Structure of PDB 7s0t Chain A

Receptor sequence

>7s0tA (length=1231) Species: 4932 (Saccharomyces cerevisiae)

SDYFRIQLNNQDYYMSKPTFLDPSHGESLPLNQFSQVPNIRVFGALPTGH
QVLCHVHGILPYMFIKYDGQITDTSTLRHQRCAQVHKTLEVKIRASFKKL
GNLNFVADVSVVKGIPFYGYHVGWNLFYKISLLNPSCLSRISELIRDGKI
FGKKFEIYESHIPYLLQWTADFNLFGCSWINVDRCYFRSPVLNSILDIDK
LTINDDLQLLLDRFCDFKCNVLSRRDFPRVGNGLIEIDILPQFIKNREKL
QHRDIHHDFLEKLGKPYVSSARDMINELTMQREYKEPPETKRHVSGHQWQ
SSGEFEAFYKKAQHKTSTIPNFENFIDKQKFSAINTPYEALPQLWPRLPQ
IEAGLRYGKRAFVYGEPPFGYQDILNKLEDEGFPKIDYKDPFFSNPVDLE
NKPYAYAGKRFEISSTHVSTRIPVQFGGETVSVYNKPTFDMFSSWKYALK
PPTYDAVQKWYNKVPSSVHDSLTHLTLEIHANTRSDKIPDPAIDEVSMII
WCLEEETFPLDLDIAYEGIMIVHKADSTFPTKIQHCINEIPVMFYESEFE
MFEALTDLVLLLDPDILSGFEIHNFSWGYIIERCQKIHQFDIVRELARVK
CSDTWGYAHSSGIMITGRHMINIWRALRSDVNLTQYTIESAAFNILHKRL
PHFSFESLTNMWNAKKSTTELKTVLNYWLSRAQINIQLLRKQDYIARNIE
QARLIGIDFHSVYYRGSQFKVESFLIRICKSESFILLSPGKKDVRKQKAL
ECVPLVMEPESAFYKSPLIVLDFQSLYPSIMIGYNYCYSTMIGRVREINL
TENNLGVSKFSLPRNILALLKNDVTIAPNGVVYAKTSVRKSTLSKMLTDI
LDVRVMIKKTMTTLKRLLNNKQLALKLLANVTYGYTSASFSGRMPCSDLA
DSIVQTGRETLEKAIDIIEKDETWNAKVVYGDTDSLFVYLPGKTAIEAFS
IGHAMAERVTQNNPKPIFLKFEKVYHPSILISKKRYVGFSYESPSQTLPI
FDAKGIETVRRDGIPAQQKIIEKCIRLLFQTKDLSKIKKYLQNEFFKIQI
GKVSAQDFCFAKEVKLGAYKSEKTAPAGAVVVKRRINAEPQYKERIPYLV
VKQLLRCVSPEFLEGLDSEYYINKILIPPLDRLFNLIGINVGNWAQEIKR
STTTLSFLIKKLKRQKEYQTLKTVCRTCSYRYTSDAGIENDHIASKCNSY
DCPVFYSRVKAERYLRDNQSVQREEALISLN

3D structure

• PDB: 7s0t Cryo-EM structure of translesion DNA synthesis polymerase zeta with a base pair mismatch.
• Chain: A
• Resolution: 3.05 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.

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	D1142 K1194 K1214 R1220 R1221 E1273 Y1279 T1284	D932 K984 K1004 R1010 R1011 E1063 Y1069 T1074
BS02	dna	A	W808 R918 G919 Q921 V956 G1094 S1097 F1100 K1193 R1195 L1322 L1323 R1324 R1357	W605 R715 G716 Q718 V753 G884 S887 F890 K983 R985 L1104 L1105 R1106 R1132
BS03	SF4	A	P854 C1446 C1449 C1468 C1473 V1475 F1476 R1479	P651 C1175 C1178 C1197 C1202 V1204 F1205 R1208
BS04	CA	A	D975 F976 D1144	D772 F773 D934
BS05	DCP	A	F976 S978 Y980 Y1093 D1144	F773 S775 Y777 Y883 D934

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0005515 protein binding
• GO:0008270 zinc ion binding
• GO:0046872 metal ion binding
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:0000724 double-strand break repair via homologous recombination
• GO:0006260 DNA replication
• GO:0006281 DNA repair
• GO:0006974 DNA damage response
• GO:0019985 translesion synthesis
• GO:0042276 error-prone translesion synthesis
• GO:0070987 error-free translesion synthesis

Cellular Component

• GO:0005634 nucleus
• GO:0005739 mitochondrion
• GO:0016035 zeta DNA polymerase complex
• GO:0043231 intracellular membrane-bounded organelle

External links

• PDB: RCSB:7s0t, PDBe:7s0t, PDBj:7s0t
• PDBsum: 7s0t
• PubMed: 35217661
• UniProt: P14284|DPOZ_YEAST DNA polymerase zeta catalytic subunit (Gene Name=REV3)