Structure of PDB 8d37 Chain A

Receptor sequence

>8d37A (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: 8d37 Pol gamma coordinates DNA synthesis and proofreading to ensure mitochondrial genome integrity.
• Chain: A
• Resolution: 2.65 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	R579 H754 N761 V762 G763 A767 K768 N803 T861 A862 S863 N864 R869 H1134 D1135	R448 H544 N551 V552 G553 A557 K558 N593 T651 A652 S653 N654 R659 H873 D874
BS02	dna	A	S306 K498 K561 S593 R597 N803 K806 R807 T849 V855 G952 Y955 G956 A957 G958 F961 M1093 T1094 S1095	S230 K397 K430 S462 R466 N593 K596 R597 T639 V645 G742 Y745 G746 A747 G748 F751 M832 T833 S834
BS03	CA	A	D890 V891 D1135	D680 V681 D874
BS04	DCP	A	D890 V891 S893 E895 R943 K947 Y951 D1135	D680 V681 S683 E685 R733 K737 Y741 D874

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:8d37, PDBe:8d37, PDBj:8d37
• PDBsum: 8d37
• PubMed: 37202477
• UniProt: P54098|DPOG1_HUMAN DNA polymerase subunit gamma-1 (Gene Name=POLG)