEF2; RAPGEF3; RAPGEF4; RAPGEF6; RCNC2; SLC9A10; SLC9A11;

References

  1. ^ Schultz SC, Shields GC, Steitz TA (August 1991). "Crystal structure of a CAP-DNA complex: the DNA is bent by 90 degrees". Science. 253 (5023): 1001–7. Bibcode:1991Sci...253.1001S. doi:10.1126/science.1653449. PMID 1653449. 

Further reading

This article incorporates text from the public domain Pfam and InterPro IPR000595

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.

Cyclic nucleotide-binding domain Provide feedback

No Pfam abstract.

Literature references

  1. Yau KW; , Proc Natl Acad Sci USA 1994;91:3481-3483.: Cyclic nucleotide-gated channels: an expanding new family of ion channels. PUBMED:7513422 EPMC:7513422


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR000595

Proteins that bind cyclic nucleotides (cAMP or cGMP) share a structural domain of about 120 residues [ PUBMED:14638413 , PUBMED:10550204 , PUBMED:1710853 ]. The best studied of these proteins is the prokaryotic catabolite gene activator (also known as the cAMP receptor protein) (gene crp) where such a domain is known to be composed of three alpha-helices and a distinctive eight-stranded, antiparallel beta-barrel structure. There are six invariant amino acids in this domain, three of which are glycine residues that are thought to be essential for maintenance of the structural integrity of the beta-barrel. cAMP- and cGMP-dependent protein kinases (cAPK and cGPK) contain two tandem copies of the cyclic nucleotide-binding domain. The cAPK's are composed of two different subunits, a catalytic chain and a regulatory chain, which contains both copies of the domain. The cGPK's are single chain enzymes that include the two copies of the domain in their N-terminal section. Vertebrate cyclic nucleotide-gated ion-channels also contain this domain. Two such cations channels have been fully characterised, one is found in rod cells where it plays a role in visual signal transduction.

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 (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets and the UniProtKB 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
(211)
Full
(78333)
Representative proteomes UniProt
(268360)
RP15
(13683)
RP35
(36188)
RP55
(73969)
RP75
(117964)
Jalview View  View  View  View  View  View  View 
HTML View             
PP/heatmap 1            

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

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

Format an alignment

  Seed
(211)
Full
(78333)
Representative proteomes UniProt
(268360)
RP15
(13683)
RP35
(36188)
RP55
(73969)
RP75
(117964)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(211)
Full
(78333)
Representative proteomes UniProt
(268360)
RP15
(13683)
RP35
(36188)
RP55
(73969)
RP75
(117964)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download  
Gzipped 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: Prosite
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Sonnhammer ELL , Finn RD
Number in seed: 211
Number in full: 78333
Average length of the domain: 88.20 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 19.91 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 57096847 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 27.5 27.5
Trusted cut-off 27.5 27.5
Noise cut-off 27.4 27.4
Model length: 89
Family (HMM) version: 31
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

Selections

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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 cNMP_binding domain has been found. There are 683 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 sequence.

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AlphaFold Structure Predictions

The list of proteins below match this family and have AlphaFold predicted structures. Click on the protein accession to view the predicted structure.

Protein Predicted structure External Information
A0A0B4KGS5 View 3D Structure Click here
A0A0G2K3D4 View 3D Structure Click here
A0A0G2KKD9 View 3D Structure Click here
A0A0K3AVF4 View 3D Structure Click here
A0A0P0V919 View 3D Structure Click here
A0A0R0F3C0 View 3D Structure Click here
A0A0R0F3J7 View 3D Structure Click here
A0A0R0LBA6 View 3D Structure Click here
A0A0R0LBA6 View 3D Structure Click here
A0A0R4IEI6 View 3D Structure Click here
A0A0R4IM06 View 3D Structure Click here
A0A0R4IM06 View 3D Structure Click here
A0A0R4IRW0 View 3D Structure Click here
A0A0R4IY63 View 3D Structure Click here
A0A142J9E8 View 3D Structure Click here
A0A1D6DWK0 View 3D Structure Click here
A0A1D6E9S9 View 3D Structure Click here
A0A1D6F9Z9 View 3D Structure Click here
A0A1D6FPS6 View 3D Structure Click here
A0A1D6G3C8 View 3D Structure Click here
A0A1D6GA20 View 3D Structure Click here
A0A1D6GBD0 View 3D Structure Click here
A0A1D6H5P9 View 3D Structure Click here
A0A1D6HBJ8 View 3D Structure Click here
A0A1D6HMV9 View 3D Structure Click here
A0A1D6HTC3 View 3D Structure Click here
A0A1D6IAL4 View 3D Structure Click here
A0A1D6JD17 View 3D Structure Click here
A0A1D6LTF1 View 3D Structure Click here
A0A1D6LW77 View 3D Structure Click here
A0A1D6M4T0 View 3D Structure Click here
A0A1D6MG59 View 3D Structure Click here
A0A1D6MVG1 View 3D Structure Click here
A0A1D6NHI0 View 3D Structure Click here
A0A1D6NTG0 View 3D Structure Click here
A0A1D6QNV1 View 3D Structure Click here
A0A1D6QNV1 View 3D Structure Click here
A0A1D6QP96 View 3D Structure Click here
A0A1D6QPH6 View 3D Structure Click here
A0A286Y9K1 View 3D Structure Click here
A0A286Y9K1 View 3D Structure Click here
A0A2R8Q8R8 View 3D Structure Click here
A0A2R8Q8R8 View 3D Structure Click here
A0A2R8QJW8 View 3D Structure Click here
A0A2R8QM30 View 3D Structure Click here
A0A2R8QNN9 View 3D Structure Click here
A0A2R8QQ34 View 3D Structure Click here
A0A2R8QQ34 View 3D Structure Click here
A0A2R8QRD5 View 3D Structure Click here
A0A2R8QTL4 View 3D Structure Click here
A0A2R8RKE8 View 3D Structure Click here
A0A2R8RTW7 View 3D Structure Click here
A0A2R8RZU5 View 3D Structure Click here
A1Z6P8 View 3D Structure Click here
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A1Z9N7 View 3D Structure Click here
A2AJ88 View 3D Structure Click here
A2AJ88 View 3D Structure Click here
A2AJ88 View 3D Structure Click here
A2ZX97 View 3D Structure Click here
A4HVF2 View 3D Structure Click here
A4HVF2 View 3D Structure Click here
A4I4G3 View 3D Structure Click here
A4I6E9 View 3D Structure Click here
A4I8L5 View 3D Structure Click here
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A4IA61 View 3D Structure Click here
A4IA61 View 3D Structure Click here
A4IAJ9 View 3D Structure Click here
A4ICQ1 View 3D Structure Click here
A8WHX9 View 3D Structure Click here
A8WI01 View 3D Structure Click here
A9C3T0 View 3D Structure Click here
A9C3T0 View 3D Structure Click here
B0S7I0 View 3D Structure Click here
B0S7I0 View 3D Structure Click here
B0S7I0 View 3D Structure Click here
B0V138 View 3D Structure Click here
B3DJX4 View 3D Structure Click here
B8JHY6 View 3D Structure Click here
B9F3N3 View 3D Structure Click here
C0PDL6 View 3D Structure Click here
D3ZTL8 View 3D Structure Click here
E1AZ71 View 3D Structure Click here
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E7F485 View 3D Structure Click here
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F1LS43 View 3D Structure Click here
F1LX27 View 3D Structure Click here
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F4HU51 View 3D Structure Click here
F4JHC9 View 3D Structure Click here
F6NQL8 View 3D Structure Click here
G5EEE2 View 3D Structure Click here
G5EFJ9 View 3D Structure Click here
H2KYN2 View 3D Structure Click here
I1JGQ1 View 3D Structure Click here
I1JK89 View 3D Structure Click here
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I1K1D3 View 3D Structure Click here
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I1K949 View 3D Structure Click here
I1K951 View 3D Structure Click here
I1KAP5 View 3D Structure Click here
I1KCH9 View 3D Structure Click here
I1KDG7 View 3D Structure Click here
I1KEI2 View 3D Structure Click here
I1KW21 View 3D Structure Click here
I1LT39 View 3D Structure Click here
I1LUV8 View 3D Structure Click here
I1M9L1 View 3D Structure Click here
I1MAJ1 View 3D Structure Click here
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I1MF38 View 3D Structure Click here
I1MUD0 View 3D Structure Click here
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I1N3P6 View 3D Structure Click here
I1NCK8 View 3D Structure Click here
I3ITL7 View 3D Structure Click here
K7KAI6 View 3D Structure Click here
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K7LG58 View 3D Structure Click here
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K7M132 View 3D Structure Click here
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M0R715 View 3D Structure Click here
M0R715 View 3D Structure Click here
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M0RB82 View 3D Structure Click here
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O05581 View 3D Structure Click here
O05884 View 3D Structure Click here
O08962 View 3D Structure Click here
O35219 View 3D Structure Click here
O54852 View 3D Structure Click here
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O60741 View 3D Structure Click here
O61827 View 3D Structure Click here
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O95259 View 3D Structure Click here
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P05987 View 3D Structure Click here
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P07278 View 3D Structure Click here
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P09456 View 3D Structure Click here
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P0A9E5 View 3D Structure Click here
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P0ACJ8 View 3D Structure Click here
P0C605 View 3D Structure Click here
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P10644 View 3D Structure Click here
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P12849 View 3D Structure Click here
P12849 View 3D Structure Click here
P13861 View 3D Structure Click here
P13861 View 3D Structure Click here
P16905 View 3D Structure Click here
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P29973 View 3D Structure Click here
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P30625 View 3D Structure Click here
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P31321 View 3D Structure Click here
P31321 View 3D Structure Click here
P31323 View 3D Structure Click here
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P31324 View 3D Structure Click here
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P34578 View 3D Structure Click here
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P36600 View 3D Structure Click here
P36600 View 3D Structure Click here
P59111 View 3D Structure Click here
P71915 View 3D Structure Click here
P81377 View 3D Structure Click here
P81377 View 3D Structure Click here
P81900 View 3D Structure Click here
P81900 View 3D Structure Click here
P92960 View 3D Structure Click here
P9WIY7 View 3D Structure Click here
P9WM61 View 3D Structure Click here
P9WMH3 View 3D Structure Click here
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Q00195 View 3D Structure Click here
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Q03611 View 3D Structure Click here
Q04958 View 3D Structure Click here
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Q08C49 View 3D Structure Click here
Q08C49 View 3D Structure Click here
Q09764 View 3D Structure Click here
Q0DDZ0 View 3D Structure Click here
Q0DNE3 View 3D Structure Click here
Q0GFG2 View 3D Structure Click here
Q0J9M1 View 3D Structure Click here
Q0JB40 View 3D Structure Click here
Q0JKV1 View 3D Structure Click here
Q12809 View 3D Structure Click here
Q13237 View 3D Structure Click here
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Q13976 View 3D Structure Click here
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Q14028 View 3D Structure Click here
Q16280 View 3D Structure Click here
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Q21534 View 3D Structure Click here
Q24278 View 3D Structure Click here
Q2FUY1 View 3D Structure Click here
Q32ME0 View 3D Structure Click here
Q38849 View 3D Structure Click here
Q38898 View 3D Structure Click here
Q38998 View 3D Structure Click here
Q39128 View 3D Structure Click here
Q3TRM4 View 3D Structure Click here
Q3TRM4 View 3D Structure Click here
Q3TRM4 View 3D Structure Click here
Q3UW12 View 3D Structure Click here
Q4CL33 View 3D Structure Click here
Q4CPG9 View 3D Structure Click here
Q4CSS9 View 3D Structure Click here
Q4CSS9 View 3D Structure Click here
Q4CY04 View 3D Structure Click here
Q4D1K8 View 3D Structure Click here
Q4D6P2 View 3D Structure Click here
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Q4DAR7 View 3D Structure Click here
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Q4DL64 View 3D Structure Click here
Q4DNL5 View 3D Structure Click here
Q4DSV5 View 3D Structure Click here
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Q4G0N8 View 3D Structure Click here
Q59V20 View 3D Structure Click here
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Q5A368 View 3D Structure Click here
Q5BK26 View 3D Structure Click here
Q5BK26 View 3D Structure Click here
Q5BK26 View 3D Structure Click here
Q5I0F6 View 3D Structure Click here
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Q5JM04 View 3D Structure Click here
Q5NCJ1 View 3D Structure Click here
Q5QNI1 View 3D Structure Click here
Q5TAH2 View 3D Structure Click here
Q60603 View 3D Structure Click here
Q60EI8 View 3D Structure Click here
Q61410 View 3D Structure Click here
Q61410 View 3D Structure Click here
Q62398 View 3D Structure Click here
Q62927 View 3D Structure Click here
Q63472 View 3D Structure Click here
Q64359 View 3D Structure Click here
Q64595 View 3D Structure Click here
Q64595 View 3D Structure Click here
Q652U9 View 3D Structure Click here
Q653P0 View 3D Structure Click here
Q653S0 View 3D Structure Click here
Q6K3D4 View 3D Structure Click here
Q6K3D4 View 3D Structure Click here
Q6K3T2 View 3D Structure Click here
Q6NW93 View 3D Structure Click here
Q6NW93 View 3D Structure Click here
Q6QI81 View 3D Structure Click here
Q6UJY2 View 3D Structure Click here
Q6ZV29 View 3D Structure Click here
Q6ZV29 View 3D Structure Click here
Q6ZV29 View 3D Structure Click here
Q75HP9 View 3D Structure Click here
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Q7KQK0 View 3D Structure Click here
Q7KQK0 View 3D Structure Click here
Q7T2E5 View 3D Structure Click here
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Q7XUW4 View 3D Structure Click here
Q7Z205 View 3D Structure Click here
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Q8IV77 View 3D Structure Click here
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Q8L7Z0 View 3D Structure Click here
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Q8MM62 View 3D Structure Click here
Q8MM62 View 3D Structure Click here
Q8MVR1 View 3D Structure Click here
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Q8NA66 View 3D Structure Click here
Q8NCM2 View 3D Structure Click here
Q8RWS9 View 3D Structure Click here
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Q8WZA2 View 3D Structure Click here
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Q920E3 View 3D Structure Click here
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Q96L42 View 3D Structure Click here
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Q9JKB0 View 3D Structure Click here
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Q9NQW8 View 3D Structure Click here
Q9NS40 View 3D Structure Click here
Q9P1Z3 View 3D Structure Click here
Q9QWS8 View 3D Structure Click here
Q9S9N5 View 3D Structure Click here
Q9SCX5 View 3D Structure Click here
Q9SJA4 View 3D Structure Click here
Q9SL29 View 3D Structure Click here
Q9SL76 View 3D Structure Click here
Q9SL76 View 3D Structure Click here
Q9SU64 View 3D Structure Click here
Q9U969 View 3D Structure Click here
Q9U969 View 3D Structure Click here
Q9U969 View 3D Structure Click here
Q9UL51 View 3D Structure Click here
Q9ULD8 View 3D Structure Click here
Q9USJ4 View 3D Structure Click here
Q9USJ4 View 3D Structure Click here
Q9VL34 View 3D Structure Click here
Q9VL34 View 3D Structure Click here
Q9VXJ8 View 3D Structure Click here
Q9VXK3 View 3D Structure Click here
Q9W2D5 View 3D Structure Click here
Q9WVJ0 View 3D Structure Click here
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