Structure of PDB 6mr8 Chain A

Receptor sequence

>6mr8A (length=320) Species: 9606 (Homo sapiens) [Search protein sequence]

LNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAK
KLPGVGTKIAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSA
ARKFVDEGIKTLEDLRKNEDKLNHHQRIGLKYFGDFEKRIPREEMLQMQD
IVLNEVKKVDSEYIATVCGSFRRGAESSGDMDVLLTHPSFTSESPKLLHQ
VVEQLQKVHFITDTLSKGETKFMGVCQLPSKEKEYPHRRIDIRLIPKDQY
YCGVLYFTGSGIFNKNMRAHALEKGFTINEYTIRPLGVTGVAGEPLPVDS
EKDIFDYIQWKYREPKDRSE

3D structure

PDB

6mr8 A guardian residue hinders insertion of a Fapy•dGTP analog by modulating the open-closed DNA polymerase transition.

Chain

Resolution

1.897 Å

3D
structure

[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]

Enzymatic activity

Enzyme Commision number

2.7.7.7: DNA-directed DNA polymerase.
4.2.99.-
4.2.99.18: DNA-(apurinic or apyrimidinic site) lyase.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)
BS01	dna	A	H34 S229 K230 G231 T233 K234 Y296	H24 S216 K217 G218 T220 K221 Y281
BS02	dna	A	S104 G105 I106 G107 P108 S109 A110 R254	S94 G95 I96 G97 P98 S99 A100 R239
BS03	dna	A	K35 Y39 P63 G64 G66 K68 I69	K25 Y29 P53 G54 G56 K58 I59
BS04	GKS	A	R149 G179 S180 Y271 F272 G276	R139 G169 S170 Y256 F257 G261
BS05	CA	A	D190 D192	D180 D182

Gene Ontology

	Molecular Function
GO:0003677	DNA binding
GO:0003684	damaged DNA binding
GO:0003887	DNA-directed DNA polymerase activity
GO:0003906	DNA-(apurinic or apyrimidinic site) endonuclease activity
GO:0005515	protein binding
GO:0008017	microtubule binding
GO:0016779	nucleotidyltransferase activity
GO:0016829	lyase activity
GO:0019899	enzyme binding
GO:0034061	DNA polymerase activity
GO:0046872	metal ion binding
GO:0051575	5'-deoxyribose-5-phosphate lyase activity
GO:0140078	class I DNA-(apurinic or apyrimidinic site) endonuclease activity

	Biological Process
GO:0001701	in utero embryonic development
GO:0006259	DNA metabolic process
GO:0006260	DNA replication
GO:0006261	DNA-templated DNA replication
GO:0006281	DNA repair
GO:0006284	base-excision repair
GO:0006287	base-excision repair, gap-filling
GO:0006290	pyrimidine dimer repair
GO:0006297	nucleotide-excision repair, DNA gap filling
GO:0006303	double-strand break repair via nonhomologous end joining
GO:0006915	apoptotic process
GO:0006954	inflammatory response
GO:0006974	DNA damage response
GO:0007435	salivary gland morphogenesis
GO:0008630	intrinsic apoptotic signaling pathway in response to DNA damage
GO:0010332	response to gamma radiation
GO:0016445	somatic diversification of immunoglobulins
GO:0016446	somatic hypermutation of immunoglobulin genes
GO:0045471	response to ethanol
GO:0048535	lymph node development
GO:0048536	spleen development
GO:0048872	homeostasis of number of cells
GO:0051402	neuron apoptotic process
GO:0055093	response to hyperoxia
GO:0071707	immunoglobulin heavy chain V-D-J recombination
GO:0071897	DNA biosynthetic process

	Cellular Component
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005737	cytoplasm
GO:0005874	microtubule
GO:0005876	spindle microtubule
GO:0032991	protein-containing complex

View graph for
Molecular Function

View graph for
Biological Process

View graph for
Cellular Component

External links

PDB	RCSB:6mr8, PDBe:6mr8, PDBj:6mr8
PDBsum	6mr8
PubMed	30649431
UniProt	P06746\|DPOLB_HUMAN DNA polymerase beta (Gene Name=POLB)

[Back to BioLiP]