Structure of PDB 7yq8 Chain B

Receptor sequence

>7yq8B (length=730) Species: 9606 (Homo sapiens) [Search protein sequence]

KGIPKLDDANDAGGKHSLECTLILTEGDSAKSLAVSGLGVIGRDRYGVFP
LRGKILNVREASHKQIMENAEINNIIKIVGLQYKKSYDDAESLKTLRYGK
IMIMTDQDQDGSHIKGLLINFIHHNWPSLLKHGFLEEFITPIVKASKNKQ
ELSFYSIPEFDEWKKHIENQKAWKIKYYKGLGTSTAKEAKEYFADMERHR
ILFRYAGPEDDAAITLAFSKKKIDDRKEWLTNFMEDRRQRRLHGLPEQFL
YGTATKHLTYNDFINKELILFSNSDNERSIPSLVDGFKPGQRKVLFTCFK
RNDKREVKVAQLAGSVAEMSAYHHGEQALMMTIVNLAQNFVGSNNINLLQ
PIGQFGTRLHGGKDAASPRYIFTMLSTLARLLFPAVDDNLLKFLYDDNQR
VEPEWYIPIIPMVLINGAEGIGTGWACKLPNYDAREIVNNVRRMLDGLDP
HPMLPNYKNFKGTIQELGQNQYAVSGEIFVVDRNTVEITELPVRTWTQVY
KEQVLEPMLNGTDKTPALISDYKEYHTDTTVKFVVKMTEEKLAQAEAAGL
HKVFKLQTTLTCNSMVLFDHMGCLKKYETVQDILKEFFDLRLSYYGLRKE
WLVGMLGAESTKLNNQARFILEKIQGKITIENRSKKDLIQMLVQRGYESD
PVKAWKEAQEKAGPDFNYILNMSLWSLTKEKVEELIKQRDAKGREVNDLK
RKSPSDLWKEDLAAFVEELDKVESQEREDV

3D structure

PDB

7yq8 ERK2-topoisomerase II regulatory axis is important for gene activation in immediate early genes.

Chain

Resolution

3.9 Å

3D
structure

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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	B	R508 L512 N513 I679 R682 K683 Y826 I877 G878 K970 K1011 T1015 T1017	R52 L56 N57 I223 R226 K227 Y370 I421 G422 K514 K555 T559 T561
BS02	dna	B	E482 G509 K510 D566 R734 K744 Y778 H780 A784 N791 E875 I877 R950 W952	E26 G53 K54 D110 R278 K288 Y322 H324 A328 N335 E419 I421 R494 W496
BS03	MG	B	D562 D564	D106 D108
BS04	EVP	B	G483 R508 M787	G27 R52 M331

Gene Ontology

	Molecular Function
GO:0003677	DNA binding
GO:0003682	chromatin binding
GO:0003916	DNA topoisomerase activity
GO:0003918	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity
GO:0005515	protein binding
GO:0005524	ATP binding
GO:0043021	ribonucleoprotein complex binding
GO:0046872	metal ion binding

	Biological Process
GO:0000712	resolution of meiotic recombination intermediates
GO:0000819	sister chromatid segregation
GO:0001764	neuron migration
GO:0006259	DNA metabolic process
GO:0006265	DNA topological change
GO:0007409	axonogenesis
GO:0030183	B cell differentiation
GO:0030900	forebrain development
GO:0045870	positive regulation of single stranded viral RNA replication via double stranded DNA intermediate
GO:0060255	regulation of macromolecule metabolic process
GO:0070301	cellular response to hydrogen peroxide
GO:0071318	cellular response to ATP
GO:0090398	cellular senescence
GO:2001034	positive regulation of double-strand break repair via nonhomologous end joining

	Cellular Component
GO:0000792	heterochromatin
GO:0005634	nucleus
GO:0005654	nucleoplasm
GO:0005730	nucleolus
GO:0005829	cytosol
GO:1990904	ribonucleoprotein complex

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Molecular Function

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Biological Process

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Cellular Component

External links

PDB	RCSB:7yq8, PDBe:7yq8, PDBj:7yq8
PDBsum	7yq8
PubMed	38097570
UniProt	Q02880\|TOP2B_HUMAN DNA topoisomerase 2-beta (Gene Name=TOP2B)

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