Structure of PDB 8fok Chain 1

Receptor sequence

>8fok1 (length=1046) Species: 4932 (Saccharomyces cerevisiae)

FQMFWLDYCEVNNTLILFGKVKLKDDNCVSAMVQINGLCRELFFLPREGK
TPTDIHEEIIPLLMDKYGLDNIRAKPQKMKYSFELPDIPSESDYLKVLLP
YQTPKSSRDTIPSDLSSDTFYHVFGGNSNIFESFVIQNRIMGPCWLDIKG
ADFSHCAVEVSVDKPQNITPTTTKTMPNLRCLSLSIQTLMNPKENKQEIV
SITLSAYRNISLDSPIPENIKPDDLCTLVRPPQSTSFPLGLAALAKQKLP
GRVRLFNNEKAMLSCFCAMLKVEDPDVIIGHRLQNVYLDVLAHRMHDLNI
PTFSSIGRRLRRTWPEKFGNMNHFFISDICSGRLICDIANEMGQSLTPKC
QSWDLSEMYQVTCEKEHKPLDIDYQNPQYQNDVNSMTMALQENITNCMIS
AEVSYRIQLLTLTKQLTNLAGNAWAQTLGGTRAGRNEYILLHEFSRNGFI
VPDKKYQGGLVFEPEKGLHKNYVLVMDFNSLYPSIIQEFNICFTTVDRNK
EDIDELPSVPPSEVDQGVLPRLLANLVDRRREVKKVMKKRVQCDIRQQAL
KLTANSMYGCLGYVNSRFYAKPLAMLVTNKGREILMNTRQLAESMNLLVV
YGDTDSVMIDTGCDNYADAIKIGLGFKRLVNERYRLLEIDIDNVFKKLLL
HAKKKYAALTVNLDKNGNGTTVLEVKGLDMKRREFCPLSRDVSIHVLNTI
LSDKDPEEALQEVYDYLEDIRIKVETNNIRIDKYKINMKLSKDPKAYPGG
KNMPAVQVALRMRKAGRVVKAGSVITFVITKSVAERAHALNEVMIKSNNL
IPDPQYYLEKQIFAPVERLLERIDSFNVVRLSEALGLDSKKYFRREGGNN
NGEDINNLQPLETTITDVERFKDTVTLELSCPSCDKRFPFGGIVSSNYYR
VSYNGLQCKHCEQLFTPLQLTSQIEHSIRAHISLYYAGWLQCDDSTCGIV
TRQVSVFGKRCLNDGCTGVMRYKYSDKQLYNQLLYFDSLFDCEKNKKQEL
KPIYLPDDLDYPKEQLTESSIKALTEQNRELMETGRSVVQKYLNDC

3D structure

• PDB: 8fok Molecular choreography of primer synthesis by the eukaryotic Pol alpha-primase.
• Chain: 1
• Resolution: 3.56 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	1	H684 F685 F686 E702 T792 R793 A794 K842 Y843 G845 Y951 G955 Y956 K1046 K1047 N1145 R1224 G1258	H323 F324 F325 E341 T431 R432 A433 K455 Y456 G458 Y558 G562 Y563 K653 K654 N752 R818 G852
BS02	rna	1	T997 K1047 R1075 R1076 K1132 S1134 K1135 K1247 R1250	T604 K654 R682 R683 K739 S741 K742 K841 R844

Gene Ontology

Molecular Function

• GO:0000166 nucleotide binding
• GO:0000510 H3-H4 histone complex chaperone activity
• GO:0003676 nucleic acid binding
• GO:0003677 DNA binding
• GO:0003682 chromatin binding
• GO:0003688 DNA replication origin binding
• GO:0003697 single-stranded 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:0000731 DNA synthesis involved in DNA repair
• GO:0006260 DNA replication
• GO:0006270 DNA replication initiation
• GO:0006272 leading strand elongation
• GO:0006273 lagging strand elongation
• GO:0006278 RNA-templated DNA biosynthetic process
• GO:0006279 premeiotic DNA replication
• GO:0006302 double-strand break repair
• GO:1902975 mitotic DNA replication initiation

Cellular Component

• GO:0005634 nucleus
• GO:0005657 replication fork
• GO:0005658 alpha DNA polymerase:primase complex
• GO:0005739 mitochondrion
• GO:0043231 intracellular membrane-bounded organelle

External links

• PDB: RCSB:8fok, PDBe:8fok, PDBj:8fok
• PDBsum: 8fok
• PubMed: 37344454
• UniProt: P13382|DPOLA_YEAST DNA polymerase alpha catalytic subunit A (Gene Name=POL1)