Structure of PDB 8b7e Chain B

Receptor sequence

>8b7eB (length=1122) Species: 4932 (Saccharomyces cerevisiae)

NNYALSAQQLLNASKIDDIDSMMGFERYVPPQYNGRFDAKDIDQIPGRVG
WLTNMHATLVSQENQGISGVDFYFLDEEGGSFKSTVVYDPYFFIACNDES
RVNDVEELVKKYLESCLKSLQIIRKEDLTMDNHLLGLQKTLIKLSFVNSN
QLFEARKLLRPILQDNANNNVQRNIYNVVDAKHLIEDIREYDVPYHVRVS
IDKDIRVGKWYKVTQQGFIEDTRKIAFADPVVMAFAIATTKPPLKFPDSA
VDQIMMISYMIDGEGFLITNREIISEDIEDFEYTPKPEYPGFFTIFNEND
EVALLQRFFEHIRDVRPTVISTFNGDFFDWPFIHNRSKIHGLDMFDEIGF
APDAEGEYKSSYCSHMDCFRWVKRDSYLPQGSQGLKAVTQSKLGYNPIEL
DPELMTPYAFEKPQHLSEYSVSDAVATYYLYMKYVHPFIFSLCTIIPLNP
DETLRKGTGTLCEMLLMVQAYQHNILLPNKHTDPIERFYDGHLLESETYV
GGHVESLEAGVFRSDLKNEFKIDPSAIDELLQELPEALKFSVEVENKSSV
DKVTNFEEIKNQITQKLLELKENNIRNELPLIYHVDVASMYPNIMTTNRL
QPDSIKAERDCTCARKLKWAWRGEFFPSKMDEYNMIKRALQNETFPNKNK
FSKKKVLTFDELSYADQVIHIKKRLTEYSRKVYHRVKVSEIVEREAIVCQ
RENPFYVDTVKSFRDRRYEFKGLAKTWKGNLSKIDPSDKHARDEAKKMIV
LYDSLQLAHKVILVSFYGYVMRKGSRWYSMEMAGITCLTGATIIQMARAL
VERVGRPLELDTDGIWCILPKSFPETYFFTLENGKKLYLSYPCSMLNYRV
HQKFTNHQYQELKDPLNYIYETHSENTIFFEVDGPYKAMILPSSKEEGKG
IKKRYAVFNEDGSLAELKGFELKRRGELQLIKNFQSDIFKVFLEGDTLEG
CYSAVASVCNRWLDVLDSHGLMLEDEDLVSLICENRSMSKTLKEYEGQKS
TSITTARRLGDFLGEDMVKDKGLQCKYIISSKPFNAPVTERAIPVAIFSA
DIPIKRSFLRRWTLDPSLEDLDIRTIIDWGYYRERLGSAIQKIITIPAAL
QGVSNPVPRVEHPDWLKRKIAT

3D structure

• PDB: 8b7e 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	Q434 V750 K751 D875 T876 K967 Y969 K982 G983 K987 R988 R989 S1051 S1053 Y1059 Q1062	Q380 V686 K687 D811 T812 K903 Y905 K918 G919 K923 R924 R925 S987 S989 Y995 Q998
BS02	dna	B	K510 G511 T512 G513 T514 T552 Y553 G555 G556 V558 R686 R744 H748 S829 G832 M835 R836 K837 I965 K966 K967 R988 K1063 T1103 Y1145 K1156	K456 G457 T458 G459 T460 T498 Y499 G501 G502 V504 R622 R680 H684 S765 G768 M771 R772 K773 I901 K902 K903 R924 K999 T1039 Y1081 K1092
BS03	dna	B	S1032 L1035 M1036	S968 L971 M972
BS04	dna	B	D1028 D1031 R1173	D964 D967 R1109
BS05	UTP	B	D640 S643 Y645 R781 K785 K824 V828 D877	D586 S589 Y591 R717 K721 K760 V764 D813
BS06	CA	B	D640 V641 D877	D586 V587 D813

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:8b7e, PDBe:8b7e, PDBj:8b7e
• PDBsum: 8b7e
• PubMed: 37819038
• UniProt: P21951|DPOE_YEAST DNA polymerase epsilon catalytic subunit A (Gene Name=POL2)