PDBsum entry 4s1z

Hydrolase

PDB id: 4s1z

Contents

Protein chains

73 a.a.

27 a.a.

25 a.a.

26 a.a.

Metals

_ZN ×5

PDB id:

4s1z

Name:

Hydrolase

Title:

Crystal structure of trabid nzf1 in complex with k29 linked di- ubiquitin

Structure:

Ubiquitin. Chain: a, b, c, d, e. Fragment: residues 1-76. Synonym: cep52, ubiquitin a-52 residue ribosomal protein fusion product 1, ubiquitin, 60s ribosomal protein l40. Engineered: yes. Ubiquitin thioesterase zranb1. Chain: f, g, h, j, i. Fragment: ranbp2-type 1 zinc finger domain residues 2-33.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: uba52, ubcep2, zranb1. Expressed in: escherichia coli. Expression_system_taxid: 469008. Bos taurus. Bovine,cow,domestic cattle,domestic cow. Organism_taxid: 9913.

Resolution:

3.03Å R-factor: 0.225 R-free: 0.270

Authors:

Y.A.Kristariyanto,S.A.Abdul Rehman,D.G.Campbell,N.A.Morrice, C.Johnson,R.Toth,Y.Kulathu

Key ref:

Y.A.Kristariyanto et al. (2015). K29-selective ubiquitin binding domain reveals structural basis of specificity and heterotypic nature of k29 polyubiquitin. Mol Cell, 58, 83-94. PubMed id: 25752573 DOI: 10.1016/j.molcel.2015.01.041

Date:

16-Jan-15 Release date: 08-Apr-15

Protein chains

P62987  (RL40_HUMAN) -  Ubiquitin-ribosomal protein eL40 fusion protein from Homo sapiens

Seq: 128 a.a.

Struc: 73 a.a.

Protein chains

A6QP16  (ZRAN1_BOVIN) -  Ubiquitin thioesterase ZRANB1 from Bos taurus

Seq: 708 a.a.

Struc: 27 a.a.

Protein chain

A6QP16  (ZRAN1_BOVIN) -  Ubiquitin thioesterase ZRANB1 from Bos taurus

Seq: 708 a.a.

Struc: 25 a.a.

Protein chain

A6QP16  (ZRAN1_BOVIN) -  Ubiquitin thioesterase ZRANB1 from Bos taurus

Seq: 708 a.a.

Struc: 26 a.a.

Enzyme reactions

• Enzyme class 2: Chains A, B, C, D, E: E.C.?
• Enzyme class 3: Chains F, G, H, J, I: E.C.3.4.19.12 - ubiquitinyl hydrolase 1.
• Reaction: Thiol-dependent hydrolysis of ester, thiolester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).

Note, where more than one E.C. class is given (as above), each may correspond to a different protein domain or, in the case of polyprotein precursors, to a different mature protein.

DOI no: 10.1016/j.molcel.2015.01.041

Mol Cell 58:83-94 (2015)

PubMed id: 25752573

K29-selective ubiquitin binding domain reveals structural basis of specificity and heterotypic nature of k29 polyubiquitin.

Y.A.Kristariyanto, S.A.Abdul Rehman, D.G.Campbell, N.A.Morrice, C.Johnson, R.Toth, Y.Kulathu.

ABSTRACT

Polyubiquitin chains regulate diverse cellular processes through the ability of ubiquitin to form chains of eight different linkage types. Although detected in yeast and mammals, little is known about K29-linked polyubiquitin. Here we report the generation of K29 chains in vitro using a ubiquitin chain-editing complex consisting of the HECT E3 ligase UBE3C and the deubiquitinase vOTU. We determined the crystal structure of K29-linked diubiquitin, which adopts an extended conformation with the hydrophobic patches on both ubiquitin moieties exposed and available for binding. Indeed, the crystal structure of the NZF1 domain of TRABID in complex with K29 chains reveals a binding mode that involves the hydrophobic patch on only one of the ubiquitin moieties and exploits the flexibility of K29 chains to achieve linkage selective binding. Further, we establish methods to study K29-linked polyubiquitin and find that K29 linkages exist in cells within mixed or branched chains containing other linkages.