3SSC | pdb_00003ssc

DNA binding domain of restriction endonuclease bound to DNA

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	MrcB N-terminal domain-like	8106443	3002855	SCOP2B (2022-06-29)
A	SCOP2 Family	MrcB N-terminal domain-like	8047208	4005504	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	MrcB N-terminal domain-like	8106443	3002855	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B		e3sscB1	A: beta-Grasp	X: Ubiquitin-related	H: Ubiquitin-like	T: ABC_tran	F:	ECOD (20:10:01)
A		e3sscA1	A: P-loop domains-like	X: Protein kinase/SAICAR synthase/ATP-grasp	H: Protein kinase	T: Ribosomal_S30AE	F:	ECOD (20:10:01)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	3.30.920.90	Alpha Beta	2-Layer Sandwich	Metal Transport, Frataxin	Chain A	CATH (4.3.0)
A	3.30.920.90	Alpha Beta	2-Layer Sandwich	Metal Transport, Frataxin	Chain A	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF12102	MrcB-like, N-terminal domain (MrcB_N)	MrcB-like, N-terminal domain	This model describes the N-terminal domain of a group of mostly uncharacterised proteins, including 5-methylcytosine-specific restriction enzyme B (also known as MrcB) from E. coli. MrcB recognises N4- and C5-methylcytosine (and 5-hydroxy-methylcytos ...	This model describes the N-terminal domain of a group of mostly uncharacterised proteins, including 5-methylcytosine-specific restriction enzyme B (also known as MrcB) from E. coli. MrcB recognises N4- and C5-methylcytosine (and 5-hydroxy-methylcytosines) produced by a broad range of DNA methylases and appears to act against 5-methylcytosine preceded by a purine residue [1]. The N-terminal domain of MrcB has been shown to be a DNA-binding domain, and the crystal structure has been solved [2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
D	DNA (5'-D(APGPCPTPAP(5CM)PCPGPGPTPCPTP*C)-3')	-	-	-
C	DNA (5'-D(TPGPAPGPAP(5CM)PCPGPGPTPAPGP*C)-3')	-	-	-
A, B	5-methylcytosine-specific restriction enzyme B	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding double-stranded DNA binding double-stranded methylated DNA binding pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid hemi-methylated DNA-binding guanyl nucleotide binding GTP binding guanyl ribonucleotide binding GTPase activity identical protein binding protein binding restriction endodeoxyribonuclease activity DNA endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA DNA nuclease activity	catabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process biological process involved in interspecies interaction between organisms response to stimulus catabolic process primary metabolic process DNA metabolic process nucleic acid metabolic process macromolecule catabolic process nucleobase-containing compound catabolic process nucleobase-containing compound metabolic process DNA catabolic process nucleic acid catabolic process metabolic process cellular process macromolecule metabolic process biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response DNA restriction-modification system defense response to symbiont response to external stimulus clearance of foreign intracellular DNA clearance of foreign intracellular nucleic acids response to biotic stimulus DNA modification defense response to other organism response to stress macromolecule modification response to external biotic stimulus	protein-containing complex catalytic complex intracellular protein-containing complex endonuclease complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR011704	ATPase, dynein-related, AAA domain	Domain
A, B	IPR052934	Methylated DNA Recognition and Restriction Enzymes	Family
A, B	IPR021961	Type IV methyl-directed restriction enzyme EcoKMcrB subunit, DNA-binding domain	Domain
A, B	IPR003593	AAA+ ATPase domain	Domain
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.