PDBsum entry 5c1b

Hydrolase

PDB id: 5c1b

Contents

Protein chains

(+ 0 more) 724 a.a.

11 a.a.

Ligands

ARG-ALA-PHE-SER-GLY-SER-GLY-ASN-ARG-LEU

AGS ×12

GOL ×2

Metals

_CL ×6

_MG ×12

Waters ×30

PDB id:

5c1b

Name:

Hydrolase

Title:

P97-delta709-728 in complex with a ufd1-shp peptide

Structure:

Transitional endoplasmic reticulum atpase. Chain: a, b, c, d, e, f. Synonym: ter atpase,15s mg(2+)-atpase p97 subunit,valosin-containing protein,vcp. Engineered: yes. Mutation: yes. Ubiquitin fusion degradation protein 1 homolog. Chain: v, u. Fragment: unp residues 221-241.

Source:

Homo sapiens. Human. Organism_taxid: 9606. Gene: vcp. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Synthetic: yes. Other_details: this sequence occurs naturally in humans

Resolution:

3.08Å R-factor: 0.200 R-free: 0.240

Authors:

P.Haenzelmann,H.Schindelin

Key ref:

P.Hänzelmann and H.Schindelin (2016). Characterization of an Additional Binding Surface on the p97 N-Terminal Domain Involved in Bipartite Cofactor Interactions. Structure, 24, 140-147. PubMed id: 26712280 DOI: 10.1016/j.str.2015.10.027

Date:

13-Jun-15 Release date: 13-Jan-16

Protein chains

P55072  (TERA_HUMAN) -  Transitional endoplasmic reticulum ATPase from Homo sapiens

Seq: 806 a.a.

Struc: 724 a.a.

Protein chain

Q92890  (UFD1_HUMAN) -  Ubiquitin recognition factor in ER-associated degradation protein 1 from Homo sapiens

Seq: 307 a.a.

Struc: 11 a.a.

Enzyme reactions

• Enzyme class 1: Chains A, B, C, D, E, F: E.C.3.6.4.6 - vesicle-fusing ATPase.
• Reaction: ATP + H2O = ADP + phosphate + H⁺

ATP (Bound ligand (Het Group name = AGS) matches with 93.75% similarity) + H2O = ADP + phosphate + H(+)

• Enzyme class 2: Chain V: E.C.?

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.

Molecule diagrams generated from .mol files obtained from the KEGG ftp site

reference

DOI no: 10.1016/j.str.2015.10.027

Structure 24:140-147 (2016)

PubMed id: 26712280

Characterization of an Additional Binding Surface on the p97 N-Terminal Domain Involved in Bipartite Cofactor Interactions.

P.Hänzelmann, H.Schindelin.

ABSTRACT

The type II AAA ATPase p97 interacts with a large number of cofactors that regulate its function by recruiting it to different cellular pathways. Most of the cofactors interact with the N-terminal (N) domain of p97, either via ubiquitin-like domains or short linear binding motifs. While some linear binding motifs form α helices, another group features short stretches of unstructured hydrophobic sequences as found in the so-called SHP (BS1, binding segment 1) motif. Here we present the crystal structure of a SHP-binding motif in complex with p97, which reveals a so far uncharacterized binding site on the p97 N domain that is different from the conserved binding surface of all other known p97 cofactors. This finding explains how cofactors like UFD1/NPL4 and p47 can utilize a bipartite binding mechanism to interact simultaneously with the same p97 monomer via their ubiquitin-like domain and SHP motif.