Structure of PDB 6tyf Chain D

Receptor sequence

>6tyfD (length=1262) Species: 1773 (Mycobacterium tuberculosis)

FFDELRIGLATAEDIRQWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPT
RDWECYCGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELAAPVTHIW
YFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDEEMRHNELSTLEAEM
AVERKAVEDQRDGELEARAQKLEADLAELEAEGAKADARRKVRDGGEREM
RQIRDRAQRELDRLEDIWSTFTKLAPKQLIVDENLYRELVDRYGEYFTGA
MGAESIQKLIENFDIDAEAESLRDVIRNGKGQKKLRALKRLKVVAAFQQS
GNSPMGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLK
RLIDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRPLKSLSDL
LKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELFKPF
VMKRLVDLNHAQNIKSAKRMVERQRPQVWDVLEEVIAEHPVLLNRAPTLH
RLGIQAFEPMLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEAQAEA
RILMLSSNNILSPASGRPLAMPRLDMVTGLYYLTTEVPGDTGEYQPASGD
HPETGVYSSPAEAIMAADRGVLSVRAKIKVRLTQLRPPVEIEAELFGHSG
WQPGDAWMAETTLGRVMFNELLPLGYPFVNKQMHKKVQAAIINDLAERYP
MIVVAQTVDKLKDAGFYWATRSGVTVSMADVLVPPRKKEILDHYEERADK
VEKQFQRGALNHDERNEALVEIWKEATDEVGQALREHYPDDNPIITIVDS
GATGNFTQTRTLAGMKGLVTNPKGEFIPRPVKSSFREGLTVLEYFINTHG
ARKGLADTALRTADSGYLTRRLVDVSQDVIVREHDCQTERGIVVELAERA
PDGTLIRDPYIETSAYARTLGTDAVDEAGNVIVERGQDLGDPEIDALLAA
GITQVKVRSVLTCATSTGVCATCYGRSMATGKLVDIGEAVGIVAAQSIGE
PGTQLTGGLPRVQELFEARVPRGKAPIADVTGRVRLEDGERFYKITIVPD
DGGEEVVYDKISKRQRLRVFKHEDGSERVLSDGDHVEVGQQLMEGSADPH
EVLRVQGPREVQIHLVREVQEVYRAQGVSIHDKHIEVIVRQMLRRVTIID
SGSTEFLPGSLIDRAEFEAENRRVVAEGGEPAAGRPVLMGITKASLATDS
WLSAASFQETTRVLTDAAINCRSDKLNGLKENVIIGKLIPAGTGINRYRN
IAVQPTEEARAA

3D structure

• PDB: 6tyf RNA extension drives a stepwise displacement of an initiation-factor structural module in initial transcription.
• Chain: D
• Resolution: 3.8 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	D	Q287 R291 R386 K409 R414 R427 A501 Q1227 E1228	Q282 R286 R381 K404 R409 R422 A496 Q1208 E1209
BS02	dna	D	P111 S112 Y116 P122 K123 R291 K294 R1038	P106 S107 Y111 P117 K118 R286 K289 R1019
BS03	rna	D	R500 D539	R495 D534

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003677 DNA binding
• GO:0003899 DNA-directed 5'-3' RNA polymerase activity
• GO:0008270 zinc ion binding
• GO:0016779 nucleotidyltransferase activity
• GO:0034062 5'-3' RNA polymerase activity
• GO:0046872 metal ion binding

Biological Process

• GO:0006351 DNA-templated transcription

Cellular Component

• GO:0000428 DNA-directed RNA polymerase complex
• GO:0005829 cytosol
• GO:0005886 plasma membrane
• GO:0009274 peptidoglycan-based cell wall

External links

• PDB: RCSB:6tyf, PDBe:6tyf, PDBj:6tyf
• PDBsum: 6tyf
• PubMed: 32127479
• UniProt: P9WGY7|RPOC_MYCTU DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)