3IKM | pdb_00003ikm

Crystal structure of human mitochondrial DNA polymerase holoenzyme

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
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Class II aaRS ABD-related	8041652	3000465	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8041653	3000058	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8041653	3000058	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Class II aaRS ABD-related	8041652	3000465	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8041653	3000058	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Class II aaRS ABD-related	8041652	3000465	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Class II aaRS ABD-related	8041652	3000465	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Class II aaRS and biotin synthetases	8041653	3000058	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)
F	CoV_NSP4_C	e3ikmF5	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: CoV_NSP4_C	ECOD (develop294)
E	Copper-bind	e3ikmE2	A: alpha bundles	X: cradle loop barrel	H: RIFT-related	T: acid protease	F: Copper-bind	ECOD (develop294)
E		e3ikmE3	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F:	ECOD (develop294)
C	CoV_NSP4_C	e3ikmC5	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F: CoV_NSP4_C	ECOD (develop294)
B	C1-set	e3ikmB2	A: alpha bundles	X: Cystatin-like	H: NTF2-like	T: NTF2-like	F: C1-set	ECOD (develop294)
B		e3ikmB3	A: alpha bundles	X: DEATH domain	H: Ten stranded beta/alpha barrel	T: Ten stranded beta/alpha barrel	F:	ECOD (develop294)
D		e3ikmD5	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F:	ECOD (develop294)
D		e3ikmD6	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F:	ECOD (develop294)
D	rve	e3ikmD7	A: alpha bundles	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: rve	ECOD (develop294)
A	DNApol_Exo	e3ikmA1	A: alpha bundles	X: Alpha-beta plaits	H: RNA-binding domain, RBD	T: RNA-binding domain, RBD	F: DNApol_Exo	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
F	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (4.3.0)
E	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
E	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (4.3.0)
C	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
C	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (4.3.0)
B	3.30.930.10	Alpha Beta	2-Layer Sandwich	BirA Bifunctional Protein	domain 2	CATH (4.3.0)
B	3.40.50.800	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Anticodon-binding domain	CATH (4.3.0)
D	3.30.420.390	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	3.30.420.390	Alpha Beta	2-Layer Sandwich	Nucleotidyltransferase	domain 5	CATH (4.3.0)
A	1.20.5.3960	Mainly Alpha	Up-down Bundle	Single alpha-helices involved in coiled-coils or other helix-helix interfaces		CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
B, C, E, F	PF03129	Anticodon binding domain (HGTP_anticodon)	Anticodon binding domain	This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases [1] it is probably the anticodon binding domain [2].	Domain
A, D	PF18136	DNA mitochondrial polymerase exonuclease domain (DNApol_Exo)	DNA mitochondrial polymerase exonuclease domain	This domain belongs to human mitochondrial DNA polymerase (Pol-gamma). Pol-gamma has a catalytic subunit, Pol gamma-A, which possesses both polymerase and proofreading exonuclease activities and an accessory subunit, Pol gamma-B, which accelerates po ...	This domain belongs to human mitochondrial DNA polymerase (Pol-gamma). Pol-gamma has a catalytic subunit, Pol gamma-A, which possesses both polymerase and proofreading exonuclease activities and an accessory subunit, Pol gamma-B, which accelerates polymerization rate and suppresses exonuclease activity. This domain is the exonuclease domain of the catalytic subunit, Pol gamma-A [1].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B, C, E, F	DNA polymerase subunit gamma-2	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 double-stranded DNA binding binding nucleic acid binding enzyme regulator activity DNA polymerase processivity factor activity 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 double-stranded DNA binding binding nucleic acid binding enzyme regulator activity DNA polymerase processivity factor activity enzyme activator activity molecular function activator activity molecular function regulator activity protein binding DNA polymerase binding enzyme binding identical protein binding	regulation of cellular process regulation of catalytic activity positive regulation of biological process regulation of transferase activity regulation of DNA biosynthetic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of molecular function positive regulation of metabolic process nucleic acid biosynthetic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process regulation of cellular process regulation of catalytic activity positive regulation of biological process regulation of transferase activity regulation of DNA biosynthetic process positive regulation of macromolecule biosynthetic process regulation of primary metabolic process nucleobase-containing compound metabolic process positive regulation of molecular function positive regulation of metabolic process nucleic acid biosynthetic process positive regulation of biosynthetic process positive regulation of macromolecule metabolic process regulation of nucleobase-containing compound metabolic process positive regulation of cellular process regulation of biosynthetic process regulation of biological process biological regulation positive regulation of catalytic activity positive regulation of DNA biosynthetic process primary metabolic process regulation of macromolecule metabolic process DNA metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process regulation of molecular function positive regulation of DNA metabolic process biosynthetic process metabolic process cellular process regulation of macromolecule biosynthetic process macromolecule metabolic process regulation of metabolic process DNA biosynthetic process positive regulation of DNA-directed DNA polymerase activity regulation of DNA metabolic process DNA-templated DNA replication DNA replication mitochondrial DNA metabolic process mitochondrial DNA replication cellular component organization organelle organization cellular component organization or biogenesis mitochondrion organization developmental process multicellular organism development multicellular organismal process embryo development ending in birth or egg hatching chordate embryonic development anatomical structure development embryo development in utero embryonic development	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial protein-containing complex protein-containing complex catalytic complex membrane-enclosed lumen transferase complex mitochondrial matrix membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle mitochondrial protein-containing complex protein-containing complex catalytic complex membrane-enclosed lumen transferase complex mitochondrial matrix DNA polymerase complex intracellular organelle lumen transferase complex, transferring phosphorus-containing groups organelle lumen gamma DNA polymerase complex intracellular protein-containing complex intracellular membraneless organelle nucleoid membraneless organelle mitochondrial nucleoid
A, D	DNA polymerase subunit gamma-1	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 exonuclease activity 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity single-stranded DNA exodeoxyribonuclease activity nuclease activity hydrolase activity, acting on ester bonds 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 exonuclease activity 3'-5' exonuclease activity hydrolase activity DNA exonuclease activity, producing 5'-phosphomonoesters DNA nuclease activity single-stranded DNA exodeoxyribonuclease activity nuclease activity hydrolase activity, acting on ester bonds 3'-5'-DNA exonuclease activity exonuclease activity single-stranded DNA 3'-5' DNA exonuclease activity chromatin binding binding protein binding enzyme binding protease binding DNA-directed DNA polymerase activity DNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups DNA binding nucleic acid binding	nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus response to stimulus DNA-templated DNA replication maintenance of fidelity DNA replication proofreading cellular response to stress nucleobase-containing compound metabolic process DNA-templated DNA replication DNA replication metabolic process cellular process primary metabolic process DNA metabolic process macromolecule metabolic process nucleic acid metabolic process cellular response to stimulus response to stimulus DNA-templated DNA replication maintenance of fidelity DNA replication proofreading cellular response to stress DNA damage response response to stress DNA repair mitochondrial DNA metabolic process mitochondrial DNA replication base-excision repair base-excision repair, gap-filling	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex mitochondrial protein-containing complex catalytic complex membrane-enclosed lumen transferase complex mitochondrial matrix membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure mitochondrion organelle cytoplasm intracellular membrane-bounded organelle protein-containing complex mitochondrial protein-containing complex catalytic complex membrane-enclosed lumen transferase complex mitochondrial matrix DNA polymerase complex intracellular organelle lumen transferase complex, transferring phosphorus-containing groups organelle lumen gamma DNA polymerase complex intracellular protein-containing complex mitochondrial chromosome intracellular membraneless organelle chromosome nucleoid membraneless organelle mitochondrial nucleoid

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B, C, E, F	IPR045864	Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)	Homologous Superfamily
B, C, E, F	IPR004154	Anticodon-binding	Domain
B, C, E, F	IPR042064	POLG2, C-terminal	Domain
B, C, E, F	IPR036621	Anticodon-binding domain superfamily	Homologous Superfamily
B, C, E, F	IPR027031	Glycyl-tRNA synthetase/DNA polymerase subunit gamma-2	Family
A, D	IPR047580	DNA polymerase gamma, palm domain	Domain
A, D	IPR019760	DNA-directed DNA polymerase, family A, conserved site	Conserved Site
A, D	IPR012337	Ribonuclease H-like superfamily	Homologous Superfamily
A, D	IPR002297	DNA-directed DNA-polymerase, family A, mitochondria	Family
A, D	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
A, D	IPR001098	DNA-directed DNA polymerase, family A, palm domain	Domain
A, D	IPR041336	DNA mitochondrial polymerase, exonuclease domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
B, C, E, F	Pharos: Q9UHN1	progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 4 progressive external ophthalmoplegia progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1 large cell medulloblastoma Mitochondrial Diseases muscular disease rhabdomyolysis leukodystrophy mitochondrial DNA depletion syndrome 4a myopathy medulloblastoma muscle tissue disease osteosarcoma
A, D	Pharos: P54098	mitochondrial DNA depletion syndrome 4a sensory ataxic neuropathy, dysarthria, and ophthalmoparesis Leigh syndrome progressive external ophthalmoplegia mitochondrial DNA depletion syndrome 4b progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1 mitochondrial DNA depletion syndrome 1 epilepsy progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1 male infertility peripheral neuropathy adrenoleukodystrophy myopathy visual epilepsy Charcot-Marie-Tooth disease mitochondrial DNA depletion syndrome 4a sensory ataxic neuropathy, dysarthria, and ophthalmoparesis Leigh syndrome progressive external ophthalmoplegia mitochondrial DNA depletion syndrome 4b progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal dominant 1 mitochondrial DNA depletion syndrome 1 epilepsy progressive external ophthalmoplegia with mitochondrial DNA deletions, autosomal recessive 1 male infertility peripheral neuropathy adrenoleukodystrophy myopathy visual epilepsy Charcot-Marie-Tooth disease spinocerebellar ataxia with epilepsy Balo concentric sclerosis peripheral nervous system disease Cholestasis in newborn motor peripheral neuropathy neurodegenerative disease autosomal dominant progressive external ophthalmoplegia autosomal recessive progressive external ophthalmoplegia inborn mitochondrial metabolism disorder parkinsonian disorder bipolar disorder leukodystrophy rhabdomyolysis drug-induced liver injury muscle tissue disease autosomal recessive juvenile Parkinson disease 2 osteosarcoma pancreatic intraductal papillary-mucinous carcinoma intellectual disability Pelizaeus-Merzbacher disease cholestasis lung cancer Schilder disease arthrogryposis muscular disease attention deficit hyperactivity disorder, inattentive type inborn errors of metabolism ovarian cancer pancreatic intraductal papillary-mucinous neoplasm with low grade dysplasia

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.