Structure of PDB 8d42 Chain A

Receptor sequence

>8d42A (length=974) Species: 9606 (Homo sapiens)

LRHNPLDIQMLSRGLHEQIFGQGGEMPGEAAVRRSVEHLQKHGLWGQPAV
PLPDVELRLPPLYGDNLDQHFRLLAQKQSLPYLEAANLLLQAQLPPKPPA
WAWAEGWTRYGPEGEAVPVAIPEERALVFDVEVCLAEGTCPTLAVAISPS
AWYSWCSQRLVEERYSWTSQLSPADLIPLEVPTDWQEQLVVGHNVSFDRA
HIREQYLIQGSRMRFLDTMSMHMAISGLSSFQRSLWIAAKISSWDWLDIS
SVNSLAEVHRLYVGGPPLEKEPRELFVKGTMKDIRENFQDLMQYCAQDVW
ATHEVFQQQLPLFLERCPHPVTLAGMLEMGVSYLPVNQNWERYLAEAQGT
YEELQREMKKSLMDLANDACQLLSGERYKEDPWLWDLEWDLQEFKQKKLG
PCSEEEEFQQDVMARACLQKLKGTTELLPKRPQHLPGHPGWYRKLCPRLD
DPAWTPGPSLLSLQMRVTPKLMALTWDGFPLHYSERHGWGYLVPGRRDNL
VVCPYRAIESLYRKHCLEQPSYHHGNGPYNDVDIPGCWFFKLPHKDGNSC
NVGSPFAKDFLPKMEDGTLQAGPGGASGPRALEINKMISFWRNAHKRISS
QMVVWLPRSALPRAVIRHPDYDEEGLYGAILPQVVTAGTITRRAVEPTWL
TASNARPDRVGSELKAMVQAPPGYTLVGADVDSQELWIAAVLGDAHFAGM
HGCTAFGWMTLQGRKSRGTDLHSKTATTVGISREHAKIFNYGRIYGAGQP
FAERLLMQFNHRLTQQEAAEKAQQMYAATKGLRWYRLWKGGTESEMFNKL
ESIATSDIPRTPVLGCCISRALEPSAVQEEFMTSRVNWVVQSSAVDYLHL
MLVAMKWLFEEFAIDGRFCISIHDEVRYLVREEDRYRAALALQITNLLTR
CMFAYKLGLNDLPQSVAFFSAVDIDRCLRKEVTMDCKTPSNPTGMERRYG
IPQGEALDIYQIIELTKGSLEKRS

3D structure

• PDB: 8d42 Pol gamma coordinates DNA synthesis and proofreading to ensure mitochondrial genome integrity.
• Chain: A
• Resolution: 2.91 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.7: DNA-directed DNA polymerase.
  3.1.11.-
  4.2.99.-

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	E200 V201 L203 F273 R309 I313 N354 S355 V378 R579 N761 V762 G763 A767 K768 N803 R807	E132 V133 L135 F197 R233 I237 N253 S254 V277 R448 N551 V552 G553 A557 K558 N593 R597
BS02	dna	A	F307 S310 K561 R562 Q595 R597 G958 F961 R964 M1093	F231 S234 K430 R431 Q464 R466 G748 F751 R754 M832
BS03	CA	A	D198 E200 C396 D399	D130 E132 C295 D298
BS04	DCP	A	H932 R943 K947 Y951 H1134	H722 R733 K737 Y741 H873

Gene Ontology

Molecular Function

• GO:0002020 protease binding
• GO:0003677 DNA binding
• GO:0003682 chromatin binding
• GO:0003887 DNA-directed DNA polymerase activity
• GO:0005515 protein binding
• GO:0008310 single-stranded DNA 3'-5' DNA exonuclease activity
• GO:0008408 3'-5' exonuclease activity
• GO:0016787 hydrolase activity
• GO:0016829 lyase activity
• GO:0051575 5'-deoxyribose-5-phosphate lyase activity

Biological Process

• GO:0006259 DNA metabolic process
• GO:0006260 DNA replication
• GO:0006261 DNA-templated DNA replication
• GO:0006264 mitochondrial DNA replication
• GO:0006281 DNA repair
• GO:0006284 base-excision repair
• GO:0006287 base-excision repair, gap-filling
• GO:0045004 DNA replication proofreading
• GO:0071897 DNA biosynthetic process

Cellular Component

• GO:0000262 mitochondrial chromosome
• GO:0005739 mitochondrion
• GO:0005759 mitochondrial matrix
• GO:0005760 gamma DNA polymerase complex
• GO:0032991 protein-containing complex
• GO:0042645 mitochondrial nucleoid
• GO:0043231 intracellular membrane-bounded organelle

External links

• PDB: RCSB:8d42, PDBe:8d42, PDBj:8d42
• PDBsum: 8d42
• PubMed: 37202477
• UniProt: P54098|DPOG1_HUMAN DNA polymerase subunit gamma-1 (Gene Name=POLG)