1NOM

DNA POLYMERASE BETA (POL B) (E.C.2.7.7.7), 31-KD DOMAIN; SOAKED IN THE PRESENCE OF MNCL2 (5 MILLIMOLAR)

External Resource: Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1noma1	All alpha proteins	SAM domain-like	PsbU/PolX domain-like	DNA polymerase beta-like, second domain	DNA polymerase beta	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
A	d1noma2	Alpha and beta proteins (a+b)	Nucleotidyltransferase	Nucleotidyltransferase	DNA polymerase beta-like	DNA polymerase beta, catalytic (31 kD) fragment	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Nucleotidyltransferase-like	8042125	3000129	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	PsbU/PolX domain-like	8042124	3000893	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)
A	DNA_pol_lambd_f	e1nomA1	A: alpha arrays	X: HhH/H2TH	H: SAM/DNA-glycosylase	T: SAM domain-like	F: DNA_pol_lambd_f	ECOD (1.6)
A	DNA_pol_B_palm	e1nomA2	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)
A	1.10.150.20	Mainly Alpha	Orthogonal Bundle	DNA polymerase	domain 1	CATH (4.3.0)
A	3.30.460.10	Alpha Beta	2-Layer Sandwich	Beta Polymerase	domain 2	CATH (4.3.0)
A	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
A	PF14791	DNA polymerase beta thumb (DNA_pol_B_thumb)	DNA polymerase beta thumb	-	Family
A	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
A	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
A	DNA POLYMERASE BETA	catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid 5'-deoxyribose-5-phosphate lyase activity lyase activity catalytic activity carbon-oxygen lyase activity DNA binding binding organic cyclic compound binding damaged DNA binding nucleic acid binding DNA-directed DNA polymerase activity DNA polymerase activity transferase activity catalytic activity, acting on DNA catalytic activity, acting on a nucleic acid 5'-deoxyribose-5-phosphate lyase activity lyase activity catalytic activity carbon-oxygen lyase activity DNA binding binding organic cyclic compound binding damaged DNA binding nucleic acid binding DNA-directed DNA polymerase activity DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups cytoskeletal protein binding microtubule binding protein binding tubulin binding DNA-(apurinic or apyrimidinic site) endonuclease activity class I DNA-(apurinic or apyrimidinic site) endonuclease activity enzyme binding cation binding ion binding metal ion binding small molecule binding	cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process developmental process cellular response to stimulus cellular response to stress response to stimulus DNA damage response response to stress cellular process nucleobase-containing compound metabolic process DNA replication metabolic process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process developmental process multicellular organismal process gland development animal organ development salivary gland development anatomical structure morphogenesis multicellular organism development gland morphogenesis salivary gland morphogenesis anatomical structure development animal organ morphogenesis exocrine system development system development immune system development lymph node development immune system process hematopoietic or lymphoid organ development multicellular organismal-level homeostasis homeostatic process homeostasis of number of cells immunoglobulin production cellular biosynthetic process somatic cell DNA recombination V(D)J recombination somatic recombination of immunoglobulin gene segments immunoglobulin heavy chain V-D-J recombination somatic diversification of immune receptors production of molecular mediator of immune response DNA recombination cellular metabolic process gene expression macromolecule biosynthetic process somatic diversification of immunoglobulins immunoglobulin V(D)J recombination biosynthetic process somatic diversification of immune receptors via germline recombination within a single locus apoptotic process cell death programmed cell death somatic diversification of immune receptors via somatic mutation somatic hypermutation of immunoglobulin genes pyrimidine dimer repair DNA repair embryo development ending in birth or egg hatching chordate embryonic development embryo development in utero embryonic development response to alcohol response to chemical response to oxygen-containing compound response to ethanol spleen development regulation of biological process regulation of cellular process signaling biological regulation intracellular signal transduction cell communication apoptotic signaling pathway intrinsic apoptotic signaling pathway in response to DNA damage signal transduction intrinsic apoptotic signaling pathway neuron apoptotic process base-excision repair response to ionizing radiation response to radiation response to abiotic stimulus response to gamma radiation base-excision repair, gap-filling defense response inflammatory response double-strand break repair double-strand break repair via nonhomologous end joining response to oxygen levels response to hyperoxia response to increased oxygen levels	intracellular anatomical structure cytoplasm cellular anatomical entity protein-containing complex polymeric cytoskeletal fiber spindle spindle microtubule intracellular organelle cytoskeleton organelle intracellular non-membrane-bounded organelle supramolecular fiber microtubule supramolecular polymer intracellular anatomical structure cytoplasm cellular anatomical entity protein-containing complex polymeric cytoskeletal fiber spindle spindle microtubule intracellular organelle cytoskeleton organelle intracellular non-membrane-bounded organelle supramolecular fiber microtubule supramolecular polymer supramolecular complex microtubule cytoskeleton non-membrane-bounded organelle membrane-bounded organelle nucleus intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A	IPR037160	DNA polymerase, thumb domain superfamily	Homologous Superfamily
A	IPR019843	DNA polymerase family X, binding site	Binding Site
A	IPR029398	DNA polymerase beta, thumb domain	Domain
A	IPR002008	DNA polymerase family X, beta-like	Family
A	IPR043519	Nucleotidyltransferase superfamily	Homologous Superfamily
A	IPR027421	DNA polymerase lambda lyase domain superfamily	Homologous Superfamily
A	IPR003583	Helix-hairpin-helix DNA-binding motif, class 1	Domain
A	IPR028207	DNA polymerase beta, palm domain	Domain
A	IPR022312	DNA polymerase family X	Family
A	IPR010996	DNA polymerase beta-like, N-terminal domain	Domain
A	IPR018944	DNA polymerase lambda, fingers domain	Domain
A	IPR002054	DNA-directed DNA polymerase X	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.