ATP cone

Available protein structures:
Pfam	structures / ECOD
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

ATP-cone
ATP-cone
	ribonucleotide reductase e441q mutant r1 protein from escherichia coli
Identifiers
Symbol	ATP-cone
Pfam	PF03477
InterPro	IPR005144
SCOP2	7r1r / SCOPe / SUPFAM
Pfam
Available protein structures:
Pfam	structures / ECOD
PDB	RCSB PDB; PDBe; PDBj
PDBsum	structure summary

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.

The ATP-cone domain also is a key part of NrdR, that controls transcription of ribonucleotide reductases in bacteria, in response to ATP and dATP levels. ^[4]

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. S2CID 8940689.
^ 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.
^ Rozman Grinberg, Inna; Martínez-Carranza, Markel; Bimai, Ornella; Nouaïria, Ghada; Shahid, Saher; Lundin, Daniel; Logan, Derek T.; Sjöberg, Britt-Marie; Stenmark, Pål (2022-05-16). "A nucleotide-sensing oligomerization mechanism that controls NrdR-dependent transcription of ribonucleotide reductases". Nature Communications. 13 (1). doi:10.1038/s41467-022-30328-1. ISSN 2041-1723. PMC 9110341. PMID 35577776.

This article incorporates text from the public domain Pfam and InterPro: IPR005144

[pmid10939243-1] 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.

[pmid8052308-2] Uhlin U, Eklund H (August 1994). "Structure of ribonucleotide reductase protein R1". Nature. 370 (6490): 533–9. doi:10.1038/370533a0. PMID 8052308. S2CID 8940689.

[pmid9309223-3] 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.

[4] Rozman Grinberg, Inna; Martínez-Carranza, Markel; Bimai, Ornella; Nouaïria, Ghada; Shahid, Saher; Lundin, Daniel; Logan, Derek T.; Sjöberg, Britt-Marie; Stenmark, Pål (2022-05-16). "A nucleotide-sensing oligomerization mechanism that controls NrdR-dependent transcription of ribonucleotide reductases". Nature Communications. 13 (1). doi:10.1038/s41467-022-30328-1. ISSN 2041-1723. PMC 9110341. PMID 35577776.

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ATP cone

References

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