Structure of PDB 6dcf Chain D

Receptor sequence

>6dcfD (length=1176) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

DVNFFDELRIGLATADDIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIF
GPTRDWECYCGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELAAPVT
HIWYFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDDEMRHNELSTLE
AEMAVEKKAVEDQRDADLEARAQKLEADLAELEAEGAKSDVRRKVRDSGE
REMRQLRDRAQRELDRLDEIWNTFTKLAPKQLIVDEVLYRELQDRYGEYF
TGAMGAESIKKLIENFDIDAEAESLREVIRSGKGQKKLRALKRLKVVAAF
QQSGNSPMGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNN
RLKRLIDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRPLKSL
SDLLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELF
KPFVMKRLVDLNHAQNIKSAKRMVERQRPQVWDVLEEVIAEHPVLLNRAP
TLHRLGIQAFEPQLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEAQ
AEARILMLSSNNILSPASGKPLAMPRLDMVTGLYYLTTLVEGATGEYQAA
TKDAPEQGVYSSPAEAIMAMDRGALSVRAKIKVRLTELRPPTDLEAQLFE
NGWKPGDAWTAETTLGRVMFNELLPKSYPFVNEQMHKKVQARIINDLAER
FPMIVVAQTVDKLKDAGFYWATRSGVTVSMADVLVQKQEILERHEAEADA
IERKYQRGALNHTERNESLVKIWQDATEEVGKALEEFYPADNPIITIVKS
GATADSGYLTRRLVDVSQDVIVREHDCETERGINVTLAERGRDAHVETSA
FARTLATDAVDANGNVIIERGHDLGDPAIDALLAAGITTVKVRSVLTCTS
ATGVCAMCYGRSMATGKLVDIGEAVGIVAAQSIGEPGTGGLPRVQELFEA
RVPRNKAPIADVAGRVRLEESDKFFKITIVPDDGGEEVVYDKLSKRQRLR
VIGTEGVLSDGDHVEVGDQLMEGAADPHEVLRVQGPREVQIHLVKEVQEV
YRAQGVSIHDKHIEVIVRQMLRRVTIIDSEFLPGSLTERAEFEAENAGRP
VLMGITKASLATDSWLSAASFQETTRVLTDAAINCRSDKLNGLKENVIIG
KLIPAGTGISRYRNIQVQPTEEARAA

3D structure

• PDB: 6dcf Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism.
• Chain: D
• Resolution: 3.45 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	C890 C967 C977	C827 C898 C908
BS02	ZN	D	C60 C62 C75 C78	C58 C60 C73 C76
BS03	MG	D	D535 D537 D539	D533 D535 D537
BS04	GLU	D	R886 I1265 S1266	R823 I1159 S1160

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:6dcf, PDBe:6dcf, PDBj:6dcf
• PDBsum: 6dcf
• PubMed: 30297823
• UniProt: A0QS66|RPOC_MYCS2 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)