Structure of PDB 6pcm Chain A

Receptor sequence

>6pcmA (length=793) Species: 246196 (Mycolicibacterium smegmatis MC2 155) [Search protein sequence]

NVRRLVIVESPTKARKIAGYLGSNYVVESSRGHIRDLPRNAADVPAKFKS
EPWARLGVNVDQNFEPLYIVSPEKKSTVTELKGLLKDVDELYLATDGDRE
GEAIAWHLLETLKPRVPVKRMVFHEITEPAIRNAAENPRDLDIALVDAQE
TRRILDRLYGYEVSPVLWKKVAPKLSAGRVQSVATRIIVQRERERMAFHS
ASYWDVTAELDASVSDPSPPKFTAKLNTVDGRRVATGRDFDSLGQLKRPD
EVLVLDEASAGALASGLRGAQLAVTSVEQKPYTRRPYAPFMTSTLQQEAA
RKLRFSSERTMSIAQRLYENGYITYMRTDSTTLSESAINAARTQARQLYG
EEYVHPSPRQYTRKVKNAQEAHEAIRPAGDVFQTPGQLHSALDTDEFRLY
ELIWQRTVASQMADARGTTLSLRIGGSASSGEQVVFNASGRTITFPGFLK
AYVSDDAESRLPNLTQGQRVDADLSADGHQTSPPARYTEASLIKALEELG
IGRPSTYSSIIKTIQDRGYVQKKGSALVPSWVAFAVVGLLEQHFGRLVDY
DFTAAMEDELDEIANGQEQRTNWLNNFYFGGEHGVEGSIARAGGLKQLVG
GNLEGIDAREVNSIKVFDDSEGRPVYVRVGRNGPYLERMVDDPDNPGEQK
PQRANLKEDLTPDELTPELAEKLFATPQEGRSLGIDPETGHEIVAKDGRF
GPYVTEVLPETGPKPRTGSLFRSMDLETVTLEDALKLLSLPRVVGVDPTT
NEEITAQNGRYGPYLKRGTDSRSLATEDQIFTITLDEALKIYA

3D structure

PDB

6pcm Mechanistic insights from structure of Mycobacterium smegmatis topoisomerase I with ssDNA bound to both N- and C-terminal domains.

Chain

Resolution

3.107 Å

3D
structure

Catalytic site residues are labeled in the structure
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Enzymatic activity

Catalytic site (original residue number in PDB)	E21 S22 D108 D110 Y339 R341
Catalytic site (residue number reindexed from 1)	E9 S10 D96 D98 Y325 R327
Enzyme Commision number	5.6.2.1: DNA topoisomerase.

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	A	S22 P23 R43 G44 H45 E112 R164 R165 D168 R169 G172 Y173 S176 P177 W180 K186 S188 A189 G190 R191 V192 Q193 Y339 R341 R528 S530 T531 R542	S10 P11 R31 G32 H33 E100 R152 R153 D156 R157 G160 Y161 S164 P165 W168 K174 S176 A177 G178 R179 V180 Q181 Y325 R327 R503 S505 T506 R517
BS02	dna	A	W180 K181 P185 G723 R724 F725 G726 Y728 T762 S764 G804 R805 Y806 Y809 S816 R817 S818	W168 K169 P173 G698 R699 F700 G701 Y703 T717 S719 G759 R760 Y761 Y764 S771 R772 S773

Gene Ontology

	Molecular Function
GO:0003677	DNA binding
GO:0003916	DNA topoisomerase activity
GO:0003917	DNA topoisomerase type I (single strand cut, ATP-independent) activity
GO:0046872	metal ion binding

	Biological Process
GO:0006265	DNA topological change

View graph for
Molecular Function

View graph for
Biological Process

External links

PDB	RCSB:6pcm, PDBe:6pcm, PDBj:6pcm
PDBsum	6pcm
PubMed	32232337
UniProt	A0R5D9\|TOP1_MYCS2 DNA topoisomerase 1 (Gene Name=topA)

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