7E62 | pdb_00007e62

Experimental Data Snapshot

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

(2021) Biophys J 120: 3355-3362

PubMed Abstract:
TAK1-binding protein 2 (TAB2) has generally been considered to bind specifically to K63-linked polyubiquitin chains via its C-terminal Npl4 zinc-finger (NZF) domain. However, a recent study showed that the NZF domain of TAB2 (TAB2-NZF) could also interact with K6-linked polyubiquitin chains. Here, we report the crystal structure of TAB2-NZF in complex with K6-linked diubiquitin (K6-Ub ₂) at 1.99-Å resolution. TAB2-NZF simultaneously interacts with the distal and proximal ubiquitin moieties of K6-Ub ₂. By comparing the structures of TAB2-NZF in complex with K6-Ub ₂ and with K63-linked diubiquitin (K63-Ub ₂), we reveal that the binding mechanism of TAB2-NZF with K6-Ub ₂ is similar to that with K63-Ub ₂, except for the flexible C-terminal region of the distal ubiquitin. Therefore, we conclude that the C-terminal flexibility of the distal ubiquitin contributes to the dual specificity of TAB2-NZF toward K6- and K63-linked ubiquitin chains. This study provides important insights into the functions of K6-linked ubiquitin chains, which are currently unclear.

Organizational Affiliation

Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Chiba, Japan.

Macromolecule Content

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ubiquitin	A, D [auth H]	76	Mus musculus	Mutation(s): 1 Gene Names: Rps27a, Uba80, Ubcep1
UniProt
Find proteins for P62983 (Mus musculus) Explore P62983 Go to UniProtKB: P62983
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62983
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Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Ubiquitin	B, E [auth I]	77	Mus musculus	Mutation(s): 1 Gene Names: Rps27a, Uba80, Ubcep1
UniProt
Find proteins for P62983 (Mus musculus) Explore P62983 Go to UniProtKB: P62983
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P62983
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
TGF-beta-activated kinase 1 and MAP3K7-binding protein 2	C, F [auth J]	55	Mus musculus	Mutation(s): 0 Gene Names: Tab2, Kiaa0733, Map3k7ip2
UniProt
Find proteins for Q99K90 (Mus musculus) Explore Q99K90 Go to UniProtKB: Q99K90
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99K90
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Reference Sequence

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
EPE Query on EPE Download:Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID C₈ H₁₈ N₂ O₄ S JKMHFZQWWAIEOD-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain I [auth J] SDF format, chain H [auth C] MOL2 format, chain I [auth J] MOL2 format, chain H [auth C] mmCIF format, chain I [auth J] mmCIF format, chain H [auth C]	H [auth C], I [auth J]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Focus chain I [auth J] Interactions & Density Focus chain H [auth C] Focus chain I [auth J]