4FCY | pdb_00004fcy

Crystal structure of the bacteriophage Mu transpososome

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	Homeodomain-like	8057699	3000001	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Homeodomain-like	8057698	3000001	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribonuclease H-like	8003608	3000143	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Mu transposase C-terminal domain-like	8003611	3000144	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Mu transposase C-terminal domain-like	8003611	3000144	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Homeodomain-like	8057698	3000001	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribonuclease H-like	8003608	3000143	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Homeodomain-like	8057699	3000001	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)
B	MMS1_N	e4fcyB1	A: a/b three-layered sandwiches	X: beta-propeller-like	H: beta-propeller	T: 7-bladed	F: MMS1_N	ECOD (v294.1)
A	AP_endonuc_2	e4fcyA1	A: a/b three-layered sandwiches	X: Cytochrome P450	H: Cytochrome P450	T: Cytochrome P450	F: AP_endonuc_2	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
B	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
B	2.30.30.130	Mainly Beta	Roll	SH3 type barrels.	Transposase, Mu, C-terminal	CATH (4.3.0)
B	6.10.250.2550	Special	Helix non-globular	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)
A	1.10.10.60	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Homeodomain-like	CATH (4.3.0)
A	3.30.420.10	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF09039	Mu DNA binding, I gamma subdomain (HTH_Tnp_Mu_2)	Mu DNA binding, I gamma subdomain	Members of this family are responsible for binding the DNA attachment sites at each end of the Mu genome. They adopt a secondary structure comprising a four helix bundle tightly packed around a hydrophobic core consisting of aliphatic and aromatic am ...	Members of this family are responsible for binding the DNA attachment sites at each end of the Mu genome. They adopt a secondary structure comprising a four helix bundle tightly packed around a hydrophobic core consisting of aliphatic and aromatic amino acid residues. Helices 1 and 2 are oriented antiparallel to each other. Helix 3 crosses helices 1 and 2 at angles of 60 and 120 degrees, respectively. Excluding the C-terminal helix 4, the fold of the I-gamma subdomain is remarkably similar to that of the homeodomain family of helix-turn-helix DNA-binding proteins, although their amino acid sequences are completely unrelated [1].	Domain
A, B	PF09299	Mu transposase, C-terminal (Mu-transpos_C)	Mu transposase, C-terminal	Members of this family are found in various prokaryotic integrases and transposases. They adopt a beta-barrel structure with Greek-key topology [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
E [auth D]	DNA (49-MER)	-	-	-
D [auth E]	DNA (13-MER)	-	-	-
C	DNA (68-MER)	-	-	-
A, B	Transposase	DNA endonuclease activity endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid hydrolase activity double-stranded DNA endonuclease activity catalytic activity DNA nuclease activity DNA binding binding nucleic acid binding transposase activity DNA endonuclease activity endonuclease activity hydrolase activity, acting on ester bonds catalytic activity, acting on DNA nuclease activity catalytic activity, acting on a nucleic acid hydrolase activity double-stranded DNA endonuclease activity catalytic activity DNA nuclease activity DNA binding binding nucleic acid binding transposase activity ligase activity cation binding ion 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 DNA recombination transposition DNA transposition latent virus replication viral process viral latency nucleobase-containing compound metabolic process DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process DNA recombination transposition DNA transposition latent virus replication viral process viral latency release from viral latency latency-replication decision viral DNA genome replication viral life cycle nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid biosynthetic process biosynthetic process viral genome replication DNA biosynthetic process cellular response to stimulus response to stimulus cellular response to stress DNA damage response response to stress DNA repair DNA integration	host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region other organism part

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR036397	Ribonuclease H superfamily	Homologous Superfamily
A, B	IPR009061	Putative DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR009057	Homedomain-like superfamily	Homologous Superfamily
A, B	IPR009004	Transposase, Mu, C-terminal	Homologous Superfamily
A, B	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
A, B	IPR004189	Bacteriophage Mu, transposase	Domain
A, B	IPR003314	Mu-type HTH domain	Domain
A, B	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, B	IPR015126	Mu DNA binding, I gamma subdomain	Domain
A, B	IPR015378	Transposase-like, Mu, C-terminal	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.