Structure of PDB 8b76 Chain B

Receptor sequence

>8b76B (length=1121) Species: 4932 (Saccharomyces cerevisiae)

NNYALSAQQLLNASKIDDIDSMMGFERYVPPQYNGRFDAKDIDQIPGRVG
WLTNMHATLVSQENQGISGVDFYFLDEEGGSFKSTVVYDPYFFIACNDES
RVNDVEELVKKYLESCLKSLQIIRKEDLTMDNHLLGLQKTLIKLSFVNSN
QLFEARKLLRPILQDNANNNVQRNIYNVDAKHLIEDIREYDVPYHVRVSI
DKDIRVGKWYKVTQQGFIEDTRKIAFADPVVMAFDIETTKPPLKFPDSAV
DQIMMISYMIDGEGFLITNREIISEDIEDFEYTPKPEYPGFFTIFNENDE
VALLQRFFEHIRDVRPTVISTFNGDFFDWPFIHNRSKIHGLDMFDEIGFA
PDAEGEYKSSYCSHMDCFRWVKRDSYLPQGSQGLKAVTQSKLGYNPIELD
PELMTPYAFEKPQHLSEYSVSDAVATYYLYMKYVHPFIFSLCTIIPLNPD
ETLRKGTGTLCEMLLMVQAYQHNILLPNKHTDPIERFYDGHLLESETYVG
GHVESLEAGVFRSDLKNEFKIDPSAIDELLQELPEALKFSVEVENKSSVD
KVTNFEEIKNQITQKLLELKENNIRNELPLIYHVDVASGYPNIMTTNRLQ
PDSIKAERDCTCARKLKWAWRGEFFPSKMDEYNMIKRALQNETFPNKNKF
SKKKVLTFDELSYADQVIHIKKRLTEYSRKVYHRVKVSEIVEREAIVCQR
ENPFYVDTVKSFRDRRYEFKGLAKTWKGNLSKIDPSDKHARDEAKKMIVL
YDSLQLAHKVILNSFYGYVMRKGSRWYSMEMAGITCLTGATIIQMARALV
ERVGRPLELDTDGIWCILPKSFPETYFFTLENGKKLYLSYPCSMLNYRVH
QKFTNHQYQELKDPLNYIYETHSENTIFFEVDGPYKAMILPSSKEEGKGI
KKRYAVFNEDGSLAELKGFELKRRGELQLIKNFQSDIFKVFLEGDTLEGC
YSAVASVCNRWLDVLDSHGLMLEDEDLVSLICENRSMSKTLKEYEGQKST
SITTARRLGDFLGEDMVKDKGLQCKYIISSKPFNAPVTERAIPVAIFSAD
IPIKRSFLRRWTLDPSLEDLDIRTIIDWGYYRERLGSAIQKIITIPAALQ
GVSNPVPRVEHPDWLKRKIAT

3D structure

• PDB: 8b76 A sensor complements the steric gate when DNA polymerase epsilon discriminates ribonucleotides.
• Chain: B
• Resolution: 2.6 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	P433 Q434 K751 D875 T876 K967 Y969 K982 G983 K987 R988 R989 S1051 S1053 Y1059 Q1062	P378 Q379 K686 D810 T811 K902 Y904 K917 G918 K922 R923 R924 S986 S988 Y994 Q997
BS02	dna	B	K510 G511 T512 G513 T514 T552 Y553 G555 G556 R686 R744 S829 G832 M835 R836 K837 I965 K966 K967 R988 T1103 Y1145 R1149 K1156	K455 G456 T457 G458 T459 T497 Y498 G500 G501 R621 R679 S764 G767 M770 R771 K772 I900 K901 K902 R923 T1038 Y1080 R1084 K1091
BS03	dna	B	S1032 L1035 M1036	S967 L970 M971
BS04	dna	B	D1028 D1031	D963 D966
BS05	CA	B	D640 V641 D877	D585 V586 D812
BS06	CA	B	D290 E292 D477	D235 E237 D422
BS07	TTP	B	Y431 D640 V641 A642 S643 G644 Y645 R781 K824 N828 D877	Y376 D585 V586 A587 S588 G589 Y590 R716 K759 N763 D812

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:8b76, PDBe:8b76, PDBj:8b76
• PDBsum: 8b76
• PubMed: 37819038
• UniProt: P21951|DPOE_YEAST DNA polymerase epsilon catalytic subunit A (Gene Name=POL2)