Structure of PDB 8c5u Chain A

Receptor sequence

>8c5uA (length=919) Species: 559292 (Saccharomyces cerevisiae S288C)

INFFEIYNSLPTLEEKKAFESALNIFNQDRQKVLENRATEAARERWKHDF
EEAKARGDISIEKNLNVKLWKWYNEMLPLVKEEINHCRSLLSEKLSDKKG
LNKVDTNRLGYGPYLTLIDPGKMCVITILELLKLNSTGEGMRTARAVISV
GKAIEMEFRSEQVLKKILWPQSIRARIGSVLISMLIQVAKVSVQGVDPVT
KAKVHGEAPAFAHGYQYHNGSKLGVLKIHKTLIRQLNGERLIASVQPQLL
PMLVEPKPWVNWRSGGYHYTQSTLLRTKDSPEQVAYLKAASDNGDIDRVY
DGLNVLGRTPWTVNRKVFDVVSQVWNKGEGFLDIPGAQDEMVLPPAPPKN
SDPSILRAWKLQVKTIANKFSSDRSNRCDTNYKLEIARAFLGEKLYFPHN
LDFRGRAYPLSPHFNHLGNDMSRGLLIFWHGKKLGPSGLKWLKIHLSNLF
GFDKLPLKDRVAFTESHLQDIKDSAENPLTGDRWWTTADKPWQALATCFE
LNEVMKMDNPEEFISHQPVHQDGTCNGLQHYAALGGDVEGATQVNLVPSD
KPQDVYAHVARLVQKRLEIAAEKGDENAKILKDKITRKVVKQTVMTNVYG
VTYVGATFQIAKQLSPIFDDRKESLDFSKYLTKHVFSAIRELFHSAHLIQ
DWLGESAKRISKSIRLDVDEKSFKNGNKPDFMSSVIWTTPLGLPIVQPYR
EESKKQVETNLQTVFISDPFAVNPVNARRQKAGLPPNFIHSLDASHMLLS
AAECGKQGLDFASVHDSYWTHASDIDTMNVVLREQFIKLHEVDLVLRLKE
EFDQRYKNYVKIGKLKRSTDLAQKIIRIRKDLSRKLGRSTTLADEIYFEK
KRQELLNSPLIEDRNVGEKMVTTVSLFEDITDLDALEGMSVLLPLRLPEI
PPKGDFDVTVLRNSQYFFS

3D structure

• PDB: 8c5u Structures illustrate step-by-step mitochondrial transcription initiation
• Chain: A
• Resolution: 3.62 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 G643 Y1026 K1081 R1151 K1154	Y217 G220 Y603 K658 R728 K731
BS02	dna	A	L519 N520 R530 A532 Y638 S644 K645 L646 R699 C801 D802 R827 Y831 P835 Y1022 V1024 T1025 Y1122 Q1129 Q1135 T1136 F1138 I1139 R1151 R1152	L134 N135 R142 A144 Y215 S221 K222 L223 R276 C378 D379 R404 Y408 P412 Y599 V601 T602 Y699 Q706 Q712 T713 F715 I716 R728 R729
BS03	rna	A	N791 R829 G841 N842 R846 T1019 Y1022 H1188 D1189	N368 R406 G418 N419 R423 T596 Y599 H765 D766

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:8c5u, PDBe:8c5u, PDBj:8c5u
• PDBsum: 8c5u
• PubMed: 37821701
• UniProt: P13433|RPOM_YEAST DNA-directed RNA polymerase, mitochondrial (Gene Name=RPO41)