Structure of PDB 8b79 Chain A

Receptor sequence

>8b79A (length=1118) Species: 4932 (Saccharomyces cerevisiae)

ALSAQQLLNASKIDDIDSMMGFERYVPPQYNGRFDAKDIDQIPGRVGWLT
NMHATLVSQEQGISGVDFYFLDEEGGSFKSTVVYDPYFFIACNDESRVND
VEELVKKYLESCLKSLQIIRKEDLTMDNHLLGLQKTLIKLSFVNSNQLFE
ARKLLRPILQDNANNNVQRNIYNVVDAKHLIEDIREYDVPYHVRVSIDKD
IRVGKWYKVTQQGFIEDTRKIAFADPVVMAFDIETTKPPLKFPDSAVDQI
MMISYMIDGEGFLITNREIISEDIEDFEYTPKPEYPGFFTIFNENDEVAL
LQRFFEHIRDVRPTVISTFNGDFFDWPFIHNRSKIHGLDMFDEIGFAPDA
EGEYKSSYCSHMDCFRWVKRDSYLPQGSQGLKAVTQSKLGYNPIELDPEL
MTPYAFEKPQHLSEYSVSDAVATYYLYMKYVHPFIFSLCTIIPLNPDETL
RKGTGTLCEMLLMVQAYQHNILLPNKHTDPIERFYDGHLLESETYVGGHV
ESLEAGVFRSDLKNEFKIDPSAIDELLQELPEALKFSVEVENKSSVDKVT
NFEEIKNQITQKLLELKENNIRNELPLIYHVDVASGYPNIMTTNRLQPDS
IKAERDCTCARKLKWAWRGEFFPSKMDEYNMIKRALQNETFPNKNKFSKK
KVLTFDELSYADQVIHIKKRLTEYSRKVYHRVKVSEIVEREAIVCQRENP
FYVDTVKSFRDRRYEFKGLAKTWKGNLSKIDPSDKHARDEAKKMIVLYDS
LQLAHKVILNSFYGYVMRKGSRWYSMEMAGITCLTGATIIQMARALVERV
GRPLELDTDGIWCILPKSFPETYFFTLENGKKLYLSYPCSMLNYRVHQKF
TNHQYQELKDPLNYIYETHSENTIFFEVDGPYKAMILPSSKEEGKGIKKR
YAVFNEDGSLAELKGFELKRRGELQLIKNFQSDIFKVFLEGDTLEGCYSA
VASVCNRWLDVLDSHGLMLEDEDLVSLICENRSMSKTLKEYEGQKSTSIT
TARRLGDFLGEDMVKDKGLQCKYIISSKPFNAPVTERAIPVAIFSADIPI
KRSFLRRWTLDPSLEDLDIRTIIDWGYYRERLGSAIQKIITIPAALQGVS
NPVPRVEHPDWLKRKIAT

3D structure

• PDB: 8b79 A sensor complements the steric gate when DNA polymerase epsilon discriminates ribonucleotides.
• Chain: A
• Resolution: 2.65 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	P433 Q434 D875 T876 K967 Y969 K982 G983 K987 R988 R989 S1051 S1053 Y1059	P375 Q376 D807 T808 K899 Y901 K914 G915 K919 R920 R921 S983 S985 Y991
BS02	dna	A	K510 G511 T512 G513 T514 T552 Y553 G555 G556 R686 R744 S829 G832 M835 R836 K837 I965 K966 K967 R968 R988 K1063 T1103 Y1145 R1149 K1156	K452 G453 T454 G455 T456 T494 Y495 G497 G498 R618 R676 S761 G764 M767 R768 K769 I897 K898 K899 R900 R920 K995 T1035 Y1077 R1081 K1088
BS03	UTP	A	D640 V641 A642 S643 G644 Y645 R781 K785 K824 N828 Y831 D877	D582 V583 A584 S585 G586 Y587 R713 K717 K756 N760 Y763 D809
BS04	CA	A	D640 V641 D877	D582 V583 D809
BS05	CA	A	D640 E945	D582 E877
BS06	CA	A	D290 E292 D477	D232 E234 D419

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:8b79, PDBe:8b79, PDBj:8b79
• PDBsum: 8b79
• PubMed: 37819038
• UniProt: P21951|DPOE_YEAST DNA polymerase epsilon catalytic subunit A (Gene Name=POL2)