1L1L | pdb_00001l1l

CRYSTAL STRUCTURE OF B-12 DEPENDENT (CLASS II) RIBONUCLEOTIDE REDUCTASE

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	d1l1la_	Alpha and beta proteins (a/b)	PFL-like glycyl radical enzymes	PFL-like glycyl radical enzymes	B12-dependent (class II) ribonucleotide reductase	B12-dependent (class II) ribonucleotide reductase	(Lactobacillus leichmannii ) [TaxId: 28039 ],	SCOPe (2.08)
B	d1l1lb_	Alpha and beta proteins (a/b)	PFL-like glycyl radical enzymes	PFL-like glycyl radical enzymes	B12-dependent (class II) ribonucleotide reductase	B12-dependent (class II) ribonucleotide reductase	(Lactobacillus leichmannii ) [TaxId: 28039 ],	SCOPe (2.08)
C	d1l1lc_	Alpha and beta proteins (a/b)	PFL-like glycyl radical enzymes	PFL-like glycyl radical enzymes	B12-dependent (class II) ribonucleotide reductase	B12-dependent (class II) ribonucleotide reductase	(Lactobacillus leichmannii ) [TaxId: 28039 ],	SCOPe (2.08)
D	d1l1ld_	Alpha and beta proteins (a/b)	PFL-like glycyl radical enzymes	PFL-like glycyl radical enzymes	B12-dependent (class II) ribonucleotide reductase	B12-dependent (class II) ribonucleotide reductase	(Lactobacillus leichmannii ) [TaxId: 28039 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2 Family	B12-dependent (class II) ribonucleotide reductase	8028585	4002265	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	PFL-like glycyl radical enzymes	8040964	3001069	SCOP2 (2022-06-29)
B	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8040964	3001069	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8040964	3001069	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PFL-like glycyl radical enzymes	8040964	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	RTPR	e1l1lA1	A: alpha arrays	X: Alpha helical domain of ribonucleotide reductases (From Topology)	H: Alpha helical domain of ribonucleotide reductases (From Topology)	T: Alpha helical domain of ribonucleotide reductases	F: RTPR	ECOD (1.6)
A	Ribonuc_red_lgC_1	e1l1lA2	A: a+b three layers	X: B12-dependent (class II) ribonucleotide reductase, insertion domain (From Topology)	H: B12-dependent (class II) ribonucleotide reductase, insertion domain (From Topology)	T: B12-dependent (class II) ribonucleotide reductase, insertion domain	F: Ribonuc_red_lgC_1	ECOD (1.6)
A	Ribonuc_red_lgC	e1l1lA3	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: Ribonuc_red_lgC	ECOD (1.6)
B	RTPR	e1l1lB1	A: alpha arrays	X: Alpha helical domain of ribonucleotide reductases (From Topology)	H: Alpha helical domain of ribonucleotide reductases (From Topology)	T: Alpha helical domain of ribonucleotide reductases	F: RTPR	ECOD (1.6)
B	Ribonuc_red_lgC_1	e1l1lB2	A: a+b three layers	X: B12-dependent (class II) ribonucleotide reductase, insertion domain (From Topology)	H: B12-dependent (class II) ribonucleotide reductase, insertion domain (From Topology)	T: B12-dependent (class II) ribonucleotide reductase, insertion domain	F: Ribonuc_red_lgC_1	ECOD (1.6)
B	Ribonuc_red_lgC	e1l1lB3	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: Ribonuc_red_lgC	ECOD (1.6)
C	RTPR	e1l1lC1	A: alpha arrays	X: Alpha helical domain of ribonucleotide reductases (From Topology)	H: Alpha helical domain of ribonucleotide reductases (From Topology)	T: Alpha helical domain of ribonucleotide reductases	F: RTPR	ECOD (1.6)
C	Ribonuc_red_lgC_1	e1l1lC2	A: a+b three layers	X: B12-dependent (class II) ribonucleotide reductase, insertion domain (From Topology)	H: B12-dependent (class II) ribonucleotide reductase, insertion domain (From Topology)	T: B12-dependent (class II) ribonucleotide reductase, insertion domain	F: Ribonuc_red_lgC_1	ECOD (1.6)
C	Ribonuc_red_lgC	e1l1lC3	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: Ribonuc_red_lgC	ECOD (1.6)
D	RTPR	e1l1lD1	A: alpha arrays	X: Alpha helical domain of ribonucleotide reductases (From Topology)	H: Alpha helical domain of ribonucleotide reductases (From Topology)	T: Alpha helical domain of ribonucleotide reductases	F: RTPR	ECOD (1.6)
D	Ribonuc_red_lgC_1	e1l1lD2	A: a+b three layers	X: B12-dependent (class II) ribonucleotide reductase, insertion domain (From Topology)	H: B12-dependent (class II) ribonucleotide reductase, insertion domain (From Topology)	T: B12-dependent (class II) ribonucleotide reductase, insertion domain	F: Ribonuc_red_lgC_1	ECOD (1.6)
D	Ribonuc_red_lgC	e1l1lD3	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: Ribonuc_red_lgC	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)
A	3.30.1620.10	Alpha Beta	2-Layer Sandwich	b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2	b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2	CATH (4.3.0)
A	3.90.1390.10	Alpha Beta	Alpha-Beta Complex	b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3	b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3	CATH (4.3.0)
B	3.20.70.20	Alpha Beta	Alpha-Beta Barrel	Anaerobic Ribonucleotide-triphosphate Reductase Large Chain		CATH (4.3.0)
B	3.30.1620.10	Alpha Beta	2-Layer Sandwich	b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2	b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2	CATH (4.3.0)
B	3.90.1390.10	Alpha Beta	Alpha-Beta Complex	b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3	b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3	CATH (4.3.0)
C	3.20.70.20	Alpha Beta	Alpha-Beta Barrel	Anaerobic Ribonucleotide-triphosphate Reductase Large Chain		CATH (4.3.0)
C	3.30.1620.10	Alpha Beta	2-Layer Sandwich	b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2	b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2	CATH (4.3.0)
C	3.90.1390.10	Alpha Beta	Alpha-Beta Complex	b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3	b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3	CATH (4.3.0)
D	3.20.70.20	Alpha Beta	Alpha-Beta Barrel	Anaerobic Ribonucleotide-triphosphate Reductase Large Chain		CATH (4.3.0)
D	3.30.1620.10	Alpha Beta	2-Layer Sandwich	b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2	b-12 dependent (class ii) ribonucleotide reductase, Chain A, Domain 2	CATH (4.3.0)
D	3.90.1390.10	Alpha Beta	Alpha-Beta Complex	b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3	b-12 dependent (class ii) ribonucleotide reductase, chain A, domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF17975	Ribonucleotide reductase alpha domain (RNR_Alpha)	Ribonucleotide reductase alpha domain	This is the alpha helical domain of ribonucleotide reductases. Family members include Ribonucleotide reductase (RNR, EC:1.17.4.1) [1, 2] which catalyse the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provi ...	This is the alpha helical domain of ribonucleotide reductases. Family members include Ribonucleotide reductase (RNR, EC:1.17.4.1) [1, 2] which catalyse the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs divide into three classes on the basis of their metallocofactor usage. This domain is found in Class II. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Many organisms have more than one class of RNR present in their genomes. Ribonucleotide reductase is an oligomeric enzyme composed of a large sub-unit (700 to 1000 residues) and a small sub-unit (300 to 400 residues) - class II RNRs are less complex, using the small molecule B12 in place of the small chain [3]. Some family members carry ATP cone domain which acts as a functional regulator. Competitive binding of ATP and dATP to an N-terminal ATP-cone domain determines enzyme activity. As the ratio of dATP to ATP increases above a certain threshold, the enzyme activity is turned off. Substrate nucleotides are recognised by relatively simple H-bonding interactions at the N-terminus of one or more alpha helices. In the monomeric class II RNR, the effector binds in a pocket formed by helices in a 130 amino acid insertion which constitutes this domain [4].	Domain
A, B, C, D	PF21995	B12-dependent ribonucleotide reductase, insertion domain (RNR-II_ins_dom)	B12-dependent ribonucleotide reductase, insertion domain	This entry represents the insertion domain of adenosylcobalamin-dependent ribonucleoside-triphosphate reductases (class II RNRs) from Lactococcus leichmannii and related sequences. RNR's are responsible for the conversion of the ribose sugar of RNA i ...	This entry represents the insertion domain of adenosylcobalamin-dependent ribonucleoside-triphosphate reductases (class II RNRs) from Lactococcus leichmannii and related sequences. RNR's are responsible for the conversion of the ribose sugar of RNA into the deoxyribose sugar of DNA, a rate-limiting step of DNA biosynthesis. RNRs are classified in class I, II and III [1]. Class II RNRs are less complex and function as a monomer in contrast to class I and III RNRs, which controls substrate specificity as efficiently as a multimeric enzymes. This insertion domain provides the interface responsible for effector binding that, in oligomeric RNRs, is formed in the dimer interface [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	RIBONUCLEOSIDE TRIPHOSPHATE REDUCTASE	vitamin binding binding cobalamin binding tetrapyrrole binding heterocyclic compound binding small molecule binding 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 nucleoside phosphate binding vitamin binding binding cobalamin binding tetrapyrrole binding heterocyclic compound binding small molecule binding 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 nucleoside phosphate binding nucleotide 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	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR013345	Ribonucleoside-triphosphate reductase, adenosylcobalamin-dependent	Family
A, B, C, D	IPR054158	B12-dependent ribonucleotide reductase, insertion domain	Domain
A, B, C, D	IPR050862	Ribonucleoside diphosphate reductase class-2	Family
A, B, C, D	IPR040763	Ribonucleotide reductase, alpha helical domain	Domain

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

Chains	Enzyme Name	Description	Catalytic Residues
A	ribonucleoside-triphosphate reductase (class II) M-CSA #140	Ribonucleotide reductase (RNR) is the enzyme responsible for the conversion of the four standard ribonucleotides, 5V -di(or tri)-phospho -adenosine, -cytidine, -guanosine, and -uridine, to their 2V -deoxyribonucleotide counterparts and thereby provides the precursors needed for both synthesis and repair of DNA. Class II enzymes are found in bacteria that can live under both aerobic and anaerobic conditions, and also in some of their phages. The prototype from this class is the monomeric enzyme from Lactobacillus leichmannii , but as more and more members of this class have been found that are predominately homodimers, the Lactobacillus enzyme seems to be rather an extreme of the class. They all, however, utilize a cobaltous cofactor, adenosylcobalamin, a vitamin B12 derivative, that interacts directly with an active site cysteine to form the reactive cysteine radical needed for ribonucleotide reduction.	Defined by 7 residues: CYS:A-119ASN:A-406CYS:A-408GLU:A-410CYS:A-419CYS:A-731CYS:A-736 Some residues are not modelled and lack atomic coordinates. Visualization is not available. Some residues are not modelled and lack atomic coordinates. Structure Motif searching is not available. EC: 1.17.4.2 (PDB Primary Data)

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.