1H7A

Structural basis for allosteric substrate specificity regulation in class III ribonucleotide reductases: NRDD in complex with dATP

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Structure Motif: Primary M-CSA Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1h7aa_	Alpha and beta proteins (a/b)	PFL-like glycyl radical enzymes	PFL-like glycyl radical enzymes	Class III anaerobic ribonucleotide reductase NRDD subunit	Class III anaerobic ribonucleotide reductase NRDD subunit	(Tequatrovirus T4 ) [TaxId: 10665 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8044519	3001069	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	NRDD	e1h7aA1	A: a/b barrels	X: Ten stranded beta/alpha barrel (From Topology)	H: Ten stranded beta/alpha barrel (From Topology)	T: Ten stranded beta/alpha barrel	F: NRDD	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.20.70.20	Alpha Beta	Alpha-Beta Barrel	Anaerobic Ribonucleotide-triphosphate Reductase Large Chain		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A	PF01228	Glycine radical (Gly_radical)	Glycine radical		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A	ANAEROBIC RIBONUCLEOTIDE-TRIPHOSPHATE REDUCTASE LARGE CHAIN	ribonucleoside-diphosphate reductase activity oxidoreductase activity oxidoreductase activity, acting on CH or CH2 groups oxidoreductase activity, acting on CH or CH2 groups, disulfide as acceptor ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor catalytic activity ribonucleoside-triphosphate reductase (thioredoxin) activity cation binding ion binding binding metal ion binding small molecule binding	nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process deoxyribose phosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process deoxyribonucleotide biosynthetic process deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process deoxyribose phosphate biosynthetic process nucleotide biosynthetic process carbohydrate derivative metabolic process deoxyribonucleotide biosynthetic process deoxyribonucleotide metabolic process nucleobase-containing small molecule metabolic process phosphate-containing compound metabolic process small molecule metabolic process phosphorus metabolic process nucleoside phosphate metabolic process carbohydrate derivative biosynthetic process 2'-deoxyribonucleotide metabolic process 2'-deoxyribonucleotide biosynthetic process nucleotide metabolic process deoxyribose phosphate metabolic process nucleobase-containing compound biosynthetic process biosynthetic process organophosphate metabolic process organophosphate biosynthetic process nucleoside phosphate biosynthetic process	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR001150	Glycine radical domain	Domain
A	IPR012833	Ribonucleoside-triphosphate reductase, anaerobic	Family
A	IPR019777	Formate C-acetyltransferase glycine radical, conserved site	Conserved Site

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

Chains	Enzyme Name	Description	Catalytic Residues
A	ribonucleoside-triphosphate reductase (class III) M-CSA #416	Ribonucleotide reductases (RNRs) catalyse the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. Providing the precursors necessary for DNA synthesis. This is a class III (anaerobic) RNR. The mechanism of the enzyme involves a glycine-centred radical (which is formed by the radical SAM superfamily protein NrdG). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. The class III enzyme from phage T4 consists of two subunits, the larger of which contains the active and allosteric sites. The protein binds a zinc ion in a position remote from the active site which has been shown to be critical for function. It is thought that this metal ion is responsible for protecting the enzyme from loss of its ground state radical.	Defined by 9 residues: ASN:A-78CYS:A-79MET:A-288CYS:A-290SER:A-292ASN:A-311TYR:A-441GLU:A-446ALA:A-580 \| Explore in 3D: M-CSA Motif Definition Search M-CSA Motif EC: 1.17.4.2 (PDB Primary Data) Search M-CSA Motif + EC 1.17.4.2 EC: 1.1.98.6 (UniProt) Search M-CSA Motif + EC 1.1.98.6

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.