Structure of PDB 3aoi Chain D

Receptor sequence

>3aoiD (length=1316) Species: 300852 (Thermus thermophilus HB8)

MKKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIF
GPIKDVRRYRMGHIELATPAAHIWFVKDVPSKIGTLLDLSATELEQVLYF
SKYIVLDPKGAILNGVPVEKRQLLTDEEYRELRYGKQETYPLPPGVDALV
KDGEEVVKGQELAPGVVSRLDGVALYRFPRRVRVEYRVQPHMNVVVPEGA
RVEAGDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYPFEDDVEV
STGDRVAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYDIDARMGAE
AIQQLLKELDLEALEKELLEEMKHPSRARRAKARKRLEVVRAFLDSGNRP
EWMILEAVPVLPPDLRPSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNE
KRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLG
KRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNV
KAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVL
VEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLL
SPASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEALAAHERGE
VALNAPIKVAGRETSVGRLKYVFANPDEALLAVAHGIVDLQDVVTVRYMG
KRLETSPGRILFARIVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFL
RLGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRK
LLQIEQAYEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFEENYPFNPL
YVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFREGLTVLEY
FISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISV
PLFQPDEVTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEEGRYLSMDD
VHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEA
VGIVAAQSIGEPGTQLTDITQGLPRVIELFEARRPKAKAVISEIDGVVRI
EETEEKLSVFVESEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPH
QLLEAKGPEAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTD
PGDSRLLEGQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKS
WLSAASFQNTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRF
TQVVDQKTLKAIEEAR

3D structure

• PDB: 3aoi Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein
• Chain: D
• Resolution: 4.3 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	R628 P706 S1091	R458 P536 S921
BS02	rna	D	R704 P706 D741 D743	R534 P536 D571 D573
BS03	ZN	D	C1112 C1194 C1204	C942 C1024 C1034
BS04	MG	D	D739 D741 D743	D569 D571 D573

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:3aoi, PDBe:3aoi, PDBj:3aoi
• PDBsum: 3aoi
• PubMed: 21124318
• UniProt: Q8RQE8|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)