Structure of PDB 1zyr Chain N

Receptor sequence

>1zyrN (length=1392) Species: 274 (Thermus thermophilus)

KKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFG
PIKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAH
IWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQ
LLTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDG
VALYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEILAELPEPYLF
GDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYPFEDDVEVSTGD
RVAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYDIDARMGAEAIQQ
LLKELDLEALEKELLEEMKHPSRARRAKARKRLEVVRAFLDSGNRPEWMI
LEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNNRLKKLLAQGAP
EIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRSLTDILSGKQGR
FRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALELFKPFLLKKMEE
KGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLLNRAPTLHRLGI
QAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLSSFAQAEARIQM
LSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGAGLEFATPEEAL
AAHERGEVALNAPIKVAGRETSVGRLKYVFANPDEALLAVAHGIVDLQDV
VTVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQLDVPQEKNSLKD
LVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGIDDAVIPEEKKQY
LEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEKVTQAVFKNFEE
NYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGETFEVPVRSSFRE
GLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVTHEIVVREADCG
TTNYISVPLFQPDEVTRSLRLRKRADIEAGLYGRVLAREVEVLGVRLEEG
RYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQKCYGYDLSMAR
PVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADITQGLPRVIELF
EARRPKAKAVISEIDGVVRIEETEEKLSVFVESEGFSKEYKLPKEARLLV
KDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEIQKVYRAQGVKL
HDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKT
PVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLK
ENVILGRLIPAGTGSDFVRFTQVVDQKTLKAIEEARKEAVEA

3D structure

• PDB: 1zyr Inhibition of bacterial RNA polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation.
• Chain: N
• Resolution: 3.0 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	STD	N	A1082 A1085 L1086 D1090	A969 A972 L973 D977
BS02	ZN	N	C60 C73	C59 C72
BS03	ZN	N	C1194 C1201 C1204	C1081 C1088 C1091
BS04	MG	N	D739 D741 D743	D626 D628 D630

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:1zyr, PDBe:1zyr, PDBj:1zyr
• PDBsum: 1zyr
• PubMed: 16122422
• UniProt: Q8RQE8|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)