7NZ3

Cryo-EM structure of apposed MukBEF-MatP monomers on DNA

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)
E [auth C1]	PF17193	e7nz3C12	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF17193	ECOD (1.6)
E [auth C1]	PF17192,PF17193	e7nz3C11	A: alpha bundles	X: STAT-like	H: MukF C-terminal domain-like (From Topology)	T: MukF C-terminal domain-like	F: PF17192,PF17193	ECOD (1.6)
F [auth C2]	PF17193	e7nz3C22	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF17193	ECOD (1.6)
F [auth C2]	PF17192,PF17193	e7nz3C21	A: alpha bundles	X: STAT-like	H: MukF C-terminal domain-like (From Topology)	T: MukF C-terminal domain-like	F: PF17192,PF17193	ECOD (1.6)
G [auth D1]	PF03882	e7nz3D11	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF03882	ECOD (1.6)
H [auth D2]	PF03882	e7nz3D21	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF03882	ECOD (1.6)
I [auth E1]	PF04288	e7nz3E12	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF04288	ECOD (1.6)
I [auth E1]	PF04288	e7nz3E11	A: a+b two layers	X: Chromosome partition protein mukE N-terminal domain (From Topology)	H: Chromosome partition protein mukE N-terminal domain (From Topology)	T: Chromosome partition protein mukE N-terminal domain	F: PF04288	ECOD (1.6)
K [auth F1]	PF04288	e7nz3F12	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF04288	ECOD (1.6)
K [auth F1]	PF04288	e7nz3F11	A: a+b two layers	X: Chromosome partition protein mukE N-terminal domain (From Topology)	H: Chromosome partition protein mukE N-terminal domain (From Topology)	T: Chromosome partition protein mukE N-terminal domain	F: PF04288	ECOD (1.6)
J [auth E2]	PF04288	e7nz3E22	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF04288	ECOD (1.6)
J [auth E2]	PF04288	e7nz3E21	A: a+b two layers	X: Chromosome partition protein mukE N-terminal domain (From Topology)	H: Chromosome partition protein mukE N-terminal domain (From Topology)	T: Chromosome partition protein mukE N-terminal domain	F: PF04288	ECOD (1.6)
L [auth F2]	PF04288	e7nz3F21	A: alpha arrays	X: HTH	H: HTH	T: winged	F: PF04288	ECOD (1.6)
L [auth F2]	PF04288	e7nz3F22	A: a+b two layers	X: Chromosome partition protein mukE N-terminal domain (From Topology)	H: Chromosome partition protein mukE N-terminal domain (From Topology)	T: Chromosome partition protein mukE N-terminal domain	F: PF04288	ECOD (1.6)
N [auth G2]	PF00550	e7nz3G21	A: alpha bundles	X: ACP-like	H: Acyl-carrier protein (ACP) (From Topology)	T: Acyl-carrier protein (ACP)	F: PF00550	ECOD (1.6)
M [auth G1]	PF00550	e7nz3G11	A: alpha bundles	X: ACP-like	H: Acyl-carrier protein (ACP) (From Topology)	T: Acyl-carrier protein (ACP)	F: PF00550	ECOD (1.6)
O [auth H1]	PF00550	e7nz3H11	A: alpha bundles	X: ACP-like	H: Acyl-carrier protein (ACP) (From Topology)	T: Acyl-carrier protein (ACP)	F: PF00550	ECOD (1.6)
P [auth H2]	PF00550	e7nz3H21	A: alpha bundles	X: ACP-like	H: Acyl-carrier protein (ACP) (From Topology)	T: Acyl-carrier protein (ACP)	F: PF00550	ECOD (1.6)
S [auth J1]	PF17414	e7nz3J11	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF17414	ECOD (1.6)
S [auth J1]	PF06303	e7nz3J12	A: alpha arrays	X: Macrodomain Ter protein MatP (From Topology)	H: Macrodomain Ter protein MatP (From Topology)	T: Macrodomain Ter protein MatP	F: PF06303	ECOD (1.6)
Q [auth I1]	PF17414	e7nz3I12	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF17414	ECOD (1.6)
Q [auth I1]	PF06303	e7nz3I11	A: alpha arrays	X: Macrodomain Ter protein MatP (From Topology)	H: Macrodomain Ter protein MatP (From Topology)	T: Macrodomain Ter protein MatP	F: PF06303	ECOD (1.6)
R [auth I2]	PF17414	e7nz3I22	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF17414	ECOD (1.6)
R [auth I2]	PF06303	e7nz3I21	A: alpha arrays	X: Macrodomain Ter protein MatP (From Topology)	H: Macrodomain Ter protein MatP (From Topology)	T: Macrodomain Ter protein MatP	F: PF06303	ECOD (1.6)
T [auth J2]	PF17414	e7nz3J22	A: alpha arrays	X: HTH	H: HTH	T: Ribbon-helix-helix	F: PF17414	ECOD (1.6)
T [auth J2]	PF06303	e7nz3J21	A: alpha arrays	X: Macrodomain Ter protein MatP (From Topology)	H: Macrodomain Ter protein MatP (From Topology)	T: Macrodomain Ter protein MatP	F: PF06303	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth A1], B [auth A2], C [auth B1], D [auth B2]	PF13558	SbcC/RAD50-like, Walker B motif (SbcC_Walker_B)	SbcC/RAD50-like, Walker B motif	This entry represents the Walker B domain of RAD50 from eukaryotes and the prokaryotic homologue SbcCD complex subunit C. RAD50-ATPase forms a complex with Mre11-nuclease that detects and processes diverse and obstructed DNA ends. This domain is sepa ...	This entry represents the Walker B domain of RAD50 from eukaryotes and the prokaryotic homologue SbcCD complex subunit C. RAD50-ATPase forms a complex with Mre11-nuclease that detects and processes diverse and obstructed DNA ends. This domain is separated of the Walker A domain by a long coiled-coil domain and forms the nucleotide-binding domain (NBD) when the coiled coils fold back on themselves and bring together Walker A and B domains [1,2,3,4]. Two RAD50-NBDs forms heterotetramers with a Mre11 nuclease dimer that assemble as catalytic head module that binds and cleaves DNA in an ATP-dependent reaction. Through secondary structural analysis, it has been suggested that there is a wide structural conservation in the Rad50/SMC protein family as seen in structural similarities between RAD50's hook and ABC-ATPase MukB's elbow region [4].	Domain
A [auth A1], B [auth A2], C [auth B1], D [auth B2]	PF16330	MukB hinge domain (MukB_hinge)	MukB hinge domain	The hinge domain of chromosome partition protein MukB is responsible for dimerisation and is also involved in protein-DNA interactions and conformational flexibility [1].	Domain
A [auth A1], B [auth A2], C [auth B1], D [auth B2]	PF04310	MukB N-terminal (MukB)	MukB N-terminal	This family represents the N-terminal region of MukB, one of a group of bacterial proteins essential for the movement of nucleoids from mid-cell towards the cell quarters (i.e. chromosome partitioning). The structure of the N-terminal domain consist ...	This family represents the N-terminal region of MukB, one of a group of bacterial proteins essential for the movement of nucleoids from mid-cell towards the cell quarters (i.e. chromosome partitioning). The structure of the N-terminal domain consists of an antiparallel six-stranded beta sheet surrounded by one helix on one side and by five helices on the other side [1]. It contains an exposed Walker A loop in an unexpected helix-loop-helix motif (in other proteins, Walker A motifs generally adopt a P loop conformation as part of a strand-loop-helix motif embedded in a conserved topology of alternating helices and (parallel) beta strands)[1].	Domain
E [auth C1], F [auth C2], G [auth D1], H [auth D2]	PF03882	MukF winged-helix domain (KicB)	MukF winged-helix domain	The kicA and kicB genes are found upstream of mukB. It has been suggested that the kicB gene encodes a killing factor and the kicA gene codes for a protein that suppresses the killing function of the kicB gene product [1]. It was also demonstrated th ...	The kicA and kicB genes are found upstream of mukB. It has been suggested that the kicB gene encodes a killing factor and the kicA gene codes for a protein that suppresses the killing function of the kicB gene product [1]. It was also demonstrated that KicA and KicB can function as a post-segregational killing system, when the genes are transferred from the E. coli chromosome onto a plasmid [1].	Domain
E [auth C1], F [auth C2], G [auth D1], H [auth D2]	PF17193	MukF C-terminal domain (MukF_C)	MukF C-terminal domain	This presumed domain is found at the C-terminus of the MukF protein.	Domain
E [auth C1], F [auth C2], G [auth D1], H [auth D2]	PF17192	MukF middle domain (MukF_M)	MukF middle domain	The kicA and kicB genes are found upstream of mukB. It has been suggested that the kicB gene encodes a killing factor and the kicA gene codes for a protein that suppresses the killing function of the kicB gene product [1]. It was also demonstrated th ...	The kicA and kicB genes are found upstream of mukB. It has been suggested that the kicB gene encodes a killing factor and the kicA gene codes for a protein that suppresses the killing function of the kicB gene product [1]. It was also demonstrated that KicA and KicB can function as a post-segregational killing system, when the genes are transferred from the E. coli chromosome onto a plasmid [1].	Domain
I [auth E1], J [auth E2], K [auth F1], L [auth F2]	PF04288	MukE-like family (MukE)	MukE-like family	-	Family
Q [auth I1], R [auth I2], S [auth J1], T [auth J2]	PF06303	MatP N-terminal domain (MatP)	MatP N-terminal domain	This family, many of whose members are YcbG, organises the macrodomain Ter of the chromosome of bacteria such as E coli. In these bacteria, insulated macrodomains influence the segregation of sister chromatids and the mobility of chromosomal DNA. Org ...	This family, many of whose members are YcbG, organises the macrodomain Ter of the chromosome of bacteria such as E coli. In these bacteria, insulated macrodomains influence the segregation of sister chromatids and the mobility of chromosomal DNA. Organisation of the Terminus region (Ter) into a macrodomain relies on the presence of a 13 bp motif called matS repeated 23 times in the 800-kb-long domain. MatS sites are the main targets in the E. coli chromosome of YcbG or MatP (macrodomain Ter protein). MatP accumulates in the cell as a discrete focus that co-localises with the Ter macrodomain. The effects of MatP inactivation reveal its role as the main organiser of the Ter macrodomain: in the absence of MatP, DNA is less compacted, the mobility of markers is increased, and segregation of the Ter macrodomain occurs early in the cell cycle. A specific organisational system is required in the Terminus region for bacterial chromosome management during the cell cycle. This entry represents the N-terminal domain of MatP.	Domain
Q [auth I1], R [auth I2], S [auth J1], T [auth J2]	PF17414	MatP C-terminal ribbon-helix-helix domain (MatP_C)	MatP C-terminal ribbon-helix-helix domain	This family, many of whose members are YcbG, organises the macrodomain Ter of the chromosome of bacteria such as E coli. In these bacteria, insulated macrodomains influence the segregation of sister chromatids and the mobility of chromosomal DNA. Org ...	This family, many of whose members are YcbG, organises the macrodomain Ter of the chromosome of bacteria such as E coli. In these bacteria, insulated macrodomains influence the segregation of sister chromatids and the mobility of chromosomal DNA. Organisation of the Terminus region (Ter) into a macrodomain relies on the presence of a 13 bp motif called matS repeated 23 times in the 800-kb-long domain. MatS sites are the main targets in the E. coli chromosome of YcbG or MatP (macrodomain Ter protein). MatP accumulates in the cell as a discrete focus that co-localises with the Ter macrodomain. The effects of MatP inactivation reveal its role as the main organiser of the Ter macrodomain: in the absence of MatP, DNA is less compacted, the mobility of markers is increased, and segregation of the Ter macrodomain occurs early in the cell cycle. A specific organisational system is required in the Terminus region for bacterial chromosome management during the cell cycle. This entry represents the C-terminal ribbon-helix-helix domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth A1], B [auth A2], C [auth B1], D [auth B2]	Chromosome partition protein MukB	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding organic cyclic compound binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding DNA binding nucleic acid binding	nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular process cell division cell cycle chromosome segregation cell cycle process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular process cell division cell cycle chromosome segregation cell cycle process cellular component organization organelle organization chromosome condensation chromosome organization cellular component organization or biogenesis	nucleoid cellular anatomical entity intracellular anatomical structure cytoplasm
E [auth C1], F [auth C2], G [auth D1], H [auth D2]	Chromosome partition protein MukF	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding	nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular process cell division cell cycle chromosome segregation cell cycle process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular process cell division cell cycle chromosome segregation cell cycle process cellular component organization organelle organization chromosome condensation chromosome organization cellular component organization or biogenesis	nucleoid cellular anatomical entity intracellular anatomical structure cytoplasm
I [auth E1], J [auth E2], K [auth F1], L [auth F2]	Chromosome partition protein MukE	-	nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular process cell division cell cycle chromosome segregation cell cycle process nucleobase-containing compound metabolic process organic cyclic compound metabolic process DNA replication organic substance metabolic process metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular process cell division cell cycle chromosome segregation cell cycle process cellular component organization organelle organization chromosome condensation chromosome organization cellular component organization or biogenesis	nucleoid cellular anatomical entity intracellular anatomical structure cytoplasm
M [auth G1], N [auth G2], O [auth H1], P [auth H2]	Acyl carrier protein	-	-	-
Q [auth I1], R [auth I2], S [auth J1], T [auth J2]	Macrodomain Ter protein	sequence-specific DNA binding DNA binding binding organic cyclic compound binding nucleic acid binding	cellular process cell cycle regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process cellular process cell cycle regulation of cellular process cellular biosynthetic process RNA metabolic process regulation of primary metabolic process nucleobase-containing compound metabolic process RNA biosynthetic process nucleic acid biosynthetic process DNA-templated transcription regulation of RNA metabolic process organic substance metabolic process organic substance biosynthetic process regulation of nucleobase-containing compound metabolic process regulation of RNA biosynthetic process regulation of biosynthetic process regulation of biological process cellular metabolic process biological regulation primary metabolic process regulation of cellular metabolic process regulation of macromolecule metabolic process nucleobase-containing compound biosynthetic process gene expression macromolecule biosynthetic process nucleic acid metabolic process regulation of cellular biosynthetic process organic cyclic compound metabolic process regulation of gene expression biosynthetic process organic cyclic compound biosynthetic process metabolic process regulation of macromolecule biosynthetic process regulation of DNA-templated transcription macromolecule metabolic process regulation of metabolic process cell division	intracellular anatomical structure cytoplasm cellular anatomical entity
U [auth K1], W [auth M1]	matS2 DNA 80 b, oligo FBA769	-	-	-
V [auth L1], X [auth N1]	matS2 DNA 80 b, oligo FBA770	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth A1], B [auth A2], C [auth B1], D [auth B2]	IPR042501	MukB, hinge domain superfamily	Homologous Superfamily
A [auth A1], B [auth A2], C [auth B1], D [auth B2]	IPR007406	MukB, N-terminal domain	Domain
A [auth A1], B [auth A2], C [auth B1], D [auth B2]	IPR032520	MukB, hinge domain	Domain
A [auth A1], B [auth A2], C [auth B1], D [auth B2]	IPR012090	Chromosome partition protein MukB	Family
A [auth A1], B [auth A2], C [auth B1], D [auth B2]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
E [auth C1], F [auth C2], G [auth D1], H [auth D2]	IPR005582	Chromosome partition protein MukF	Family
E [auth C1], F [auth C2], G [auth D1], H [auth D2]	IPR036388	Winged helix-like DNA-binding domain superfamily	Homologous Superfamily
E [auth C1], F [auth C2], G [auth D1], H [auth D2]	IPR036141	MukF, middle domain superfamily	Homologous Superfamily
E [auth C1], F [auth C2], G [auth D1], H [auth D2]	IPR036390	Winged helix DNA-binding domain superfamily	Homologous Superfamily
E [auth C1], F [auth C2], G [auth D1], H [auth D2]	IPR033439	Chromosome partition protein MukF, winged-helix domain	Domain
E [auth C1], F [auth C2], G [auth D1], H [auth D2]	IPR038198	MukF, C-terminal domain superfamily	Homologous Superfamily
E [auth C1], F [auth C2], G [auth D1], H [auth D2]	IPR033441	Chromosome partition protein MukF, C-terminal domain	Domain
E [auth C1], F [auth C2], G [auth D1], H [auth D2]	IPR033440	Chromosome partition protein MukF, middle domain	Domain
I [auth E1], J [auth E2], K [auth F1], L [auth F2]	IPR042038	MukE, N-terminal domain	Homologous Superfamily
I [auth E1], J [auth E2], K [auth F1], L [auth F2]	IPR042037	MukE, C-terminal domain	Homologous Superfamily
I [auth E1], J [auth E2], K [auth F1], L [auth F2]	IPR007385	Prokaryotic chromosome segregation/condensation protein MukE	Family
Q [auth I1], R [auth I2], S [auth J1], T [auth J2]	IPR013321	Arc-type ribbon-helix-helix	Homologous Superfamily
Q [auth I1], R [auth I2], S [auth J1], T [auth J2]	IPR009390	Macrodomain Ter protein, MatP	Family
Q [auth I1], R [auth I2], S [auth J1], T [auth J2]	IPR035375	MatP, C-terminal ribbon-helix-helix domain	Domain
Q [auth I1], R [auth I2], S [auth J1], T [auth J2]	IPR038339	MatP, N-terminal domain superfamily	Homologous Superfamily
Q [auth I1], R [auth I2], S [auth J1], T [auth J2]	IPR035087	MatP, N-terminal	Domain