Structure of PDB 4gfh Chain F

Receptor sequence

>4gfhF (length=1098) Species: 559292 (Saccharomyces cerevisiae S288C)

SASDKYQKISQLEHILKRPDTYIGSVETQEQLQWIYDEETDCMIEKNVTI
VPGLFKIFDEILVNAADNKVRDPSMKRIDVNIHAEEHTIEVKNDGKGIPI
EIHNKENIYIPEMIFGHLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEF
ILETADLNVGQKYVQKWENNMSICHPPKITSYKKGPSYTKVTFKPDLTRF
GMKELDNDILGVMRRRVYDINGSVRDINVYLNGKSLKIRNFKNYVELYLK
SLIPTILYERINNRWEVAFAVSDISFQQISFVNSIATTMGGTHVNYITDQ
IVKKISEILKKKKKKSVKSFQIKNNMFIFINCLIENPAFTSQTKEQLTTR
VKDFGSRCEIPLEYINKIMKTDLATRMFEIASRITNYPKLEDANKAGTKE
GYKCTLVLTEGDSALSLAVAGLAVVGRDYYGCYPLRGKMLNVREASADQI
LKNAEIQAIKKIMGLQHRKKYEDTKSLRYGHLMIMTDQDHDGSHIKGLII
NFLESSFPGLLDIQGFLLEFITPIIKVSITKPTKNTIAFYNMPDYEKWRE
EESHKFTWKQKYYTSLAQEVREYFSNLDRHLKIFHSLQGNDKDYIDLAFS
KKKADDRKEWLRQYEPGTVLDPTLKEIPISDFINKELILFSLADNIRSIP
NVLDGFKPGQRKVLYGCFKKNLKSELKVAQLAPYVSECTAYHHGEQSLAQ
TIIGLAQNFVGSNNIYLLLPNGAFGTRATGGKDAAAARYIYTELNKLTRK
IFHPADDPLYKYIQEDEKTVEPEWYLPILPMILVNGAEGIGTGWSTYIPP
FNPLEIIKNIRHLMNDEELEQMHPWFRGWTGTIEEIEPLRYRMYGRIEQI
GDNVLEITELPARTWTSTIKEYLLLGLSGNDKIKPWIKDMEEQHDDNIKF
IITLSPEEMAKTRKIGFYERFKLISPISLMNMVAFDPHGKIKKYNSVNEI
LSEFYYVRLEYYQKRKDHMSERLQWEVEKYSFQVKFIKMIIEKELTVTNK
PRNAIIQELENLGFPRFNKEGKPYYGSEELYGTYEYLLGMRIWSLTKERY
QKLLKQKQEKETELENLLKLSAKDIWNTDLKAFEVGYQEFLQRDAEAR

3D structure

• PDB: 4gfh Structure of a topoisomerase II-DNA-nucleotide complex reveals a new control mechanism for ATPase activity.
• Chain: F
• 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	F	K428 D451 R475	K389 D412 R436
BS02	dna	F	K428 D451 R475	K389 D412 R436
BS03	dna	F	D530 R690 K700 Y734 H736 S740 K775 E831 I833	D491 R647 K657 Y691 H693 S697 K732 E788 I790
BS04	dna	F	K477 L479 N480 H533 R650 K651 Y782 I833 G834 T835 G836 W837 S838 K965 P969 N974	K438 L440 N441 H494 R607 K608 Y739 I790 G791 T792 G793 W794 S795 K922 P926 N931
BS05	dna	F	D530 R690 K700 Y734 H736 S740 K775 E831 I833 W908	D491 R647 K657 Y691 H693 S697 K732 E788 I790 W865
BS06	dna	F	K477 M478 L479 N480 H533 R650 K651 R781 Y782 I833 G834 T835 G836 W837 S838 K965 P969 N974	K438 M439 L440 N441 H494 R607 K608 R738 Y739 I790 G791 T792 G793 W794 S795 K922 P926 N931
BS07	MG	F	E66 N70	E60 N64
BS08	ANP	F	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)