Structure of PDB 5vi8 Chain D

Receptor sequence

>5vi8D (length=1248) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

VNFFDELRIGLATADDIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFG
PTRDWECYCGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELAAPVTH
IWYFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDDEMRHNELSTLEA
EMAVEKKAVEDQRDADLEARAQKLEADLAELEAEGAKSDVRRKVRDSGER
EMRQLRDRAQRELDRLDEIWNTFTKLAPKQLIVDEVLYRELQDRYGEYFT
GAMGAESIKKLIENFDIDAEAESLREVIRSGKGQKKLRALKRLKVVAAFQ
QSGNSPMGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNR
LKRLIDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRPLKSLS
DLLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELFK
PFVMKRLVDLNHAQNIKSAKRMVERQRPQVWDVLEEVIAEHPVLLNRAPT
LHRLGIQAFEPQLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEAQA
EARILMLSSNNILSPASGKPLAMPRLDMVTGLYYLTTLVEGATGEYQAAT
KDAPEQGVYSSPAEAIMAMDRGALSVRAKIKVRLTELRPPTDLEAQLFEN
GWKPGDAWTAETTLGRVMFNELLPKSYPFVNEQMHKKVQARIINDLAERF
PMIVVAQTVDKLKDAGFYWATRSGVTVSMADVLVPPQKQEILERHEAEAD
AIERKYQRGALNHTERNESLVKIWQDATEEVGKALEEFYPADNPIITIVK
SGATGNLTQTRTLAGMKGLVTNPKGEFIPRPIKSSFREGLTVLEYFINTH
GARKGLADTALRTADSGYLTRRLVDVSQDVIVREHDCETERGINVTLAER
GPDIRDAHVETSAFARTLATDAVDANGNVIIERGHDLGDPAIDALLAAGI
TTVKVRSVLTCTSATGVCAMCYGRSMATGKLVDIGEAVGIVAAQSIGEPG
TQLTGGLPRVQELFEARVPRNKAPIADVAGRVRLEESDKFFKITIVPDDG
GEEVVYDKLSKRQRLRVIGVLSDGDHVEVGDQLMEGAADPHEVLRVQGPR
EVQIHLVKEVQEVYRAQGVSIHDKHIEVIVRQMLRRVTIIDSGSTEFLPG
SLTERAEFEAENRRVVAAGRPVLMGITKASLATDSWLSAASFQETTRVLT
DAAINCRSDKLNGLKENVIIGKLIPAGTGISRYRNIQVQPTEEARAAA

3D structure

• PDB: 5vi8 Structural insights into the mycobacteria transcription initiation complex from analysis of X-ray crystal structures.
• Chain: D
• Resolution: 2.76 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 C974 C977	C887 C961 C968 C971
BS02	ZN	D	C60 C75	C57 C72
BS03	MG	D	D535 D537 D539	D532 D534 D536

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:5vi8, PDBe:5vi8, PDBj:5vi8
• PDBsum: 5vi8
• PubMed: 28703128
• UniProt: A0QS66|RPOC_MYCS2 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)