Structure of PDB 8b6k Chain B

Receptor sequence

>8b6kB (length=1108) Species: 4932 (Saccharomyces cerevisiae)

ALSAQQLLNASKIDDIDSMMGFERYVPPQYNGRFDAKDIDQIPGRVGWLT
NMHATLVSQEQGISGVDFYFLDEEGGSFKSTVVYDPYFFIACNDESRVND
VEELVKKYLESCLKSLQIIRKEDLTMDNHLLGLQKTLIKLSFVNSNQLFE
ARKLLRPILQDNANNNVQRNIYNKVDAKHLIEDIREYDVPYHVRVSIDKD
IRVGKWYKVTQQGFIEDTRKIAFADPVVMAFAIATTKPPLKFPDSAVDQI
MMISYMIDGEGFLITNREIISEDIEDFEYTPKPEYPGFFTIFNENDEVAL
LQRFFEHIRDVRPTVISTFNGDFFDWPFIHNRSKIHGLDMFDEIGFAPDA
EGEYKSSYCSHMDCFRWVKRDSYLPQGSQGLKAVTQSKLGYNPIELDPEL
MTPYAFEKPQHLSEYSVSDAVATYYLYMKYVHPFIFSLCTIIPLNPDETL
RKGTGTLCEMLLMVQAYQHNILLPNKHTDPIERFYDGHLLESETYVGGHV
ESLEAGVFRSDLKNEFKIDPSAIDELLQELPEALKFSVEVENKSSVDKVT
NFEEIKNQITQKLLELKENNIRNELPLIYHVDVASGYPNIMTTNRLQPDS
IKTCARKLKWAWRGEFFPSKMDEYNMIKRALQNETFPNKKKKVLTFDELS
YADQVIHIKKRLTEYSRKVYHRVKVSEIVEREAIVCQRENPFYVDTVKSF
RDRRYEFKGLAKTWKGNLSKIDPSDKHARDEAKKMIVLYDSLQLAHKVIL
NSFYGYVMRKGSRWYSMEMAGITCLTGATIIQMARALVERVGRPLELDTD
GIWCILPKSFPETYFFTLENGKKLYLSYPCSMLNYRVHQKFTNHQYQELK
DPLNYIYETHSENTIFFEVDGPYKAMILPSSKEEGKGIKKRYAVFNEDGS
LAELKGFELKRRGELQLIKNFQSDIFKVFLEGDTLEGCYSAVASVCNRWL
DVLDSHGLMLEDEDLVSLICENRSMSKTLKEYEGQKSTSITTARRLGDFL
GEDMVKDKGLQCKYIISSKPFNAPVTERAIPVAIFSADIPIKRSFLRRWT
LDPSLEDLDIRTIIDWGYYRERLGSAIQKIITIPAALQGVSNPVPRVEHP
DWLKRKIA

3D structure

• PDB: 8b6k A sensor complements the steric gate when DNA polymerase epsilon discriminates ribonucleotides.
• Chain: B
• Resolution: 2.5 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.
  3.1.11.-

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)	Binding affinity
BS01	dna	B	S1032 L1035 M1036	S955 L958 M959
BS02	dna	B	P433 Q434 G435 D875 T876 K967 Y969 K982 G983 K987 R988 R989 S1053 Y1059 Q1062	P375 Q376 G377 D798 T799 K890 Y892 K905 G906 K910 R911 R912 S976 Y982 Q985
BS03	dna	B	K510 G511 T512 G513 T514 T552 Y553 G555 G556 R686 N828 S829 Y831 G832 M835 R836 K837 I965 K966 K967 R968 R988 K1063 V1102 T1103 Y1145 K1156	K452 G453 T454 G455 T456 T494 Y495 G497 G498 R613 N751 S752 Y754 G755 M758 R759 K760 I888 K889 K890 R891 R911 K986 V1025 T1026 Y1068 K1079
BS04	CA	B	D640 V641 D877	D582 V583 D800
BS05	DCP	B	V641 S643 Y645 R781 K824 N828 Y831 D877	V583 S585 Y587 R704 K747 N751 Y754 D800

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003887 DNA-directed DNA polymerase activity

Biological Process

• GO:0006260 DNA replication
• GO:0006281 DNA repair

Cellular Component

• GO:0008622 epsilon DNA polymerase complex

External links

• PDB: RCSB:8b6k, PDBe:8b6k, PDBj:8b6k
• PDBsum: 8b6k
• PubMed: 37819038
• UniProt: P21951|DPOE_YEAST DNA polymerase epsilon catalytic subunit A (Gene Name=POL2)