Structure of PDB 8b79 Chain B

Receptor sequence

>8b79B (length=1119) Species: 4932 (Saccharomyces cerevisiae)

NYALSAQQLLNASKIDDIDSMMGFERYVPPQYNGRFDAKDIDQIPGRVGW
LTNMHATLVSQQGISGVDFYFLDEEGGSFKSTVVYDPYFFIACNDESRVN
DVEELVKKYLESCLKSLQIIRKEDLTMDNHLLGLQKTLIKLSFVNSNQLF
EARKLLRPILQDNANNNVQRNIYNVVDAKHLIEDIREYDVPYHVRVSIDK
DIRVGKWYKVTQQGFIEDTRKIAFADPVVMAFDIETTKPPLKFPDSAVDQ
IMMISYMIDGEGFLITNREIISEDIEDFEYTPKPEYPGFFTIFNENDEVA
LLQRFFEHIRDVRPTVISTFNGDFFDWPFIHNRSKIHGLDMFDEIGFAPD
AEGEYKSSYCSHMDCFRWVKRDSYLPQGSQGLKAVTQSKLGYNPIELDPE
LMTPYAFEKPQHLSEYSVSDAVATYYLYMKYVHPFIFSLCTIIPLNPDET
LRKGTGTLCEMLLMVQAYQHNILLPNKHTDPIERFYDGHLLESETYVGGH
VESLEAGVFRSDLKNEFKIDPSAIDELLQELPEALKFSVEVENKSSVDKV
TNFEEIKNQITQKLLELKENNIRNELPLIYHVDVASGYPNIMTTNRLQPD
SIKAERDCTCARKLKWAWRGEFFPSKMDEYNMIKRALQNETFPNKNKFSK
KKVLTFDELSYADQVIHIKKRLTEYSRKVYHRVKVSEIVEREAIVCQREN
PFYVDTVKSFRDRRYEFKGLAKTWKGNLSKIDPSDKHARDEAKKMIVLYD
SLQLAHKVILNSFYGYVMRKGSRWYSMEMAGITCLTGATIIQMARALVER
VGRPLELDTDGIWCILPKSFPETYFFTLENGKKLYLSYPCSMLNYRVHQK
FTNHQYQELKDPLNYIYETHSENTIFFEVDGPYKAMILPSSKEEGKGIKK
RYAVFNEDGSLAELKGFELKRRGELQLIKNFQSDIFKVFLEGDTLEGCYS
AVASVCNRWLDVLDSHGLMLEDEDLVSLICENRSMSKTLKEYEGQKSTSI
TTARRLGDFLGEDMVKDKGLQCKYIISSKPFNAPVTERAIPVAIFSADIP
IKRSFLRRWTLDPSLEDLDIRTIIDWGYYRERLGSAIQKIITIPAALQGV
SNPVPRVEHPDWLKRKIAT

3D structure

• PDB: 8b79 A sensor complements the steric gate when DNA polymerase epsilon discriminates ribonucleotides.
• Chain: B
• 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	B	Q434 D875 T876 K967 Y969 K982 G983 K987 R988 R989 S1051 S1053 Y1059 Q1062	Q377 D808 T809 K900 Y902 K915 G916 K920 R921 R922 S984 S986 Y992 Q995
BS02	dna	B	K510 G511 T512 G513 T514 T552 Y553 G555 R686 R744 S829 G832 M835 R836 K837 I965 K966 K967 R968 R988 K1063 V1102 T1103 Y1145 R1149 K1156	K453 G454 T455 G456 T457 T495 Y496 G498 R619 R677 S762 G765 M768 R769 K770 I898 K899 K900 R901 R921 K996 V1035 T1036 Y1078 R1082 K1089
BS03	dna	B	D1028 D1031 R1173	D961 D964 R1106
BS04	UTP	B	D640 V641 S643 G644 Y645 R781 K824 N828 Y831 D877	D583 V584 S586 G587 Y588 R714 K757 N761 Y764 D810
BS05	CA	B	D640 V641 D877	D583 V584 D810
BS06	CA	B	D640 E945	D583 E878
BS07	CA	B	D290 E292 D477	D233 E235 D420

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)