Structure of PDB 6c04 Chain D

Receptor sequence

>6c04D (length=1267) Species: 1773 (Mycobacterium tuberculosis)

GAMLDVNFFDELRIGLATAEDIRQWSYGEVKKPETINYRTLKPEKDGLFC
EKIFGPTRDWECYCGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELA
APVTHIWYFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDEEMRHNEL
STLEAEMAVERKAVEDQRDGELEARAQKLEADLAELEAEGAKADARRKVR
DGGEREMRQIRDRAQRELDRLEDIWSTFTKLAPKQLIVDENLYRELVDRY
GEYFTGAMGAESIQKLIENFDIDAEAESLRDVIRNGKGQKKLRALKRLKV
VAAFQQSGNSPMGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVI
NRNNRLKRLIDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRP
LKSLSDLLKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMA
LELFKPFVMKRLVDLNHAQNIKSAKRMVERQRPQVWDVLEEVIAEHPVLL
NRAPTLHRLGIQAFEPMLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLS
AEAQAEARILMLSSNNILSPASGRPLAMPRLDMVTGLYYLTTEVPGDTGE
YQPASGDHPETGVYSSPAEAIMAADRGVLSVRAKIKVRLTQLRPPVEIEA
ELFGHSGWQPGDAWMAETTLGRVMFNELLPLGYPFVNKQMHKKVQAAIIN
DLAERYPMIVVAQTVDKLKDAGFYWATRSGVTVSMADVLVPPRKKEILDH
YEERADKVEKQFQRGALNHDERNEALVEIWKEATDEVGQALREHYPDDNP
IITIVDSGATGNFTQTRTLAGMKGLVTNPKGEFIPRPVKSSFREGLTVLE
YFINTHGARKGLADTALRTADSGYLTRRLVDVSQDVIVREHDCQTERGIV
VELAERAPDGTLIRDPYIETSAYARTLGTDAVDEAGNVIVERGQDLGDPE
IDALLAAGITQVKVRSVLTCATSTGVCATCYGRSMATGKLVDIGEAVGIV
AAQSIGEPGTQLTMITGGLPRVQELFEARVPRGKAPIADVTGRVRLEDGE
RFYKITIVPDDGGEEVVYDKISKRQRLRVFKRVLSDGDHVEVGQQLMEGS
ADPHEVLRVQGPREVQIHLVREVQEVYRAQGVSIHDKHIEVIVRQMLRRV
TIIDSGSTEFLPGSLIDRAEFEAENRRVVAEGGEPAAGRPVLMGITKASL
ATDSWLSAASFQETTRVLTDAAINCRSDKLNGLKENVIIGKLIPAGTGIN
RYRNIAVQPTEEARAAA

3D structure

• PDB: 6c04 Fidaxomicin jamsMycobacterium tuberculosisRNA polymerase motions needed for initiation via RbpA contacts.
• Chain: D
• Resolution: 3.27 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	D	V110 R421 R427 T867 A868 Q1227 E1228	V112 R423 R429 T869 A870 Q1212 E1213
BS02	ZN	D	C975 C978	C977 C980
BS03	ZN	D	C60 C62 C75 C78	C62 C64 C77 C80
BS04	MG	D	D535 D537 D539	D537 D539 D541

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
• GO:0005829 cytosol
• GO:0005886 plasma membrane
• GO:0009274 peptidoglycan-based cell wall

External links

• PDB: RCSB:6c04, PDBe:6c04, PDBj:6c04
• PDBsum: 6c04
• PubMed: 29480804
• UniProt: P9WGY7|RPOC_MYCTU DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)