Structure of PDB 3aoh Chain D

Receptor sequence

>3aohD (length=1349) Species: 300852 (Thermus thermophilus HB8)

KKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFG
PIKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAH
IWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQ
LLTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDG
VALYRFPRRVRVEYVTEPKDYRVQPHMNVVVPEGARVEAGDKIVAAIDPE
EEVIAEAEGVVHLHEPASILVVKARVYPFEDDVEVSTGDRVAPGDVLADG
GKVKSDVYGRVEVDLVRNVVRVVESYDIDARMGAEAIQQLLKELDLEALE
KELLEEMKHPSRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDL
RPSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNG
RRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGP
QLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQRDIKD
EVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEA
FNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDI
ILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVAGRETS
VGRLKYVFANPDEALLAVAHGIVDLQDVVTVRYMGKRLETSPGRILFARI
VAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALK
YYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTD
RERYDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQI
RQLCGLRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADTA
LRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVPLFQPDEVTRSLRLR
KRADIEAGLYGRVLAREVEVLGVRLEEGRYLSMDDVHLLIKAAEAGEIQE
VPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQ
LTTQGLPRVIELFEARRPKAKAVISEIDGVVRIEETEEKLSVFVESEGFS
KEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVE
EIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDV
EALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEA
AIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLKAIEEAR

3D structure

• PDB: 3aoh Crystal structure of bacterial RNA polymerase bound with a transcription inhibitor protein
• Chain: D
• Resolution: 4.1 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	R628 P706 S1091	R493 P571 S956
BS02	rna	D	R704 A705 P706 D741 D743	R569 A570 P571 D606 D608
BS03	MG	D	D739 D741 D743	D604 D606 D608

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