Structure of PDB 3l4k Chain A

Receptor sequence

>3l4kA (length=721) Species: 4932 (Saccharomyces cerevisiae) [Search protein sequence]

SRITNYPKLEDANKAGTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYG
CYPLRGKMLNVREASADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGH
LMIMTDQDHDGSHIKGLIINFLESSFPGLLDIQGFLLEFITPIIKVSITK
PTKNTIAFYNMPDYEKWREEESHKFTWKQKYYKGLGTSLAQEVREYFSNL
DRHLKIFHSLQGNDKDYIDLAFSKKKADDRKEWLRQYEPGTVLDPTLKEI
PISDFINKELILFSLADNIRSIPNVLDGFKPGQRKVLYGCFKKNLKSELK
VAQLAPYVSECTAYHHGEQSLAQTIIGLAQNFVGSNNIYLLLPNGAFGTR
ATGGKDAAAARYIYTELNKLTRKIFHPADDPLYKYIQEDEKTVEPEWYLP
ILPMILVNGAEGIGTGWSTYIPPFNPLEIIKNIRHLMNDEELEQMHPWFR
GWTGTIEEIEPLRYRMYGRIEQIGDNVLEITELPARTWTSTIKEYLLLGL
SGNDKIKPWIKDMEEQHDDNIKFIITLSPEEMAKTRKIGFYERFKLISPI
SLMNMVAFDPHGKIKKYNSVNEILSEFYYVRLEYYQKRKDHMSERLQWEV
EKYSFQVKFIKMIIEKELTVTNKPRNAIIQELENLGFPRFNKEGKPYYGS
EELYGTYEYLLGMRIWSLTKERYQKLLKQKQEKETELENLLKLSAKDIWN
TDLKAFEVGYQEFLQRDAEAR

3D structure

PDB

3l4k A novel and unified two-metal mechanism for DNA cleavage by type II and IA topoisomerases.

Chain

Resolution

2.98 Å

3D
structure

[Spin on]
[Spin off]
[Reset orientation]

[High quality]
[Low quality]

[White background]
[Black background]

[Download]
[Download structure with residue number starting from 1]

Enzymatic activity

Enzyme Commision number

5.6.2.2: DNA topoisomerase (ATP-hydrolyzing).

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)
BS01	dna	A	E449 S485 D530 R690 K700 Y734 H736 S740 K775 E831 I833 W908	E29 S65 D110 R270 K280 Y314 H316 S320 K355 E411 I413 W488
BS02	dna	A	K477 L479 N480 H533 F642 A647 R650 K651 Y782 I833 G834 G836 W837 S838 K925 K965 P969 N974	K57 L59 N60 H113 F222 A227 R230 K231 Y362 I413 G414 G416 W417 S418 K505 K545 P549 N554
BS03	dna	A	R690 K700 Y734 H736 S740 K775 E831 I833 W908	R270 K280 Y314 H316 S320 K355 E411 I413 W488
BS04	dna	A	K477 L479 N480 H533 F642 R650 K651 R781 Y782 I833 G834 T835 G836 W837 S838 K925 K965 P969 N974	K57 L59 N60 H113 F222 R230 K231 R361 Y362 I413 G414 T415 G416 W417 S418 K505 K545 P549 N554
BS05	ZN	A	H735 E808	H315 E388
BS06	ZN	A	E449 D526	E29 D106
BS07	ZN	A	D526 D528	D106 D108
BS08	TSP	A	E449 D530 H736	E29 D110 H316

Gene Ontology

	Molecular Function
GO:0003677	DNA binding
GO:0003918	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
GO:0005524	ATP binding

	Biological Process
GO:0006259	DNA metabolic process
GO:0006265	DNA topological change

View graph for
Molecular Function

View graph for
Biological Process

External links

PDB	RCSB:3l4k, PDBe:3l4k, PDBj:3l4k
PDBsum	3l4k
PubMed	20485342
UniProt	P06786\|TOP2_YEAST DNA topoisomerase 2 (Gene Name=TOP2)

[Back to BioLiP]