Structure of PDB 8q63 Chain A

Receptor sequence

>8q63A (length=915) Species: 559292 (Saccharomyces cerevisiae S288C)

INFFEIYNSLPTLEEKKAFESALNIFNQDRQKVLENRATEAARERWKHDF
EEAKARGDISIEKNLNVKLWKWYNEMLPLVKEEINHCRSLLSEKLSDKKG
LNKVDTNRLGYGPYLTLIDPGKMCVITILELLKLNSTGEGMRTARAVISV
GKAIEMEFRSEQVLKKILWPQSIRARIGSVLISMLIQVAKVSVQGVDPVT
KAKVHGEAPAFAHGYQYHNGSKLGVLKIHKTLIRQLNGERLIASVQPQLL
PMLVEPKPWVNWRSGGYHYTQSTLLRTKDSPEQVAYLKAASDNGDIDRVY
DGLNVLGRTPWTVNRKVFDVVSQVWNKGEGFLDIPGAQDEMVLPPAPPPS
ILRAWKLQVKTIANKFSSDRSNRCDTNYKLEIARAFLGEKLYFPHNLDFR
GRAYPLSPHFNHLGNDMSRGLLIFWHGKKLGPSGLKWLKIHLSNLFGFDK
LPLKDRVAFTESHLQDIKDSAENPLTGDRWWTTADKPWQALATCFELNEV
MKMDNPEEFISHQPVHQDGTCNGLQHYAALGGDVEGATQVNLVPSDKPQD
VYAHVARLVQKRLEIAAEKGDENAKILKDKITRKVVKQTVMTNVYGVTYV
GATFQIAKQLSPIFDDRKESLDFSKYLTKHVFSAIRELFHSAHLIQDWLG
ESAKRISKSIRLDVDEKSFKNGNKPDFMSSVIWTTPLGLPIVQPYREESK
KQVETNLQTVFISDPFAVNPVNARRQKAGLPPNFIHSLDASHMLLSAAEC
GKQGLDFASVHDSYWTHASDIDTMNVVLREQFIKLHEVDLVLRLKEEFDQ
RYKNYVKIGKLKRSTDLAQKIIRIRKDLSRKLGRSTTLADEIYFEKKRQE
LLNSPLIEDRNVGEKMVTTVSLFEDITDLDALEGMSVLLPLRLPEIPPKG
DFDVTVLRNSQYFFS

3D structure

• PDB: 8q63 Structures illustrate step-by-step mitochondrial transcription initiation
• Chain: A
• Resolution: 3.68 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	Y640 H641 N642 G643 Y1026 K1081 K1085	Y217 H218 N219 G220 Y599 K654 K658
BS02	dna	A	L519 N520 R530 I536 Q594 Y638 S644 K645 R699 C801 D802 Y805 R827 Y831 P835 Y1022 T1025 V1027 Y1122 Q1129 Q1135 T1136 V1137 F1138 R1151 R1152 K1237	L134 N135 R142 I148 Q171 Y215 S221 K222 R276 C374 D375 Y378 R400 Y404 P408 Y595 T598 V600 Y695 Q702 Q708 T709 V710 F711 R724 R725 K810
BS03	rna	A	R829 L840 G841 N842 R846 K1035 V1187 H1188 D1189	R402 L413 G414 N415 R419 K608 V760 H761 D762

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:8q63, PDBe:8q63, PDBj:8q63
• PDBsum: 8q63
• PubMed: 37821701
• UniProt: P13433|RPOM_YEAST DNA-directed RNA polymerase, mitochondrial (Gene Name=RPO41)