Summary: ATP cone domain
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ATP cone Edit Wikipedia article
ATP-cone | |||||||||
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![]() ribonucleotide reductase e441q mutant r1 protein from escherichia coli
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Identifiers | |||||||||
Symbol | ATP-cone | ||||||||
Pfam | PF03477 | ||||||||
InterPro | IPR005144 | ||||||||
SCOP | 7r1r | ||||||||
SUPERFAMILY | 7r1r | ||||||||
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In molecular biology, the ATP-cone is an evolutionarily mobile, ATP-binding regulatory domain which is found in a variety of proteins including ribonucleotide reductases, phosphoglycerate kinases and transcriptional regulators.[1]
In ribonucleotide reductase protein R1 from Escherichia coli this domain is located at the N terminus, and is composed mostly of helices.[2] It forms part of the allosteric effector region and contains the general allosteric activity site in a cleft located at the tip of the N-terminal region.[3] This site binds either ATP (activating) or dATP (inhibitory), with the base bound in a hydrophobic pocket and the phosphates bound to basic residues. Substrate binding to this site is thought to affect enzyme activity by altering the relative positions of the two subunits of ribonucleotide reductase.
References
- ^ Aravind L, Wolf YI, Koonin EV (April 2000). "The ATP-cone: an evolutionarily mobile, ATP-binding regulatory domain". J. Mol. Microbiol. Biotechnol. 2 (2): 191–4. PMID 10939243.
- ^ Uhlin U, Eklund H (August 1994). "Structure of ribonucleotide reductase protein R1". Nature. 370 (6490): 533–9. doi:10.1038/370533a0. PMID 8052308.
- ^ Eriksson M, Uhlin U, Ramaswamy S, Ekberg M, Regnstrom K, Sjoberg BM, Eklund H (August 1997). "Binding of allosteric effectors to ribonucleotide reductase protein R1: reduction of active-site cysteines promotes substrate binding". Structure. 5 (8): 1077–92. doi:10.1016/S0969-2126(97)00259-1. PMID 9309223.
This article incorporates text from the public domain Pfam and InterPro IPR005144
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Literature references
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Aravind L, Wolf YI, Koonin EV; , J Mol Microbiol Biotechnol 2000;2:191-194.: The ATP-cone: an evolutionarily mobile, ATP-binding regulatory domain. PUBMED:10939243 EPMC:10939243
External database links
SCOP: | 7r1r |
This tab holds annotation information from the InterPro database.
InterPro entry IPR005144
The ATP-cone is an evolutionarily mobile, ATP-binding regulatory domain which is found in a variety of proteins including ribonucleotide reductases, phosphoglycerate kinases and transcriptional regulators [PUBMED:10939243].
In ribonucleotide reductase protein R1 (SWISSPROT) from Escherichia coli this domain is located at the N terminus, and is composed mostly of helices [PUBMED:8052308]. It forms part of the allosteric effector region and contains the general allosteric activity site in a cleft located at the tip of the N-terminal region [PUBMED:9309223]. This site binds either ATP (activating) or dATP (inhibitory), with the base bound in a hydrophobic pocket and the phosphates bound to basic residues. Substrate binding to this site is thought to affect enzyme activity by altering the relative positions of the two subunits of ribonucleotide reductase.
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, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...
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Seed (129) |
Full (12549) |
Representative proteomes | UniProt (58411) |
NCBI (65864) |
Meta (3565) |
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RP15 (2103) |
RP35 (6304) |
RP55 (12123) |
RP75 (21026) |
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PP/heatmap | 1 |
1Cannot generate PP/Heatmap alignments for seeds; no PP data available
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Seed (129) |
Full (12549) |
Representative proteomes | UniProt (58411) |
NCBI (65864) |
Meta (3565) |
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---|---|---|---|---|---|---|---|---|---|
RP15 (2103) |
RP35 (6304) |
RP55 (12123) |
RP75 (21026) |
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Raw Stockholm | |||||||||
Gzipped |
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.
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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
Seed source: | Aravind L |
Previous IDs: | none |
Type: | Domain |
Sequence Ontology: | SO:0000417 |
Author: |
Aravind L |
Number in seed: | 129 |
Number in full: | 12549 |
Average length of the domain: | 89.20 aa |
Average identity of full alignment: | 25 % |
Average coverage of the sequence by the domain: | 18.47 % |
HMM information
HMM build commands: |
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 47079205 -E 1000 --cpu 4 HMM pfamseq
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Model details: |
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Model length: | 86 | ||||||||||||
Family (HMM) version: | 17 | ||||||||||||
Download: | download the raw HMM for this family |
Species distribution
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Interactions
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 ATP-cone domain has been found. There are 130 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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