Structure of PDB 4m8o Chain A

Receptor sequence

>4m8oA (length=1126) Species: 559292 (Saccharomyces cerevisiae S288C)

ALSAQQLLNASKIDDIDSMMGFERYVPPQYNGRFDAKDIDQIPGRVGWLT
NMHATLVSQEVTTNQGISGVDFYFLDEEGGSFKSTVVYDPYFFIACNDES
RVNDVEELVKKYLESCLKSLQIIRKEDLTMDNHLLGLQKTLIKLSFVNSN
QLFEARKLLRPILQDNANNNVQRNIYNVKVDAKHLIEDIREYDVPYHVRV
SIDKDIRVGKWYKVTQQGFIEDTRKIAFADPVVMAFAIATTKPPLKFPDS
AVDQIMMISYMIDGEGFLITNREIISEDIEDFEYTPKPEYPGFFTIFNEN
DEVALLQRFFEHIRDVRPTVISTFNGDFFDWPFIHNRSKIHGLDMFDEIG
FAPDAEGEYKSSYCSHMDCFRWVKRDSYLPQGSQGLKAVTQSKLGYNPIE
LDPELMTPYAFEKPQHLSEYSVSDAVATYYLYMKYVHPFIFSLCTIIPLN
PDETLRKGTGTLCEMLLMVQAYQHNILLPNKHTDPIERFYDGHLLESETY
VGGHVESLEAGVFRSDLKNEFKIDPSAIDELLQELPEALKFSVEVENKSS
VDKVTNFEEIKNQITQKLLELKENNIRNELPLIYHVDVASMYPNIMTTNR
LQPDSIKAERDCASCTCARKLKWAWRGEFFPSKMDEYNMIKRALQNETFP
NKNKFSKKKVLTFDELSYADQVIHIKKRLTEYSRKVYHRVKVSEIVEREA
IVCQRENPFYVDTVKSFRDRRYEFKGLAKTWKGNLSKIDPSDKHARDEAK
KMIVLYDSLQLAHKVILNSFYGYVMRKGSRWYSMEMAGITCLTGATIIQM
ARALVERVGRPLELDTDGIWCILPKSFPETYFFTLENGKKLYLSYPCSML
NYRVHQKFTNHQYQELKDPLNYIYETHSENTIFFEVDGPYKAMILPSSKE
EGKGIKKRYAVFNEDGSLAELKGFELKRRGELQLIKNFQSDIFKVFLEGD
TLEGCYSAVASVCNRWLDVLDSHGLMLEDEDLVSLICENRSMSKTLKEYE
GQKSTSITTARRLGDFLGEDMVKDKGLQCKYIISSKPFNAPVTERAIPVA
IFSADIPIKRSFLRRWTLDPSLEDLDIRTIIDWGYYRERLGSAIQKIITI
PAALQGVSNPVPRVEHPDWLKRKIAT

3D structure

• PDB: 4m8o Structural basis for processive DNA synthesis by yeast DNA polymerase epsilon.
• Chain: A
• Resolution: 2.2 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 K751 D875 T876 K967 Y969 K982 K987 R988 R989 S1051 S1053 Y1059	P380 Q381 K691 D815 T816 K907 Y909 K922 K927 R928 R929 S991 S993 Y999
BS02	dna	A	K510 G511 T512 G513 T514 T552 Y553 G555 G556 R686 S829 G832 M835 R836 K837 I965 K966 K967 R988 K1063 V1102 T1103 Y1145 R1149 K1156	K457 G458 T459 G460 T461 T499 Y500 G502 G503 R626 S769 G772 M775 R776 K777 I905 K906 K907 R928 K1003 V1042 T1043 Y1085 R1089 K1096
BS03	DTP	A	D640 V641 A642 S643 M644 Y645 R781 K785 K824 N828 D877	D587 V588 A589 S590 M591 Y592 R721 K725 K764 N768 D817
BS04	MG	A	D640 V641 D877	D587 V588 D817
BS05	ZN	A	C665 C668 C763	C612 C615 C703

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:4m8o, PDBe:4m8o, PDBj:4m8o
• PDBsum: 4m8o
• PubMed: 24292646
• UniProt: P21951|DPOE_YEAST DNA polymerase epsilon catalytic subunit A (Gene Name=POL2)