Structure of PDB 6yxu Chain D

Receptor sequence

>6yxuD (length=1269) Species: 246196 (Mycolicibacterium smegmatis MC2 155)

FFDELRIGLATADDIRNWSYGEVKKPETINYRTLKPEKDGLFCEKIFGPT
RDWECYCGKYKRVRFKGIICERCGVEVTRAKVRRERMGHIELAAPVTHIW
YFKGVPSRLGYLLDLAPKDLEKIIYFAAYVITSVDDEMRHNELSTLEAEM
AVEKKAVEDQRDADLEARAQKLEADLAELEAEGAKSDVRRKVRDSGEREM
RQLRDRAQRELDRLDEIWNTFTKLAPKQLIVDEVLYRELQDRYGEYFTGA
MGAESIKKLIENFDIDAEAESLREVIRSGKGQKKLRALKRLKVVAAFQQS
GNSPMGMVLDAVPVIPPELRPMVQLDGGRFATSDLNDLYRRVINRNNRLK
RLIDLGAPEIIVNNEKRMLQESVDALFDNGRRGRPVTGPGNRPLKSLSDL
LKGKQGRFRQNLLGKRVDYSGRSVIVVGPQLKLHQCGLPKLMALELFKPF
VMKRLVDLNHAQNIKSAKRMVERQRPQVWDVLEEVIAEHPVLLNRAPTLH
RLGIQAFEPQLVEGKAIQLHPLVCEAFNADFDGDQMAVHLPLSAEAQAEA
RILMLSSNNILSPASGKPLAMPRLDMVTGLYYLTTLVEGATGEYQAATKD
APEQGVYSSPAEAIMAMDRGALSVRAKIKVRLTELRPPTDLEAQLFENGW
KPGDAWTAETTLGRVMFNELLPKSYPFVNEQMHKKVQARIINDLAERFPM
IVVAQTVDKLKDAGFYWATRSGVTVSMADVLVPPQKQEILERHEAEADAI
ERKYQRGALNHTERNESLVKIWQDATEEVGKALEEFYPADNPIITIVKSG
ATGNLTQTRTLAGMKGLVTNPKGEFIPRPIKSSFREGLTVLEYFINTHGA
RKGLADTALRTADSGYLTRRLVDVSQDVIVREHDCETERGINVTLAERGP
DGTLIRDAHVETSAFARTLATDAVDANGNVIIERGHDLGDPAIDALLAAG
ITTVKVRSVLTCTSATGVCAMCYGRSMATGKLVDIGEAVGIVAAQSIGEP
GTQLTMRTFDIVGGLPRVQELFEARVPRNKAPIADVAGRVRLEESDKFFK
ITIVPDDGGEEVVYDKLSKRQRLRVITHEDGTEGVLSDGDHVEVGDQLME
GAADPHEVLRVQGPREVQIHLVKEVQEVYRAQGVSIHDKHIEVIVRQMLR
RVTIIDSGSTEFLPGSLTERAEFEAENRRVVAEGGEPAAGRPVLMGITKA
SLATDSWLSAASFQETTRVLTDAAINCRSDKLNGLKENVIIGKLIPAGTG
ISRYRNIQVQPTEEARAAA

3D structure

• PDB: 6yxu Mycobacterial HelD is a nucleic acids-clearing factor for RNA polymerase.
• Chain: D
• Resolution: 3.08 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	C885 C962 C969 C972
BS02	ZN	D	C60 C62 C75	C55 C57 C70
BS03	MG	D	D535 D537 D539	D530 D532 D534

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:6yxu, PDBe:6yxu, PDBj:6yxu
• PDBsum: 6yxu
• PubMed: 33339823
• UniProt: A0QS66|RPOC_MYCS2 DNA-directed RNA polymerase subunit beta' (Gene Name=rpoC)