Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5C51

Probing the Structural and Molecular Basis of Nucleotide Selectivity by Human Mitochondrial DNA Polymerase gamma

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0002020	molecular_function	protease binding
A	0003677	molecular_function	DNA binding
A	0003682	molecular_function	chromatin binding
A	0003887	molecular_function	DNA-directed DNA polymerase activity
A	0005515	molecular_function	protein binding
A	0005739	cellular_component	mitochondrion
A	0005759	cellular_component	mitochondrial matrix
A	0005760	cellular_component	gamma DNA polymerase complex
A	0006259	biological_process	DNA metabolic process
A	0006260	biological_process	DNA replication
A	0006261	biological_process	DNA-templated DNA replication
A	0006264	biological_process	mitochondrial DNA replication
A	0006281	biological_process	DNA repair
A	0006284	biological_process	base-excision repair
A	0006287	biological_process	base-excision repair, gap-filling
A	0008310	molecular_function	single-stranded DNA 3'-5' DNA exonuclease activity
A	0008408	molecular_function	3'-5' exonuclease activity
A	0016787	molecular_function	hydrolase activity
A	0016829	molecular_function	lyase activity
A	0032991	cellular_component	protein-containing complex
A	0042645	cellular_component	mitochondrial nucleoid
A	0043231	cellular_component	intracellular membrane-bounded organelle
A	0045004	biological_process	DNA replication proofreading
A	0051575	molecular_function	5'-deoxyribose-5-phosphate lyase activity
A	0071897	biological_process	DNA biosynthetic process
B	0001701	biological_process	in utero embryonic development
B	0003677	molecular_function	DNA binding
B	0003690	molecular_function	double-stranded DNA binding
B	0003887	molecular_function	DNA-directed DNA polymerase activity
B	0005515	molecular_function	protein binding
B	0005737	cellular_component	cytoplasm
B	0005739	cellular_component	mitochondrion
B	0005759	cellular_component	mitochondrial matrix
B	0005760	cellular_component	gamma DNA polymerase complex
B	0006260	biological_process	DNA replication
B	0006261	biological_process	DNA-templated DNA replication
B	0006264	biological_process	mitochondrial DNA replication
B	0007005	biological_process	mitochondrion organization
B	0030337	molecular_function	DNA polymerase processivity factor activity
B	0032042	biological_process	mitochondrial DNA metabolic process
B	0042645	cellular_component	mitochondrial nucleoid
B	0042802	molecular_function	identical protein binding
B	0070182	molecular_function	DNA polymerase binding
B	0071897	biological_process	DNA biosynthetic process
B	1900264	biological_process	positive regulation of DNA-directed DNA polymerase activity
C	0001701	biological_process	in utero embryonic development
C	0003677	molecular_function	DNA binding
C	0003690	molecular_function	double-stranded DNA binding
C	0003887	molecular_function	DNA-directed DNA polymerase activity
C	0005515	molecular_function	protein binding
C	0005737	cellular_component	cytoplasm
C	0005739	cellular_component	mitochondrion
C	0005759	cellular_component	mitochondrial matrix
C	0005760	cellular_component	gamma DNA polymerase complex
C	0006260	biological_process	DNA replication
C	0006261	biological_process	DNA-templated DNA replication
C	0006264	biological_process	mitochondrial DNA replication
C	0007005	biological_process	mitochondrion organization
C	0030337	molecular_function	DNA polymerase processivity factor activity
C	0032042	biological_process	mitochondrial DNA metabolic process
C	0042645	cellular_component	mitochondrial nucleoid
C	0042802	molecular_function	identical protein binding
C	0070182	molecular_function	DNA polymerase binding
C	0071897	biological_process	DNA biosynthetic process
C	1900264	biological_process	positive regulation of DNA-directed DNA polymerase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	3
Details	binding site for residue MG A 4001

Chain	Residue
A	ASP1135
A	1RY4003
P	DOC24

site_id	AC2
Number of Residues	5
Details	binding site for residue MG A 4002

Chain	Residue
A	ASP890
A	VAL891
A	ASP892
A	ASP1135
A	1RY4003

site_id	AC3
Number of Residues	16
Details	binding site for residue 1RY A 4003

Chain	Residue
A	ASP890
A	VAL891
A	ASP892
A	SER893
A	GLN894
A	ARG943
A	LYS947
A	ARG948
A	TYR951
A	ASP1135
A	MG4001
A	MG4002
P	DOC24
T	DG4
T	DG5
A	ARG853

Functional Information from PROSITE/UniProt

site_id	PS00447
Number of Residues	20
Details	DNA_POLYMERASE_A DNA polymerase family A signature. RehAKrfnYGriYgaGqpfA

Chain	Residue	Details
A	ARG943-ALA962

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	MOD_RES: Phosphoserine => ECO:0007744\|PubMed:23186163

Chain	Residue	Details
B	SER38
C	SER38

site_id	SWS_FT_FI2
Number of Residues	5
Details	BINDING: BINDING => ECO:0000269\|PubMed:37202477, ECO:0007744\|PDB:8D37

Chain	Residue	Details
A	LYS316
A	LEU816
A	GLY903
A	ARG953
A	ALA1105

site_id	SWS_FT_FI3
Number of Residues	2
Details	BINDING: BINDING => ECO:0000305\|PubMed:26056153, ECO:0007744\|PDB:4ZTZ

Chain	Residue	Details
A	PRO589
A	GLN879

site_id	SWS_FT_FI4
Number of Residues	3
Details	BINDING: BINDING => ECO:0000269\|PubMed:26056153, ECO:0000269\|PubMed:37202477, ECO:0007744\|PDB:4ZTZ, ECO:0007744\|PDB:8D37

Chain	Residue	Details
A	MET603
A	ALA957
A	PHE961

site_id	SWS_FT_FI5
Number of Residues	4
Details	BINDING: BINDING => ECO:0000305\|PubMed:37202477, ECO:0007744\|PDB:8D37

Chain	Residue	Details
A	SER764
A	LYS773
A	THR778
A	GLU873

site_id	SWS_FT_FI6
Number of Residues	6
Details	BINDING: BINDING => ECO:0000269\|PubMed:26056153, ECO:0007744\|PDB:4ZTZ

Chain	Residue	Details
A	TRP859
A	ALA900
A	VAL901
A	ALA905
A	SER1104
A	ASP1145

site_id	SWS_FT_FI7
Number of Residues	2
Details	SITE: Critical for replication fidelity and mismatch recognition => ECO:0000269\|PubMed:37202477

Chain	Residue	Details
A	SER863
A	MET1112

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)