Structure of PDB 2a68 Chain D

Receptor sequence

>2a68D (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: 2a68 Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins.
• Chain: D
• Resolution: 2.5 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	ZN	D	C60 C73	C59 C72
BS02	ZN	D	C1112 C1204	C999 C1091
BS03	MG	D	G24 E25 V26 H92	G23 E24 V25 H91
BS04	MG	D	K131 I133 D155	K130 I132 D154
BS05	MG	D	P772 D1208 E1219	P659 D1095 E1106
BS06	MG	D	V80 T81	V79 T80
BS07	MG	D	R796 F1017	R683 F904
BS08	MG	D	A13 S14 P15 I18	A12 S13 P14 I17
BS09	MG	D	A100 M512 I513	A99 M399 I400
BS10	MG	D	Y63 K71 V72	Y62 K70 V71
BS11	MG	D	G870 K871 R872	G757 K758 R759
BS12	MG	D	A370 I371 D372	A257 I258 D259
BS13	MG	D	P957 E958	P844 E845
BS14	MG	D	D583 R586	D470 R473
BS15	MG	D	Q794 K797	Q681 K684
BS16	MG	D	K1307 E1308 A1309 R1310	K1194 E1195 A1196 R1197
BS17	MG	D	D542 T592	D429 T479
BS18	MG	D	K217 D372	K216 D259
BS19	MG	D	N909 K912	N796 K799
BS20	MG	D	P248 F251	P247 F250
BS21	MG	D	R1096 F1440	R983 F1327
BS22	MG	D	V1486 V1487	V1373 V1374
BS23	MG	D	F919 L920	F806 L807
BS24	MG	D	I1283 E1284	I1170 E1171
BS25	MG	D	K149 R150	K148 R149
BS26	MG	D	D1090 F1241	D977 F1128
BS27	MG	D	Y1205 V1221 A1225 H1367	Y1092 V1108 A1112 H1254

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:2a68, PDBe:2a68, PDBj:2a68
• PDBsum: 2a68
• PubMed: 16096056
• UniProt: Q8RQE8|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)