Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6UOK

Y271G DNA polymerase beta substrate complex with templating cytosine and incoming r8-oxo-GTP

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0001701	biological_process	in utero embryonic development
A	0003677	molecular_function	DNA binding
A	0003684	molecular_function	damaged DNA binding
A	0003887	molecular_function	DNA-directed DNA polymerase activity
A	0003906	molecular_function	DNA-(apurinic or apyrimidinic site) endonuclease activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005737	cellular_component	cytoplasm
A	0005874	cellular_component	microtubule
A	0005876	cellular_component	spindle microtubule
A	0006259	biological_process	DNA metabolic process
A	0006260	biological_process	DNA replication
A	0006261	biological_process	DNA-templated 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	0006290	biological_process	pyrimidine dimer repair
A	0006297	biological_process	nucleotide-excision repair, DNA gap filling
A	0006303	biological_process	double-strand break repair via nonhomologous end joining
A	0006915	biological_process	apoptotic process
A	0006954	biological_process	inflammatory response
A	0006974	biological_process	DNA damage response
A	0007435	biological_process	salivary gland morphogenesis
A	0008017	molecular_function	microtubule binding
A	0008630	biological_process	intrinsic apoptotic signaling pathway in response to DNA damage
A	0010332	biological_process	response to gamma radiation
A	0016445	biological_process	somatic diversification of immunoglobulins
A	0016446	biological_process	somatic hypermutation of immunoglobulin genes
A	0016779	molecular_function	nucleotidyltransferase activity
A	0016829	molecular_function	lyase activity
A	0019899	molecular_function	enzyme binding
A	0032991	cellular_component	protein-containing complex
A	0034061	molecular_function	DNA polymerase activity
A	0045471	biological_process	response to ethanol
A	0046872	molecular_function	metal ion binding
A	0048535	biological_process	lymph node development
A	0048536	biological_process	spleen development
A	0048872	biological_process	homeostasis of number of cells
A	0051402	biological_process	neuron apoptotic process
A	0051575	molecular_function	5'-deoxyribose-5-phosphate lyase activity
A	0055093	biological_process	response to hyperoxia
A	0071707	biological_process	immunoglobulin heavy chain V-D-J recombination
A	0071897	biological_process	DNA biosynthetic process
A	0140078	molecular_function	class I DNA-(apurinic or apyrimidinic site) endonuclease activity
F	0001701	biological_process	in utero embryonic development
F	0003677	molecular_function	DNA binding
F	0003684	molecular_function	damaged DNA binding
F	0003887	molecular_function	DNA-directed DNA polymerase activity
F	0003906	molecular_function	DNA-(apurinic or apyrimidinic site) endonuclease activity
F	0005515	molecular_function	protein binding
F	0005634	cellular_component	nucleus
F	0005654	cellular_component	nucleoplasm
F	0005737	cellular_component	cytoplasm
F	0005874	cellular_component	microtubule
F	0005876	cellular_component	spindle microtubule
F	0006259	biological_process	DNA metabolic process
F	0006260	biological_process	DNA replication
F	0006261	biological_process	DNA-templated DNA replication
F	0006281	biological_process	DNA repair
F	0006284	biological_process	base-excision repair
F	0006287	biological_process	base-excision repair, gap-filling
F	0006290	biological_process	pyrimidine dimer repair
F	0006297	biological_process	nucleotide-excision repair, DNA gap filling
F	0006303	biological_process	double-strand break repair via nonhomologous end joining
F	0006915	biological_process	apoptotic process
F	0006954	biological_process	inflammatory response
F	0006974	biological_process	DNA damage response
F	0007435	biological_process	salivary gland morphogenesis
F	0008017	molecular_function	microtubule binding
F	0008630	biological_process	intrinsic apoptotic signaling pathway in response to DNA damage
F	0010332	biological_process	response to gamma radiation
F	0016445	biological_process	somatic diversification of immunoglobulins
F	0016446	biological_process	somatic hypermutation of immunoglobulin genes
F	0016779	molecular_function	nucleotidyltransferase activity
F	0016829	molecular_function	lyase activity
F	0019899	molecular_function	enzyme binding
F	0032991	cellular_component	protein-containing complex
F	0034061	molecular_function	DNA polymerase activity
F	0045471	biological_process	response to ethanol
F	0046872	molecular_function	metal ion binding
F	0048535	biological_process	lymph node development
F	0048536	biological_process	spleen development
F	0048872	biological_process	homeostasis of number of cells
F	0051402	biological_process	neuron apoptotic process
F	0051575	molecular_function	5'-deoxyribose-5-phosphate lyase activity
F	0055093	biological_process	response to hyperoxia
F	0071707	biological_process	immunoglobulin heavy chain V-D-J recombination
F	0071897	biological_process	DNA biosynthetic process
F	0140078	molecular_function	class I DNA-(apurinic or apyrimidinic site) endonuclease activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	1
Details	binding site for residue CL B 101

Chain	Residue
B	DG3

site_id	AC2
Number of Residues	4
Details	binding site for residue NA E 101

Chain	Residue
E	DC3
F	LYS60
F	LEU62
F	VAL65

site_id	AC3
Number of Residues	5
Details	binding site for residue NA F 401

Chain	Residue
F	HOH513
C	DG9
F	THR101
F	VAL103
F	ILE106

site_id	AC4
Number of Residues	4
Details	binding site for residue MN F 402

Chain	Residue
F	ASP190
F	ASP192
F	8GT406
F	HOH507

site_id	AC5
Number of Residues	2
Details	binding site for residue MN F 403

Chain	Residue
F	ASP145
F	HIS252

site_id	AC6
Number of Residues	2
Details	binding site for residue MN F 404

Chain	Residue
F	ASP124
F	HOH501

site_id	AC7
Number of Residues	4
Details	binding site for residue NA F 405

Chain	Residue
F	ASP190
F	ASP192
F	ASP256
F	8GT406

site_id	AC8
Number of Residues	20
Details	binding site for residue 8GT F 406

Chain	Residue
B	DC6
B	DG7
C	DOC10
F	GLY179
F	SER180
F	ARG183
F	SER188
F	GLY189
F	ASP190
F	ASP192
F	GLY271
F	PHE272
F	THR273
F	GLY274
F	ASP276
F	ASN279
F	MN402
F	NA405
F	MN408
F	HOH507

site_id	AC9
Number of Residues	2
Details	binding site for residue MN F 407

Chain	Residue
F	ASP314
F	ASP318

site_id	AD1
Number of Residues	1
Details	binding site for residue MN F 408

Chain	Residue
F	8GT406

site_id	AD2
Number of Residues	1
Details	binding site for residue EDO A 401

Chain	Residue
A	HIS51

site_id	AD3
Number of Residues	5
Details	binding site for residue NA A 402

Chain	Residue
A	LYS60
A	LEU62
A	VAL65
A	HOH517
D	DC3

site_id	AD4
Number of Residues	5
Details	binding site for residue NA A 403

Chain	Residue
A	THR101
A	VAL103
A	ILE106
A	HOH519
P	DG9

site_id	AD5
Number of Residues	4
Details	binding site for residue MN A 404

Chain	Residue
A	ASP190
A	ASP192
A	8GT405
A	HOH515

site_id	AD6
Number of Residues	15
Details	binding site for residue 8GT A 405

Chain	Residue
A	ARG149
A	GLY179
A	SER180
A	SER188
A	GLY189
A	ASP190
A	ASP192
A	PHE272
A	ASP276
A	MN404
A	NA406
A	HOH515
P	DOC10
T	DC6
T	DG7

site_id	AD7
Number of Residues	4
Details	binding site for residue NA A 406

Chain	Residue
A	ASP190
A	ASP192
A	ASP256
A	8GT405

site_id	AD8
Number of Residues	1
Details	binding site for residue MG D 101

Chain	Residue
D	DG4

site_id	AD9
Number of Residues	11
Details	binding site for Di-nucleotide DG P 9 and DOC P 10

Chain	Residue
A	VAL103
A	GLY105
A	ILE106
A	ARG254
A	NA403
A	8GT405
P	DC8
T	DC6
T	DG7
T	DC8
T	DG9

Functional Information from PROSITE/UniProt

site_id	PS00522
Number of Residues	20
Details	DNA_POLYMERASE_X DNA polymerase family X signature. GSFrRGaesSgDMDVLLthP

Chain	Residue	Details
F	GLY179-PRO198

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	2
Details	ACT_SITE: Nucleophile; Schiff-base intermediate with DNA; for 5'-dRP lyase activity => ECO:0000269\|PubMed:9572863

Chain	Residue	Details
F	LYS72
A	LYS72

site_id	SWS_FT_FI2
Number of Residues	12
Details	BINDING: BINDING => ECO:0000269\|PubMed:12517346, ECO:0000269\|PubMed:8841120, ECO:0000269\|PubMed:9287163, ECO:0007744\|PDB:1BPX, ECO:0007744\|PDB:1BPZ, ECO:0007744\|PDB:1MQ3, ECO:0007744\|PDB:1ZQO, ECO:0007744\|PDB:1ZQQ

Chain	Residue	Details
F	LYS60
A	THR101
A	VAL103
A	ILE106
F	LEU62
F	VAL65
F	THR101
F	VAL103
F	ILE106
A	LYS60
A	LEU62
A	VAL65

site_id	SWS_FT_FI3
Number of Residues	6
Details	BINDING: BINDING => ECO:0000269\|PubMed:8841119, ECO:0007744\|PDB:8ICW, ECO:0007744\|PDB:8ICX, ECO:0007744\|PDB:8ICY

Chain	Residue	Details
F	ARG149
F	SER180
F	GLY189
A	ARG149
A	SER180
A	GLY189

site_id	SWS_FT_FI4
Number of Residues	2
Details	BINDING: BINDING => ECO:0000269\|PubMed:8841119, ECO:0007744\|PDB:8ICX

Chain	Residue	Details
F	ARG183
A	ARG183

site_id	SWS_FT_FI5
Number of Residues	6
Details	BINDING: BINDING => ECO:0000269\|PubMed:9287163, ECO:0007744\|PDB:1BPY

Chain	Residue	Details
F	ASP190
F	ASP192
F	ASP256
A	ASP190
A	ASP192
A	ASP256

site_id	SWS_FT_FI6
Number of Residues	2
Details	MOD_RES: N6-acetyllysine => ECO:0000250\|UniProtKB:Q8K409

Chain	Residue	Details
F	LYS72
A	LYS72

site_id	SWS_FT_FI7
Number of Residues	4
Details	MOD_RES: Omega-N-methylarginine; by PRMT6 => ECO:0000269\|PubMed:16600869

Chain	Residue	Details
F	ARG83
F	ARG152
A	ARG83
A	ARG152

site_id	SWS_FT_FI8
Number of Residues	8
Details	CROSSLNK: Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin) => ECO:0000269\|PubMed:19713937, ECO:0000269\|PubMed:21362556

Chain	Residue	Details
F	LYS41
F	LYS61
F	LYS81
A	LYS41
A	LYS61
A	LYS81

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