Structure of PDB 4wqs Chain D

Receptor sequence

>4wqsD (length=1151) Species: 300852 (Thermus thermophilus HB8)

KKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFG
PIKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAH
IWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQ
LLTDEEYRELRYARMGAEAIQQLLKELDLEALEKELLEEMKHPSRARRAK
ARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLN
DLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPV
TNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQ
CGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWDAL
EEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFD
GDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYY
ITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKY
VFANPDEALLAVAHGIVDLQDVVTVRYMGKRLETSPGRILFARIVAEAVE
DEKVAWELIQLDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTF
STTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQ
ILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGL
RGLMQKPSGETRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTR
KLVDVTHEIVVREADCGTTNYISVPLFQPDEVTRSLRLRKRADIEAGLYG
RVLAREVEVLGVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQT
RYGVCQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGV
AGAADITQGLPRVIELFEARRPKAAIDPHQLLEAKGPEAVERYLVEEIQK
VYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALN
ERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAG
KKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLKAIEEARKEAVE
A

3D structure

• PDB: 4wqs The Ratcheted and Ratchetable Structural States of RNA Polymerase Underlie Multiple Transcriptional Functions.
• Chain: D
• Resolution: 4.306 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	R486 A487 R534 A536 R586 K610 R628 A705 P706 Q744 T1088 A1089 Y1093 R1096 F1440 Q1441 N1442	R195 A196 R243 A245 R295 K319 R337 A414 P415 Q453 T792 A793 Y797 R800 F1086 Q1087 N1088
BS02	rna	D	K54 Q529 V530 D531 Q611 R704 A705 P706 N737 A738 D739 D741 G742 D743 Q744	K53 Q238 V239 D240 Q320 R413 A414 P415 N446 A447 D448 D450 G451 D452 Q453
BS03	dna	D	V108 R1266 K1426	V107 R970 K1072
BS04	ZN	D	K62 C73	K61 C72
BS05	ZN	D	C1112 R1189 C1194 C1204	C816 R893 C898 C908

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003677 DNA binding
• GO:0003899 DNA-directed 5'-3' RNA polymerase activity
• GO:0005515 protein binding
• 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

External links

• PDB: RCSB:4wqs, PDBe:4wqs, PDBj:4wqs
• PDBsum: 4wqs
• PubMed: 25601758
• UniProt: Q8RQE8|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)