2IHM

Polymerase mu in ternary complex with gapped 11mer DNA duplex and bound incoming nucleotide

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
G [auth A]	d2ihma1	All alpha proteins	SAM domain-like	DNA polymerase beta, N-terminal domain-like	automated matches	automated matches	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
G [auth A]	d2ihma2	All alpha proteins	SAM domain-like	PsbU/PolX domain-like	automated matches	automated matches	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
G [auth A]	d2ihma3	Alpha and beta proteins (a+b)	Nucleotidyltransferase	Nucleotidyltransferase	automated matches	automated matches	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
H [auth B]	d2ihmb1	All alpha proteins	SAM domain-like	DNA polymerase beta, N-terminal domain-like	automated matches	automated matches	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
H [auth B]	d2ihmb2	All alpha proteins	SAM domain-like	PsbU/PolX domain-like	automated matches	automated matches	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
H [auth B]	d2ihmb3	Alpha and beta proteins (a+b)	Nucleotidyltransferase	Nucleotidyltransferase	automated matches	automated matches	house mouse (Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
G [auth A]	DNA_pol_lambd_f	e2ihmA4	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: DNA_pol_lambd_f	ECOD (1.6)
G [auth A]	HHH_8	e2ihmA2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_8	ECOD (1.6)
G [auth A]	DNA_pol_B_palm	e2ihmA3	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: DNA_pol_B_palm	ECOD (1.6)
H [auth B]	DNA_pol_lambd_f	e2ihmB2	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: DNA_pol_lambd_f	ECOD (1.6)
H [auth B]	HHH_8	e2ihmB3	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: HHH_8	ECOD (1.6)
H [auth B]	DNA_pol_B_palm	e2ihmB1	A: a+b three layers	X: Nucleotidyltransferase-like	H: Nucleotidyltransferase (From Topology)	T: Nucleotidyltransferase	F: DNA_pol_B_palm	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
G [auth A]	1.10.150.110	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
G [auth A]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
G [auth A]	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
G [auth A]	3.30.210.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 3	CATH (4.3.0)
H [auth B]	1.10.150.110	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
H [auth B]	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
H [auth B]	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
H [auth B]	3.30.210.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
G [auth A], H [auth B]	PF14716	Helix-hairpin-helix domain (HHH_8)	Helix-hairpin-helix domain	-	Domain
G [auth A], H [auth B]	PF14791	DNA polymerase beta thumb (DNA_pol_B_thumb)	DNA polymerase beta thumb	-	Family
G [auth A], H [auth B]	PF14792	DNA polymerase beta palm (DNA_pol_B_palm)	DNA polymerase beta palm	The catalytic region of DNA polymerase beta is split into three domains. An N-terminal fingers domain, a central palm domain and a C-terminal thumb domain. This entry represents the palm domain [1].	Domain
G [auth A], H [auth B]	PF10391	Fingers domain of DNA polymerase lambda (DNA_pol_lambd_f)	Fingers domain of DNA polymerase lambda	DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. DNA_pol_lambd_f is the centr ...	DNA polymerases catalyse the addition of dNMPs onto the 3-prime ends of DNA chains. There is a general polymerase fold consisting of three subdomains that have been likened to the fingers, palm, and thumb of a right hand. DNA_pol_lambd_f is the central three-helical region of DNA polymerase lambda referred to as the F and G helices of the fingers domain. Contacts with DNA involve this conserved helix-hairpin-helix motif in the fingers region which interacts with the primer strand. This motif is common to several DNA binding proteins and confers a sequence-independent interaction with the DNA backbone [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C [auth D], F [auth E]	5'-D(PGPCPCPG)-3'	-	-	-
G [auth A], H [auth B]	DNA polymerase mu	catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding cation binding ion binding catalytic activity, acting on DNA DNA-directed DNA polymerase activity DNA polymerase activity catalytic activity, acting on a nucleic acid transferase activity nucleotidyltransferase activity catalytic activity transferase activity, transferring phosphorus-containing groups DNA binding binding organic cyclic compound binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding	developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process anatomical structure development developmental process multicellular organismal process cellular developmental process hemopoiesis B cell activation cell activation cell development mononuclear cell differentiation lymphocyte differentiation lymphocyte activation leukocyte activation B cell differentiation cell differentiation immune system process anatomical structure development cellular process leukocyte differentiation immune system development production of molecular mediator of immune response immunoglobulin production somatic diversification of immune receptors via somatic mutation gene expression macromolecule biosynthetic process somatic diversification of immunoglobulins multicellular organism development biosynthetic process somatic diversification of immune receptors metabolic process macromolecule metabolic process somatic hypermutation of immunoglobulin genes system development nucleobase-containing compound metabolic process DNA recombination primary metabolic process DNA metabolic process nucleic acid metabolic process cellular response to stimulus double-strand break repair response to stimulus double-strand break repair via nonhomologous end joining cellular response to stress DNA damage response response to stress DNA repair	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle nucleus intracellular membrane-bounded organelle
A [auth T], D [auth U]	5'-D(CPGPGPCPAPAPTPAPCPTP*G)-3'	-	-	-
B [auth P], E [auth Q]	5'-D(CPAPGPTPAPT)-3'	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G [auth A], H [auth B]	IPR028207	DNA polymerase beta, palm domain	Domain
G [auth A], H [auth B]	IPR037160	DNA polymerase, thumb domain superfamily	Homologous Superfamily
G [auth A], H [auth B]	IPR019843	DNA polymerase family X, binding site	Binding Site
G [auth A], H [auth B]	IPR022312	DNA polymerase family X	Family
G [auth A], H [auth B]	IPR010996	DNA polymerase beta-like, N-terminal domain	Domain
G [auth A], H [auth B]	IPR001726	DNA nucleotidylexotransferase (TdT) / DNA-directed DNA/RNA polymerase mu	Family
G [auth A], H [auth B]	IPR029398	DNA polymerase beta, thumb domain	Domain
G [auth A], H [auth B]	IPR018944	DNA polymerase lambda, fingers domain	Domain
G [auth A], H [auth B]	IPR043519	Nucleotidyltransferase superfamily	Homologous Superfamily
G [auth A], H [auth B]	IPR001357	BRCT domain	Domain
G [auth A], H [auth B]	IPR027421	DNA polymerase lambda lyase domain superfamily	Homologous Superfamily
G [auth A], H [auth B]	IPR036420	BRCT domain superfamily	Homologous Superfamily
G [auth A], H [auth B]	IPR002054	DNA-directed DNA polymerase X	Domain
G [auth A], H [auth B]	IPR027249	DNA-directed DNA/RNA polymerase mu	Family

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.