Structure of PDB 4gfh Chain A

Receptor sequence

>4gfhA (length=1102) Species: 559292 (Saccharomyces cerevisiae S288C)

SASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTI
VPGLFKIFDEILVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPI
EIHNKENIYIPEMIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEF
ILETADLNVGQKYVQKWENNMSICHPPKITSYKKGPSYTKVTFKPDLTRF
GMKELDNDILGVMRRRVYDINGSVRDINVYLNGKSLKIRNFKNYVELYLK
SLIPTILYERINNRWEVAFAVSDISFQQISFVNSIATTMGGTHVNYITDQ
IVKKISEILKKKKKKSVKSFQIKNNMFIFINCLIENPAFTSQTKEQLTTR
VKDFGSRCEIPLEYINKIMKTDLATRMFEIADANESRITNYPKLEDANKA
GTKEGYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNVREAS
ADQILKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIK
GLIINFLESSFPGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYE
KWREEESHKFTWKQKYYTSLAQEVREYFSNLDRHLKIFHSLQGNDKDYID
LAFSKKKADDRKEWLRQYEPGTVLDPTLKEIPISDFINKELILFSLADNI
RSIPNVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTAYHHGEQ
SLAQTIIGLAQNFVGSNNIYLLLPNGAFGTRATGGKDAAAARYIYTELNK
LTRKIFHPADDPLYKYIQEDEKTVEPEWYLPILPMILVNGAEGIGTGWST
YIPPFNPLEIIKNIRHLMNDEELEQMHPWFRGWTGTIEEIEPLRYRMYGR
IEQIGDNVLEITELPARTWTSTIKEYLLLGLSGNDKIKPWIKDMEEQHDD
NIKFIITLSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNS
VNEILSEFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELT
VTNKPRNAIIQELENLGFPRFNKEGKPYYGSEELYGTYEYLLGMRIWSLT
KERYQKLLKQKQEKETELENLLKLSAKDIWNTDLKAFEVGYQEFLQRDAE
AR

3D structure

• PDB: 4gfh Structure of a topoisomerase II-DNA-nucleotide complex reveals a new control mechanism for ATPase activity.
• Chain: A
• Resolution: 4.408 Å

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)	Binding affinity
BS01	dna	A	D530 R690 K700 Y734 H736 S740 K775 E831 I833 W908	D495 R651 K661 Y695 H697 S701 K736 E792 I794 W869
BS02	dna	A	K477 L479 N480 H533 R650 K651 Y782 I833 G834 T835 G836 W837 S838 K965 P969 N974	K442 L444 N445 H498 R611 K612 Y743 I794 G795 T796 G797 W798 S799 K926 P930 N935
BS03	dna	A	D530 R690 K700 Y734 H736 S740 K775 E831 I833 W908	D495 R651 K661 Y695 H697 S701 K736 E792 I794 W869
BS04	dna	A	K477 M478 L479 N480 H533 A647 R650 K651 R781 Y782 I833 G834 T835 G836 S838 K965 P969 N974	K442 M443 L444 N445 H498 A608 R611 K612 R742 Y743 I794 G795 T796 G797 S799 K926 P930 N935
BS05	dna	A	K428 D451 R475	K393 D416 R440
BS06	dna	A	K428 D451 R475	K393 D416 R440
BS07	ANP	A	N70 N74 I104 F121 S127 S128 G140 R141 N142 G143 Y144 G145 A146 K147 T195 Q365 K367	N64 N68 I98 F115 S121 S122 G134 R135 N136 G137 Y138 G139 A140 K141 T189 Q342 K344

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

External links

• PDB: RCSB:4gfh, PDBe:4gfh, PDBj:4gfh
• PDBsum: 4gfh
• PubMed: 23022727
• UniProt: P06786|TOP2_YEAST DNA topoisomerase 2 (Gene Name=TOP2)