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	UNK_F_TYPE	e5zmmF1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: UNK_F_TYPE	ECOD (1.6)
F	HNH_5	e5zmmF2	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: HNH_5	ECOD (1.6)
E	UNK_F_TYPE	e5zmmE1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: UNK_F_TYPE	ECOD (1.6)
E	UNK_F_TYPE	e5zmmE3	A: a+b complex topology	X: head domain of ScoMcrA (From Topology)	H: head domain of ScoMcrA (From Topology)	T: head domain of ScoMcrA	F: UNK_F_TYPE	ECOD (1.6)
E	HNH_5	e5zmmE2	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: HNH_5	ECOD (1.6)
D	UNK_F_TYPE	e5zmmD3	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: UNK_F_TYPE	ECOD (1.6)
D	UNK_F_TYPE	e5zmmD2	A: alpha complex topology	X: sulfur-binding domain (SBD) of ScoMcrA (From Topology)	H: sulfur-binding domain (SBD) of ScoMcrA (From Topology)	T: sulfur-binding domain (SBD) of ScoMcrA	F: UNK_F_TYPE	ECOD (1.6)
D	UNK_F_TYPE	e5zmmD1	A: a+b complex topology	X: head domain of ScoMcrA (From Topology)	H: head domain of ScoMcrA (From Topology)	T: head domain of ScoMcrA	F: UNK_F_TYPE	ECOD (1.6)
D	HNH_5	e5zmmD4	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: HNH_5	ECOD (1.6)
C	UNK_F_TYPE	e5zmmC1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: UNK_F_TYPE	ECOD (1.6)
C	UNK_F_TYPE	e5zmmC3	A: a+b complex topology	X: head domain of ScoMcrA (From Topology)	H: head domain of ScoMcrA (From Topology)	T: head domain of ScoMcrA	F: UNK_F_TYPE	ECOD (1.6)
C	HNH_5	e5zmmC2	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: HNH_5	ECOD (1.6)
B	UNK_F_TYPE	e5zmmB4	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: UNK_F_TYPE	ECOD (1.6)
B	UNK_F_TYPE	e5zmmB2	A: beta barrels	X: Stalk domain of SBV glycoprotein Gc (From Topology)	H: Stalk domain of SBV glycoprotein Gc (From Topology)	T: Stalk domain of SBV glycoprotein Gc	F: UNK_F_TYPE	ECOD (1.6)
B	UNK_F_TYPE	e5zmmB1	A: a+b complex topology	X: head domain of ScoMcrA (From Topology)	H: head domain of ScoMcrA (From Topology)	T: head domain of ScoMcrA	F: UNK_F_TYPE	ECOD (1.6)
B	HNH_5	e5zmmB3	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: HNH_5	ECOD (1.6)
A	UNK_F_TYPE	e5zmmA1	A: beta barrels	X: cradle loop barrel	H: RIFT-related	T: PUA domain	F: UNK_F_TYPE	ECOD (1.6)
A	UNK_F_TYPE	e5zmmA3	A: a+b complex topology	X: head domain of ScoMcrA (From Topology)	H: head domain of ScoMcrA (From Topology)	T: head domain of ScoMcrA	F: UNK_F_TYPE	ECOD (1.6)
A	HNH_5	e5zmmA2	A: few secondary structure elements	X: His-Me finger endonucleases (From Homology)	H: His-Me finger endonucleases	T: His-Me finger endonucleases	F: HNH_5	ECOD (1.6)

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.