Structure of PDB 4xlr Chain D

Receptor sequence

>4xlrD (length=1490) Species: 271 (Thermus aquaticus)

KKEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFG
PIKDYECACGKYKRQRFEGKVCERCGVEVTRSIVRRYRMGHIELATPAAH
IWFVKDVPSKIGTLLDLSATELEQVLYFNKYIVLDPKGAVLDGVPVEKRQ
LLTDEEYRELRYGKQETYPLPAGVDALVKDGEEVVKGQELAPGVVSRMDG
VALYRFPRRVRVDYLRKERAALRIPLSAWVEKEAYRPGEVLAELSEPYLF
RAEESGVVELKDLAEGHLIYLRQEEEVVARYFLPAGMTPLVVEGEIVEVG
QPLAEGKGLLRLPRHMTAKEVEAEEEGDSVHLTLFLEWTEPKDYKVAPHM
NVIVPEGAKVQAGEKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVY
PFEDDVEVTTGDRVAPGDVLADGGKVKSEIYGRVEVDLVRNVVRVVESYD
IDARMGAEAIQELLKELDLEKLERELLEEMKHPSRARRAKARKRLEVVRA
FLDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRN
NRLKKLLAQGAPEIIIRNEKRMLQEAVDAVIDNGRRGSPVTNPGSERPLR
SLTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALE
LFKPFLLKKMEEKAFAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVL
LNRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPL
SSFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKG
AGMAFATPEEALAAYERGEVALNAPIVVAGRETSVGRLKFVFANPDEALL
AVAHGLLDLQDVVTVRYLGRRLETSPGRILFARIVGEAVGDEKVAQELIQ
MDVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTLSTTSGITIGI
DDAVIPEEKQRYLEEADRKLRQIEQAYEMGFLTDRERYDQVIQLWTETTE
KVTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGMRGLMQKPSGE
TFEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDV
AHEIVVREADCGTTNYISVPLFQMDEVTRTLRLRKRSDIESGLYGRVLAR
EVEALGRRLEEGRYLSLEDVHFLIKAAEAGEVREVPVRSPLTCQTRYGVC
QKCYGYDLSMARPVSIGEAVGVVAAESIGEPGTQLTMTQGLPRVIELFEA
RRPKAKAVISEIDGVVRIEEGEDRLSVFVESEGFSKEYKLPKDARLLVKD
GDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVDEIQKVYRAQGVKLHD
KHIEIVVRQMLKYVEVTDPGDSRLLEGQVLEKWDVEALNERLIAEGKVPV
AWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAIAGKKDELIGLKEN
VILGRLIPAGTGSDFVRFTQVVDQRTLKAIEEARKEAVEA

3D structure

• PDB: 4xlr CarD uses a minor groove wedge mechanism to stabilize the RNA polymerase open promoter complex.
• Chain: D
• Resolution: 4.3 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	Y34 A120 R1266 R1267 K1426	Y33 A119 R1251 R1252 K1411
BS02	dna	D	R534 R586 K610 R622 R628 T1088 A1089 G1092 Y1093 Q1441 N1442	R533 R585 K609 R621 R627 T1087 A1088 G1091 Y1092 Q1426 N1427
BS03	rna	D	R704 D741 G742 D743 Q744	R703 D740 G741 D742 Q743
BS04	ZN	D	C1112 C1194 C1201 C1204	C1111 C1193 C1200 C1203
BS05	ZN	D	C58 C73 C76	C57 C72 C75
BS06	MG	D	D739 D741 D743	D738 D740 D742

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003677 DNA binding
• GO:0003899 DNA-directed 5'-3' RNA polymerase activity
• 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:4xlr, PDBe:4xlr, PDBj:4xlr
• PDBsum: 4xlr
• PubMed: 26349034
• UniProt: Q9KWU6|RPOC_THEAQ DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)