Structure of PDB 8ap1 Chain A

Receptor sequence

>8ap1A (length=918) Species: 559292 (Saccharomyces cerevisiae S288C)

INFFEIYNSLPTLEEKKAFESALNIFNQDRQKVLENRATEAARERWKHDF
EEAKARKNLNVKLWKWYNEMLPLVKEEINHCRSLLSEKLSDKKGLNKVDT
NRLGYGPYLTLIDPGKMCVITILELLKLNSTGGVIEGMRTARAVISVGKA
IEMEFRSEQVLKSESQAKILWPQSIRARIGSVLISMLIQVAKVSVQGVDP
VTKAKVHGEAPAFAHGYQYHNGSKLGVLKIHKTLIRQLNGERLIASVQPQ
LLPMLVEPKPWVNWRSGGYHYTQSTLLRTKDSPEQVAYLKAASDNGDIDR
VYDGLNVLGRTPWTVNRKVFDVVSQVWNKGEGFLDIPGAQDEMVLPPAPP
KNSDPSILRAWKLQVKTIANKFSSDRSNRCDTNYKLEIARAFLGEKLYFP
HNLDFRGRAYPLSPHFNHLGNDMSRGLLIFWHGKKLGPSGLKWLKIHLSN
LFGFDKLPLKDRVAFTESHLQDIKDSAENPLTGDRWWTTADKPWQALATC
FELNEVMKMDNPEEFISHQPVHQDGTCNGLQHYAALGGDVEGATQVNLVP
SDKPQDVYAHVARLVQKRLEIAAEKGDENAKILKDKITRKVVKQTVMTNV
YGVTYVGATFQIAKQLSPIFDDRKESLDFSKYLTKHVFSAIRELFHSAHL
IQDWLGESAKRISKSIRLDVDEKSFKNGNKPDFMSSVIWTTPLGLPIVQP
YREESKKQVETNLQTVFISDPFAVNPVNARRQKAGLPPNFIHSLDASHML
LSAAECGKQGLDFASVHDSYWTHASDIDTMNVVLREQFIKLHEVDLVLRL
KEEFDQRYKNYVKIGKLKRSTDLAQKIIRIRKDLSRKLGRSTTLADEIYF
EKKRQELLNSPLIEDRNVGEKMVTTVSLFEDITDLDAMSVLLPLRLPEIP
PKGDFDVTVLRNSQYFFS

3D structure

• PDB: 8ap1 Structures illustrate step-by-step mitochondrial transcription initiation
• Chain: A
• Resolution: 3.47 Å

Enzymatic activity

• Enzyme Commision number: 2.7.7.6: DNA-directed RNA 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	L486 Y640 N642 G643 K645 R780 F1031	L95 Y219 N221 G222 K224 R359 F610
BS02	dna	A	I536 Y638 S644 K645 G647 R699 F826 R827 T1019 G1023 V1024 T1025 Q1032 Y1122 Q1129 Q1135 T1136 F1138 R1151	I145 Y217 S223 K224 G226 R278 F405 R406 T598 G602 V603 T604 Q611 Y701 Q708 Q714 T715 F717 R730
BS03	MG	A	D945 G946 D1189	D524 G525 D768
BS04	GTP	A	D945 G946 C948 N949 Y979 R1010 K1014 Q1015 M1018 T1019 Y1022 H1163 D1189	D524 G525 C527 N528 Y558 R589 K593 Q594 M597 T598 Y601 H742 D768

Gene Ontology

Molecular Function

• GO:0001018 mitochondrial promoter sequence-specific DNA binding
• GO:0003677 DNA binding
• GO:0003896 DNA primase activity
• GO:0003899 DNA-directed 5'-3' RNA polymerase activity
• GO:0016779 nucleotidyltransferase activity
• GO:0034062 5'-3' RNA polymerase activity

Biological Process

• GO:0000002 mitochondrial genome maintenance
• GO:0006269 DNA replication, synthesis of primer
• GO:0006351 DNA-templated transcription
• GO:0006390 mitochondrial transcription

Cellular Component

• GO:0000428 DNA-directed RNA polymerase complex
• GO:0005737 cytoplasm
• GO:0005739 mitochondrion
• GO:0005759 mitochondrial matrix
• GO:0034245 mitochondrial DNA-directed RNA polymerase complex
• GO:0042645 mitochondrial nucleoid
• GO:0043231 intracellular membrane-bounded organelle

External links

• PDB: RCSB:8ap1, PDBe:8ap1, PDBj:8ap1
• PDBsum: 8ap1
• PubMed: 37821701
• UniProt: P13433|RPOM_YEAST DNA-directed RNA polymerase, mitochondrial (Gene Name=RPO41)