Structure of PDB 5x22 Chain N

Receptor sequence

>5x22N (length=1500) Species: 300852 (Thermus thermophilus HB8)

KEVRKVRIALASPEKIRSWSYGEVEKPETINYRTLKPERDGLFDERIFGP
IKDYECACGKYKRQRFEGKVCERCGVEVTKSIVRRYRMGHIELATPAAHI
WFVKDVPSKIGTLLDLSATELEQVLYFSKYIVLDPKGAILNGVPVEKRQL
LTDEEYRELRYGKQETYPLPPGVDALVKDGEEVVKGQELAPGVVSRLDGV
ALYRFPRRVRVEYVKKERAGLRLPLAAWVEKEAYKPGEILAELPEPYLFR
AEEEGVVELKELEEGAFLVLRREDEPVATYFLPVGMTPLVVHGEIVEKGQ
PLAEAKGLLRMPRQVRAAQVEAEEEGETVYLTLFLEWTEPKDYRVQPHMN
VVVPEGARVEAGDKIVAAIDPEEEVIAEAEGVVHLHEPASILVVKARVYP
FEDDVEVSTGDRVAPGDVLADGGKVKSDVYGRVEVDLVRNVVRVVESYDI
DARMGAEAIQQLLKELDLEALEKELLEEMKHPSRARRAKARKRLEVVRAF
LDSGNRPEWMILEAVPVLPPDLRPMVQVDGGRFATSDLNDLYRRLINRNN
RLKKLLAQGAPEIIIRNEKRMLQEAVDALLDNGRRGAPVTNPGSDRPLRS
LTDILSGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKRMALEL
FKPFLLKKMEEKGIAPNVKAARRMLERQRDIKDEVWDALEEVIHGKVVLL
NRAPTLHRLGIQAFQPVLVEGQSIQLHPLVCEAFNADFDGDQMAVHVPLS
SFAQAEARIQMLSAHNLLSPASGEPLAKPSRDIILGLYYITQVRKEKKGA
GLEFATPEEALAAHERGEVALNAPIKVAGRETSVGRLKYVFANPDEALLA
VAHGIVDLQDVVTVRYMGKRLETSPGRILFARIVAEAVEDEKVAWELIQL
DVPQEKNSLKDLVYQAFLRLGMEKTARLLDALKYYGFTFSTTSGITIGID
DAVIPEEKKQYLEEADRKLLQIEQAYEMGFLTDRERYDQILQLWTETTEK
VTQAVFKNFEENYPFNPLYVMAQSGARGNPQQIRQLCGLRGLMQKPSGET
FEVPVRSSFREGLTVLEYFISSHGARKGGADTALRTADSGYLTRKLVDVT
HEIVVREADCGTTNYISVPLFQPDEVTRSLRLRKRADIEAGLYGRVLARE
VEVLGVRLEEGRYLSMDDVHLLIKAAEAGEIQEVPVRSPLTCQTRYGVCQ
KCYGYDLSMARPVSIGEAVGIVAAQSIGEPGTQLTMRTFHTGGVAGAADI
TQGLPRVIELFEARRPKAKAVISEIDGVVRIEETEEKLSVFVESEGFSKE
YKLPKEARLLVKDGDYVEAGQPLTRGAIDPHQLLEAKGPEAVERYLVEEI
QKVYRAQGVKLHDKHIEIVVRQMMKYVEVTDPGDSRLLEGQVLEKWDVEA
LNERLIAEGKTPVAWKPLLMGVTKSALSTKSWLSAASFQNTTHVLTEAAI
AGKKDELIGLKENVILGRLIPAGTGSDFVRFTQVVDQKTLKAIEEARKEA

3D structure

• PDB: 5x22 Antibacterial Nucleoside-Analog Inhibitor of Bacterial RNA Polymerase.
• Chain: N
• Resolution: 3.35 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	K610 R622 R628 A705 P706 T1088 A1089 Y1093 N1442	K608 R620 R626 A703 P704 T1086 A1087 Y1091 N1440
BS02	dna	N	R1266 K1426	R1264 K1424
BS03	rna	N	R704 D743	R702 D741
BS04	ZN	N	C1194 C1201 C1204	C1192 C1199 C1202
BS05	ZN	N	C58 C73 C76	C56 C71 C74
BS06	MG	N	D739 D741 D743	D737 D739 D741
BS07	MG	N	W897 E898 I900	W895 E896 I898
BS08	2TM	N	R704 P706 N737 M1238	R702 P704 N735 M1236

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:5x22, PDBe:5x22, PDBj:5x22
• PDBsum: 5x22
• PubMed: 28622509
• UniProt: Q8RQE8|RPOC_THET8 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)