Structure of PDB 6eyd Chain D

Receptor sequence

>6eydD (length=1241) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

VNFFDELRIGLATADDIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFG
PTRDWECYCGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELAAPVTH
IWYFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDDEMRHNELSTLEA
EMAVEKKAVEDQRDADLEARAQKLEADLAELEDVRRKVRDSGEREMRQLR
DRAQRELDRLDEIWNTFTKLAPKQLIVDEVLYRELQDRYGEYFTGAMGAE
SIKKLIENFDIDAEAESLREVIRSGKGQKKLRALKRLKVVAAFQQSGNSP
MGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLKRLID
LGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRPLKSLSDLLKGK
QGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELFKPFVMKR
LVDLNHAQNIKSAKRMVERQRPQVWDVLEEVIAEHPVLLNRAPTLHRLGI
QAFEPQLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEAQAEARILM
LSSNNILSPASGKPLAMPRLDMVTGLYYLTTLVEGATGEYQAATKDAPEQ
GVYSSPAEAIMAMDRGALSVRAKIKVRLTELRPPTDLEAQLFENGWKPGD
AWTAETTLGRVMFNELLPKSYPFVNEQMHKKVQARIINDLAERFPMIVVA
QTVDKLKDAGFYWATRSGVTVSMADVLVPPQKQEILERHEAEADAIERKY
QRGALNHTERNESLVKIWQDATEEVGKALEEFYPADNPIITIVKSGATGN
LTQTRTLAGMKGLVTNPKGEFIPRPIKSSFREGLTVLEYFINTHGARKGL
ADTALRTADSGYLTRRLVDVSQDVIVREHDCETERGINVTLAERGPDIRD
AHVETSAFARTLATDAVDANGNVIIERGHDLGDPAIDALLAAGITTVKVR
SVLTCTSATGVCAMCYGRSMATGKLVDIGEAVGIVAAQSIGEPGTQLTGG
LPRVQELFEARVPRNKAPIADVAGRVRLEESDKFFKITIVPDDGGEEVVY
DKLSKRQRLRVGVLSDGDHVEVGDQLMEGAADPHEVLRVQGPREVQIHLV
KEVQEVYRAQGVSIHDKHIEVIVRQMLRRVTIIDSGSTEFLPGSLTERAE
FEAENRRVVAAGRPVLMGITKASLATDSWLSAASFQETTRVLTDAAINCR
SDKLNGLKENVIIGKLIPAGTGISRYRNIQVQPTEEARAAA

3D structure

• PDB: 6eyd The Core and Holoenzyme Forms of RNA Polymerase fromMycobacterium smegmatis.
• Chain: D
• Resolution: 4.22 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	C967 C977	C955 C965
BS02	ZN	D	C60 C75	C57 C72
BS03	MG	D	D537 D539	D528 D530

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:6eyd, PDBe:6eyd, PDBj:6eyd
• PDBsum: 6eyd
• PubMed: 30478083
• UniProt: A0QS66|RPOC_MYCS2 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)