Structure of PDB 5c53 Chain A

Receptor sequence

>5c53A (length=983) Species: 9606 (Homo sapiens)

MLSRGLHEQIFGQGGEMPGEAAVRRSVEHLQKHGLWGQPAVPLPDVELRL
PPLYGDNLDQHFRLLAQKQSLPYLEAANLLLQAQLPPKPPAWAWAEGWTR
YGPEGEAVPVAIPEERALVFDVEVCLAEGTCPTLAVAISPSAWYSWCSQR
LVEERYSWTSQLSPADLIPLEVQEQLVVGHNVSFDRAHIREQYLIQGSRM
RFLDTMSMHMAISGLSSFQRSLWIAAKAISSWDWLDISSVNSLAEVHRLY
VGGPPLEKEPRELFVKGTMKDIRENFQDLMQYCAQDVWATHEVFQQQLPL
FLERCPHPVTLAGMLEMGVSYLPVNQNWERYLAEAQGTYEELQREMKKSL
MDLANDACQLLSGERYKEDPWLWDLEWDLQEFKQKKAKKVKKEPATALGP
CSEEEEFQQDVMARACLQKLKGTTELLPKRPQHLPGHPGWYRKLCPRLDD
PAWTPGPSLLSLQMRVTPKLMALTWDGFPLHYSERHGWGYLNLAKLPTGT
TLESAGVVCPYRAIESLYRKHCLEPYNDVDIPGCWFFKLPHKDGNSCNVG
SPFAKDFLPKMEDGTLQAGPGGASGPRALEINKMISFWRNAHKRISSQMV
VWLPRSALPRAVIRHPDYDEEGLYGAILPQVVTAGTITRRAVEPTWLTAS
NARPDRVGSELKAMVQAPPGYTLVGADVDSQELWIAAVLGDAHFAGMHGC
TAFGWMTLQGRKSRGTDLHSKTATTVGISREHAKIFNYGRIYGAGQPFAE
RLLMQFNHRLTQQEAAEKAQQMYAATKGLLRKVQRETARKSQWKKWEVVA
ERAWKGGTESEMFNKLESIATSDIPRTPVLGCCISRALEPSAVQEEFMTS
RVNWVVQSSAVDYLHLMLVAMKWLFEEFAIDGRFCISIHDEVRYLVREED
RYRAALALQITNLLTRCMFAYKLGLNDLPQSVAFFSAVDIDRCLRKEVTM
DCKTPSNPTGMERRYGIPQGEALDIYQIIELTK

3D structure

• PDB: 5c53 Probing the structural and molecular basis of nucleotide selectivity by human mitochondrial DNA polymerase gamma.
• Chain: A
• Resolution: 3.567 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	S305 S306 R309 K498 K561 S593 Q595 M596 R597 N803 K806 R807 T849 I850 P857 I948 G952 Y955 G958 F961 K1050 E1091 M1093 T1094 N1098	S216 S217 R220 K385 K429 S461 Q463 M464 R465 N590 K593 R594 T636 I637 P644 I735 G739 Y742 G745 F748 K805 E846 M848 T849 N853	PDBbind-CN: Kd=0.9uM
BS02	dna	A	R579 S764 P765 D769 N803 L860 A862 R869	R447 S551 P552 D556 N590 L647 A649 R656	PDBbind-CN: Kd=0.9uM
BS03	MG	A	D890 V891 D1135	D677 V678 D890
BS04	4Y3	A	S893 Q894 E895 K947 Y951 D1135	S680 Q681 E682 K734 Y738 D890

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:5c53, PDBe:5c53, PDBj:5c53
• PDBsum: 5c53
• PubMed: 26124101
• UniProt: P54098|DPOG1_HUMAN DNA polymerase subunit gamma-1 (Gene Name=POLG)