Structure of PDB 2o5j Chain D

Receptor sequence

>2o5jD (length=1264) 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
QLTMRTFHTGGVAGAADITQGLPRVIELFEARRPKAKAIDPHQLLEAKGP
EAVERYLVEEIQKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLE
GQVLEKWDVEALNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQ
NTTHVLTEAAIAGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKT
LKAIEEARKEAVEA

3D structure

• PDB: 2o5j Structural basis for substrate loading in bacterial RNA polymerase.
• Chain: D
• 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	D	S485 R486 A487 R488 R534 R586 K610 R622 R628 T1088 A1089 Y1093 R1096 Q1441 N1442	S301 R302 A303 R304 R350 R402 K426 R438 R444 T904 A905 Y909 R912 Q1200 N1201
BS02	rna	D	Q529 V530 D531 R598 Q611 K671 D741 G742 D743	Q345 V346 D347 R414 Q427 K487 D557 G558 D559
BS03	dna	D	K494 E1264 R1266 K1426	K310 E1080 R1082 K1185
BS04	ZN	D	C1112 C1194 C1204	C928 C1010 C1020
BS05	MG	D	D739 D741 D743	D555 D557 D559
BS06	APC	D	R704 N737 D739 R1029 M1238 R1239 H1242	R520 N553 D555 R845 M1054 R1055 H1058

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:2o5j, PDBe:2o5j, PDBj:2o5j
• PDBsum: 2o5j
• PubMed: 17581591
• UniProt: Q8RQE8|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)