Structure of PDB 6cce Chain D

Receptor sequence

>6cceD (length=1195) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

DVNFFDELRIGLATADDIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIF
GPTKVRRERMGHIELAAPVTHIWYFKGVPSRLGYLLDLAPKDLEKIIYFA
AYVITSVDDEMRHNELSTLEAEMAVEKKAVEDQRDADLEARAQKLEADLA
ELEAEGAKSDVRRKVRDSGEREMRQLRDRAQRELDRLDEIWNTFTKLAPK
QLIVDEVLYRELQDRYGEYFTGAMGAESIKKLIENFDIDAEAESLREVIR
SGKGQKKLRALKRLKVVAAFQQSGNSPMGMVLDAVPVIPPELRPMVQLDG
GRFATSDLNDLYRRVINRNNRLKRLIDLGAPEIIVNNEKRMLQESVDALF
DNGRRGRPVTGPGNRPLKSLSDLLKGKQGRFRQNLLGKRVDYSGRSVIVV
GPQLKLHQCGLPKLMALELFKPFVMKRLVDLNHAQNIKSAKRMVERQRPQ
VWDVLEEVIAEHPVLLNRAPTLHRLGIQAFEPQLVEGKAIQLHPLVCEAF
NADFDGDQMAVHLPLSAEAQAEARILMLSSNNILSPASGKPLAMPRLDMV
TGLYYLTTLVEGATGEYQAATKDAPEQGVYSSPAEAIMAMDRGALSVRAK
IKVRLTELRPPTDLEAQLFENGWKPGDAWTAETTLGRVMFNELLPKSYPF
VNEQMHKKVQARIINDLAERFPMIVVAQTVDKLKDAGFYWATRSGVTVSM
ADVLVPPQKQEILERHEAEADAIERKYQRGALNHTERNESLVKIWQDATE
EVGKALEEFYPADNPIITIVKSGATGNLTQTRTLAGMKGLVTNPKGEFIP
RPIKSSFREGLTVLEYFINTHGARKGLADTALRTADSGYLTRRLVDVSQD
VIVREHDCETERGINVTLAEIRDAHVETSAFARTLATDAVDANGNVIIER
GHDLGDPAIDALLAAGITTVKVRSVLTCTSATGVCAMCYGRSMATGKLVD
IGEAVGIVAAQSIGEPGTQLTGGLPRVQELFEARVPRNKAPIADVAGRVR
LEESDKFFKITIVPDDGGEEVVYDKLSKRQRLRVIGVLSDGDHVEVGDQL
MEGAADPHEVLRVQGPREVQIHLVKEVQEVYRAQGVSIHDKHIEVIVRQM
LRRVTITERAEFEAAGRPVLMGITKASLATDSWLSAASFQETTRVLTDAA
INCRSDKLNGLKENVIIGKLIPAGTGISRYRNIQVQPTEEARAAA

3D structure

• PDB: 6cce Rifamycin congeners kanglemycins are active against rifampicin-resistant bacteria via a distinct mechanism.
• Chain: D
• Resolution: 3.05 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	C858 C928 C938
BS02	MG	D	D535 D537 D539	D503 D505 D507
BS03	GLU	D	R886 I1265 S1266 R1267	R854 I1177 S1178 R1179

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