Structure of PDB 6ovy Chain D

Receptor sequence

>6ovyD (length=1485) Species: 274 (Thermus thermophilus)

EVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGPI
KDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHIW
FVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQLL
TDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGVA
LYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEILAELPEPYLFRA
EEEGVVELKELEEGAFLVLRREDEPVATYFLPVGMTPLVVHGEIVEKGQP
LAEAKGLLRMPRQVRAAQVEAEEEGETVYLTLFLEWTEPKDYRVQPHMNV
VVPEGARVEAGDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYPF
EDDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYDID
ARMGAEAIQQLLKELDLEALEKELLEEMKHPSRARRAKARKRLEVVRAFL
DSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNR
LKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSL
TDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELF
KPFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLN
RAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSS
FAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAG
LEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVFANPDEALLAV
AHGIVDLQDVVTVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQLD
VPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDD
AVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKV
TQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETF
EVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTH
EIVVREADCGTTNYISVPLFQPDEVTRSLRLRKRADIEAGLYGRVLAREV
EVLGVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQK
CYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMTQGLPRVIELFEARR
PKAKAVISEIDGVVRIEETEEKLSVFVESEGFSKEYKLPKEARLLVKDGD
YVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKH
IEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAW
KPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKENVI
LGRLIPAGTGSDFVRFTQVVDQKTLKAIEEARKEA

3D structure

• PDB: 6ovy Structural basis of reiterative transcription from the pyrG and pyrBI promoters by bacterial RNA polymerase.
• Chain: D
• Resolution: 2.999 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	R586 K610 R622 R628 P706 T1088 A1089 G1092 Y1093 Q1441 N1442	R583 K607 R619 R625 P703 T1085 A1086 G1089 Y1090 Q1424 N1425
BS02	dna	D	R1266 K1426	R1249 K1409
BS03	rna	D	R704 A705 D741 D743	R701 A702 D738 D740
BS04	MG	D	D739 D741 D743	D736 D738 D740
BS05	ZN	D	C58 C73	C55 C70
BS06	ZN	D	C1112 C1194 C1201 C1204	C1109 C1191 C1198 C1201

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