PDBsum entry: 1p3q

Translation

PDB-id

1p3q


	Biological unit* = asymmetric unit, as shown (as deduced by PQS*)

Contents

Description

Header details

Protein chains

Waters ×176

* Residue conservation analysis

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PDB id:

1p3q

Name:

Translation

Title:

Mechanism of ubiquitin recognition by the cue domain of vps9

Structure:

Vacuolar protein sorting-associated protein vps9. Chain: q, r. Fragment: cue domain. Synonym: vps9p. Engineered: yes. Mutation: yes. Ubiquitin. Chain: u, v

Source:

Saccharomyces cerevisiae. Baker's yeast. Organism_taxid: 4932. Gene: vps9. Expressed in: escherichia coli. Expression_system_taxid: 562. Bos taurus. Bovine. Organism_taxid: 9913.

Biological unit:

Tetramer (from PQS)

UniProt:

Chain Q: P54787 (VPS9_YEAST)

Seq:

Struc:


Seq:				451 a.a.

Struc:				45 a.a.*

Chain R: P54787 (VPS9_YEAST)

Seq:

Struc:


Seq:				451 a.a.

Struc:				36 a.a.*

Chains U, V: P62990 (UBIQ_BOVIN)

Seq:

76 a.a.

Struc:

74 a.a.

Key:		PfamA domain
		Secondary structure			CATH domain

* PDB and UniProt seqs differ at 4 residue positions (black crosses)

Resolution:

1.70Å

R-factor:

0.260

R-free:

0.277

Authors:

G.Prag,S.Misra,E.A.Jones,R.Ghirlando,B.A.Davies, B.F.Horazdovsky,J.H.Hurley

Key ref:

G.Prag et al. (2003). Mechanism of ubiquitin recognition by the CUE domain of Vps9p.. Cell, 113, 609-620. [PubMed id: 12787502] [DOI: 10.1016/S0092-8674(03)00364-7]

Date:

18-Apr-03

Release date:

24-Jun-03

Related entries:

1mn3
apo structure of yeast vps9-cue domain

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Key reference

DOI no: 10.1016/S0092-8674(03)00364-7 Cell 113:609-620 (2003)

PubMed id: 12787502

Mechanism of ubiquitin recognition by the CUE domain of Vps9p.

G.Prag, S.Misra, E.A.Jones, R.Ghirlando, B.A.Davies, B.F.Horazdovsky, J.H.Hurley.

ABSTRACT

Coupling of ubiquitin conjugation to ER degradation (CUE) domains are approximately 50 amino acid monoubiquitin binding motifs found in proteins of trafficking and ubiquitination pathways. The 2.3 A structure of the Vps9p-CUE domain is a dimeric domain-swapped variant of the ubiquitin binding UBA domain. The 1.7 A structure of the CUE:ubiquitin complex shows that one CUE dimer binds one ubiquitin molecule. The bound CUE dimer is kinked relative to the unbound CUE dimer and wraps around ubiquitin. The CUE monomer contains two ubiquitin binding surfaces on opposite faces of the molecule that cannot bind simultaneously to a single ubiquitin molecule. Dimerization of the CUE domain allows both surfaces to contact a single ubiquitin molecule, providing a mechanism for high-affinity binding to monoubiquitin.

Selected figure(s)

Figure 2.
Figure 2. Structure of the CUE Dimer:Ubiqui- tin Complex Figure 3.
Figure 3. Conformational Changes in the CUE Domain

The above figures are reprinted by permission from Cell Press: Cell (2003, 113, 609-620) copyright 2003.

Figures were selected by the author.

Literature references that cite this PDB file's key reference

PubMed id Reference

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PDB codes: 2jy7 2jy8

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PDB code: 2qho

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Diverse polyubiquitin interaction properties of ubiquitin-associated domains.

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GAT (GGA and Tom1) domain responsible for ubiquitin binding and ubiquitination.

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12860974 J.D.Schnell, and L.Hicke (2003).
Non-traditional functions of ubiquitin and ubiquitin-binding proteins.

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Cell Struct Funct, 28, 443-453.

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Regulation of membrane protein transport by ubiquitin and ubiquitin-binding proteins.

Annu Rev Cell Dev Biol, 19, 141-172.

14592861 O.Cremona, C.Collesi, and E.Raiteri (2003).
Protein ubiquitylation and synaptic function.

Ann N Y Acad Sci, 998, 33-40.

14621999 Q.Wang, A.M.Goh, P.M.Howley, and K.J.Walters (2003).
Ubiquitin recognition by the DNA repair protein hHR23a.

Biochemistry, 42, 13529-13535.

12970176 T.D.Mueller, and J.Feigon (2003).
Structural determinants for the binding of ubiquitin-like domains to the proteasome.

EMBO J, 22, 4634-4645.

PDB codes: 1p98 1p9c 1p9d

The most recent references are shown first. Citation data come partly from CiteXplore and partly from an automated harvesting procedure. Note that this is likely to be only a partial list as not all journals are covered by either method. However, we are continually building up the citation data so more and more references will be included with time. Where a reference describes a PDB structure, the PDB codes are shown on the right.