Structure of PDB 6oy5 Chain D

Receptor sequence

>6oy5D (length=1484) Species: 274 (Thermus thermophilus)

KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGP
IKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHI
WFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQL
LTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGV
ALYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEILAELPEPYLFR
AEEEGVVELKELEEGAFLVLRREDEPVATYFLPVGMTPLVVHGEIVEKGQ
PLAEAKGLLRMPRQVRAAQVEAEEEGETVYLTLFLEWTEPKDYRVQPHMN
VVVPEGARVEAGDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYP
FEDDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYDI
DARMGAEAIQQLLKELDLEALEKELLEEMKHPSRARRAKARKRLEVVRAF
LDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNN
RLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRS
LTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALEL
FKPFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLL
NRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLS
SFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGA
GLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVFANPDEALLA
VAHGIVDLQDVVTVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQL
DVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGID
DAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEK
VTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGET
FEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVT
HEIVVREADCGTTNYISVPLFQPDEVTRSLRLRKRADIEAGLYGRVLARE
VEVLGVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQ
KCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTQGLPRVIELFEARRP
KAKAVISEIDGVVRIEETEEKLSVFVESEGFSKEYKLPKEARLLVKDGDY
VEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHI
EIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWK
PLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVIL
GRLIPAGTGSDFVRFTQVVDQKTLKAIEEARKEA

3D structure

• PDB: 6oy5 Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase.
• Chain: D
• Resolution: 3.1 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	S485 R586 K610 R622 R628 P706 T1088 A1089 G1092 Y1093 Q1441 N1442	S483 R584 K608 R620 R626 P704 T1086 A1087 G1090 Y1091 Q1423 N1424
BS02	dna	D	R1266 K1426	R1248 K1408
BS03	rna	D	R704 A705 D743	R702 A703 D741
BS04	MG	D	D739 D741 D743	D737 D739 D741
BS05	ZN	D	C58 C73 C76	C56 C71 C74
BS06	ZN	D	C1194 C1204	C1192 C1202
BS07	GTP	D	R704 N737 R1029	R702 N735 R1027

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:6oy5, PDBe:6oy5, PDBj:6oy5
• PDBsum: 6oy5
• PubMed: 31965171
• UniProt: Q8RQE8|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)