Structure of PDB 2ppb Chain N

Receptor sequence

>2ppbN (length=1314) Species: 300852 (Thermus thermophilus HB8)

KKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFG
PIKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAH
IWFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQ
LLTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDG
VALYRFASILVVKARVYPFEDDVEVSTGDRVAPGDVLADGGKVKSDVYGR
VEVDLVRNVVRVVESYDIDARMGAEAIQQLLKELDLEALEKELLEEMKHP
SRARRAKARKRLEVVRAFLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGR
FATSDLNDLYRRLINRNNRLKKLLAQGAPEIIIRNEKRMLQEAVDALLDN
GRRGAPVTNPGSDRPLRSLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVG
PQLKLHQCGLPKRMALELFKPFLLKKMEEKGIAPNVKAARRMLERQRDIK
DEVWDALEEVIHGKVVLLNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCE
AFNADFDGDQMAVHVPLSSFAQAEARIQMLSAHNLLSPASGEPLAKPSRD
IILGLYYITQVRKEKKGAGLEFATPEEALAAHERGEVALNAPIKVAGRET
SVGRLKYVFANPDEALLAVAHGIVDLQDVVTVRYMGKRLETSPGRILFAR
IVAEAVEDEKVAWELIQLDVPQEKNSLKDLVYQAFLRLGMEKTARLLDAL
KYYGFTFSTTSGITIGIDDAVIPEEKKQYLEEADRKLLQIEQAYEMGFLT
DRERYDQILQLWTETTEKVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQ
IRQLCGLRGLMQKPSGETFEVPVRSSFREGLTVLEYFISSHGARKGGADT
ALRTADSGYLTRKLVDVTHEIVVREADCGTTNYISVPLFQPDEVTRSLRL
RKRADIEAGLYGRVLAREVEVLGVRLEEGRYLSMDDVHLLIKAAEAGEIQ
EVPVRSPLTCQTRYGVCQKCYGYDLSMARPVSIGEAVGIVAAQSIGEPGT
QLTMRTFHTDITQGLPRVIELFEARRPKAKAVISEIDGVVRIEETEEKLS
VFVESEGFSKEYKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGP
EAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLE
GQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQ
NTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKT
LKAIEEARKEAVEA

3D structure

• PDB: 2ppb Structural basis for substrate loading in bacterial RNA polymerase.
• 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	dna	N	R486 A487 R488 R534 R586 K610 K621 R628 T1088 A1089 Y1093 R1096 Q1441 N1442	R302 A303 R304 R350 R402 K426 K437 R444 T904 A905 Y909 R912 Q1250 N1251
BS02	rna	N	D55 R598 Q611 K671 R704 D743	D54 R414 Q427 K487 R520 D559
BS03	dna	N	V108 R1266	V107 R1075
BS04	APC	N	P706 N737 R1029	P522 N553 R845
BS05	STD	N	A1082 A1085 L1086 R1087 D1090 P1257	A898 A901 L902 R903 D906 P1066
BS06	ZN	N	C73 C76	C72 C75
BS07	ZN	N	C1112 C1204	C928 C1020
BS08	MG	N	D739 D741 D743	D555 D557 D559

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:2ppb, PDBe:2ppb, PDBj:2ppb
• PDBsum: 2ppb
• PubMed: 17581591
• UniProt: Q8RQE8|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)