Structure of PDB 8b67 Chain A

Receptor sequence

>8b67A (length=1085) Species: 4932 (Saccharomyces cerevisiae)

NYALSAQQLLNASKIDDIDSMMGFERYVPPQYNGRFDAKDIDQIPGRVGW
LTNMHATLVSQENQGISGVDFYFLDEEGGSFKSTVVYDPYFFIACNDESR
VNDVEELVKKYLESCLKSLQIIRKEDLTMDNHLLGLQKTLIKLSFVNSNQ
LFEARKLLRPILQDNQRNIYNVDAKHLIEDIREYDVPYHVRVSIDKDIRV
GKWYKVTQQGFIEDTRKIAFADPVVMAFDIETTKPPLKFPDSAVDQIMMI
SYMIDGEGFLITNREIISEDIEDFEYTPKPEYPGFFTIFNENDEVALLQR
FFEHIRDVRPTVISTFNGDFFDWPFIHNRSKIHGLDMFDEIGFAPDAEGE
YKSSYCSHMDCFRWVKRDSYLPQGSQGLKAVTQSKLGYNPIELDPELMTP
YAFEKPQHLSEYSVSDAVATYYLYMKYVHPFIFSLCTIIPLNPDETLRKG
TGTLCEMLLMVQAYQHNILLPNKHTDPIERFYDGHLLESETYVGGHVESL
EAGVFRSDLKNEFKIDPSAIDELLQELPEALKFSVEVENKSSVDKVTNFE
EIKNQITQKLLELKENNIRNELPLIYHVDVASGYPNIMTTNRLQPDSIKA
ERDCTCARKLKWAWRGEFFPSKMDEYNMIKRALQNETFPNVLTFDELSYA
DQVIHIKKRLTEYSRKVYHRVKVSEIVEREAIVCQRENPFYVDTVKSFRD
RRYEFKGLAKTMIVLYDSLQLAHKVILNSFYGYVMRKGSRWYSMEMAGIT
CLTGATIIQMARALVERVGRPLELDTDGIWCILPKSFPETYFFTLENGKK
LYLSYPCSMLNYRVHQKFTNHQYQELKDPLNYIYETHSENTIFFEVDGPY
KAMILPSSKEEGKGIKKRYAVFNEDGSLAELKGFELKRRGELQLIKNFQS
DIFKVFLEGDTLEGCYSAVASVCNRWLDVLDSHGLMLEDEDLVSLICENR
SMSKTLKEYEGQKSTSITTARRLGDFLGEDMVKDKGLQCKYIISSKPFNA
PVTERAIPVAIFSADIPIKRSFLRRWTLDPSLEDLDIRTIIDWGYYRERL
GSAIQKIITIPAALQGVSNPVPRVEHPDWLKRKIA

3D structure

• PDB: 8b67 A sensor complements the steric gate when DNA polymerase epsilon discriminates ribonucleotides.
• Chain: A
• 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	A	Q434 R749 K751 D875 T876 K967 Y969 K982 G983 K987 R988 R989 S1053 Y1059	Q373 R670 K672 D775 T776 K867 Y869 K882 G883 K887 R888 R889 S953 Y959
BS02	dna	A	K510 G511 T512 G513 T514 T552 Y553 G555 G556 V558 R686 N828 S829 Y831 G832 M835 R836 I965 K966 K967 R988 K1063 T1103 Y1145 R1149 K1156	K449 G450 T451 G452 T453 T491 Y492 G494 G495 V497 R615 N728 S729 Y731 G732 M735 R736 I865 K866 K867 R888 K963 T1003 Y1045 R1049 K1056
BS03	CA	A	D640 V641 D877	D579 V580 D777
BS04	CA	A	D640 E945	D579 E845
BS05	CA	A	D290 E292 D477	D229 E231 D416
BS06	CTP	A	Y431 D640 V641 S643 Y645 R781 K824 N828 Y831 D877	Y370 D579 V580 S582 Y584 R702 K724 N728 Y731 D777

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:8b67, PDBe:8b67, PDBj:8b67
• PDBsum: 8b67
• PubMed: 37819038
• UniProt: P21951|DPOE_YEAST DNA polymerase epsilon catalytic subunit A (Gene Name=POL2)