5ZMM | pdb_00005zmm

Structure of the Type IV phosphorothioation-dependent restriction endonuclease ScoMcrA

External Resource: Annotation

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

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	HNH	e5zmmF1	A: a/b three-layered sandwiches	X: PriB N-terminal domain-like	H: Aconitase iron-sulfur domain	T: Aconitase iron-sulfur domain	F: HNH	ECOD (v294.1)
E	HNH	e5zmmE1	A: a/b three-layered sandwiches	X: HUP domain-like	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: HNH	ECOD (v294.1)
D	HNH	e5zmmD4	A: a/b three-layered sandwiches	X: P-loop domains-like	H: a+b domain in acetyl-CoA synthetase-like proteins	T: a+b domain in acetyl-CoA synthetase-like proteins	F: HNH	ECOD (v294.1)
C	HNH	e5zmmC1	A: a/b three-layered sandwiches	X: HUP domain-like	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: HNH	ECOD (v294.1)
B	RAI1	e5zmmB3	A: a/b three-layered sandwiches	X: P-loop domains-like	H: a+b domain in acetyl-CoA synthetase-like proteins	T: a+b domain in acetyl-CoA synthetase-like proteins	F: RAI1	ECOD (v294.1)
B	ATP-gua_Ptrans	e5zmmB4	A: a/b three-layered sandwiches	X: Ten stranded beta/alpha barrel	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: ATP-gua_Ptrans	ECOD (v294.1)
A	HNH	e5zmmA1	A: a/b three-layered sandwiches	X: HUP domain-like	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: HNH	ECOD (v294.1)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F	PF01844	HNH endonuclease (HNH)	HNH endonuclease	-	Family
A, B, C, D, E A, B, C, D, E, F	PF26348	ScoMcrA-like, SRA domain (SRA_ScoMcrA)	ScoMcrA-like, SRA domain	This entry represents the SRA domain found in the endonuclease ScoMcrA and related type IV restriction enzymes. This domain has a detectable similarity to known PUA domains. The ScoMcrA SRA domain mediates dimerization and does not engage in interact ...	This entry represents the SRA domain found in the endonuclease ScoMcrA and related type IV restriction enzymes. This domain has a detectable similarity to known PUA domains. The ScoMcrA SRA domain mediates dimerization and does not engage in interactions with the phosphorothioated DNA [1].	Domain
A, B, C, D, E A, B, C, D, E, F	PF26345	ScoMcrA-like, N-terminal head domain (ScoMcrA_N)	ScoMcrA-like, N-terminal head domain	This entry represents the N-terminal head domain found in the endonuclease ScoMcrA and related type IV restriction enzymes. This domain exhibits substantial positional variance with respect to the other domains of ScoMcrA [1]. It folds into an alpha/ ...	This entry represents the N-terminal head domain found in the endonuclease ScoMcrA and related type IV restriction enzymes. This domain exhibits substantial positional variance with respect to the other domains of ScoMcrA [1]. It folds into an alpha/beta structure composed of three-stranded antiparallel beta-sheet and array of alpha-helices packed on it. The function of this domain is unknown.	Domain
A, B, C, D, E A, B, C, D, E, F	PF26340	ScoMcrA-like, DNA sulfur-binding domain (DNA-SBD_ScoMcrA)	ScoMcrA-like, DNA sulfur-binding domain	This entry represents the DNA sulfur-binding domain (SBD) found in the endonuclease ScoMcrA and related type IV restriction enzymes. This domain recognises the sulfur atom in phosphorothioated DNA (PT-DNA). The recognition of the PT-DNA by SBD is pho ...	This entry represents the DNA sulfur-binding domain (SBD) found in the endonuclease ScoMcrA and related type IV restriction enzymes. This domain recognises the sulfur atom in phosphorothioated DNA (PT-DNA). The recognition of the PT-DNA by SBD is phosphorothioate-dependent and also DNA sequence-specific [1,2]. Residues involved in sulfur recognition are highly conserved across homologues. This domain adopts an alpha/beta fold consisting of a small three-stranded beta-sheet elaborated with alpha-helices [1,2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	Uncharacterized protein McrA	binding nucleic acid binding endonuclease activity nuclease activity catalytic activity, acting on a nucleic acid catalytic activity cation binding transition metal ion binding zinc ion binding ion binding metal ion binding small molecule binding	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR058813	ScoMcrA-like, DNA sulfur-binding domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR058712	ScoMcrA-like, SRA domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR058807	ScoMcrA-like, N-terminal head domain	Domain
A, B, C, D, E A, B, C, D, E, F	IPR003615	HNH nuclease	Domain
A, B, C, D, E A, B, C, D, E, F	IPR002711	HNH endonuclease	Domain

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.