PDBsum entry 1s3s

Protein binding

PDB id: 1s3s

Contents

Protein chains

(+ 0 more) 436 a.a. *

118 a.a. *

107 a.a. *

24 a.a. *

Ligands

ADP ×6

Waters ×63

* Residue conservation analysis

PDB id:

1s3s

Name:

Protein binding

Title:

Crystal structure of aaa atpase p97/vcp nd1 in complex with p47 c

Structure:

Transitional endoplasmic reticulum atpase (ter atpase) (15s mg(2+)- atpase p97 subunit) (valosin containing protein) (vcp) [contains: valosin]. Chain: a, b, c, d, e, f. Fragment: nd1 domains (1-458). Engineered: yes. P47 protein. Chain: g, h, i. Fragment: c-terminal domain (244-370).

Source:

Mus musculus. House mouse. Organism_taxid: 10090. Gene: vcp. Expressed in: escherichia coli. Expression_system_taxid: 562. Rattus norvegicus. Norway rat. Organism_taxid: 10116.

Biol. unit:

Nonamer (from PQS)

Resolution:

2.90Å R-factor: 0.248 R-free: 0.294

Authors:

I.Dreveny,H.Kondo,K.Uchiyama,A.Shaw,X.Zhang,P.S.Freemont

Key ref:

I.Dreveny et al. (2004). Structural basis of the interaction between the AAA ATPase p97/VCP and its adaptor protein p47. EMBO J, 23, 1030-1039. PubMed id: 14988733 DOI: 10.1038/sj.emboj.7600139

Date:

14-Jan-04 Release date: 30-Mar-04

Protein chains

Q01853  (TERA_MOUSE) -  Transitional endoplasmic reticulum ATPase from Mus musculus

Seq: 806 a.a.

Struc: 436 a.a.*

Protein chain

O35987  (NSF1C_RAT) -  NSFL1 cofactor p47 from Rattus norvegicus

Seq: 370 a.a.

Struc: 118 a.a.

Protein chain

O35987  (NSF1C_RAT) -  NSFL1 cofactor p47 from Rattus norvegicus

Seq: 370 a.a.

Struc: 107 a.a.

Protein chain

O35987  (NSF1C_RAT) -  NSFL1 cofactor p47 from Rattus norvegicus

Seq: 370 a.a.

Struc: 24 a.a.*

* PDB and UniProt seqs differ at 11 residue positions (black crosses)

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 + H2O = ADP (Bound ligand (Het Group name = ADP) corresponds exactly) + phosphate + H(+)

• Enzyme class 2: Chains G, H, I: 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: 10.1038/sj.emboj.7600139

EMBO J 23:1030-1039 (2004)

PubMed id: 14988733

Structural basis of the interaction between the AAA ATPase p97/VCP and its adaptor protein p47.

I.Dreveny, H.Kondo, K.Uchiyama, A.Shaw, X.Zhang, P.S.Freemont.

ABSTRACT

The AAA ATPase p97/VCP is involved in many cellular events including ubiquitin-dependent processes and membrane fusion. In the latter, the p97 adaptor protein p47 is of central importance. In order to provide insight into the molecular basis of p97 adaptor binding, we have determined the crystal structure of p97 ND1 domains complexed with p47 C-terminal domain at 2.9 A resolution. The structure reveals that the p47 ubiquitin regulatory X domain (UBX) domain interacts with the p97 N domain via a loop (S3/S4) that is highly conserved in UBX domains, but is absent in ubiquitin, which inserts into a hydrophobic pocket between the two p97 N subdomains. Deletion of this loop and point mutations in the loop significantly reduce p97 binding. This hydrophobic binding site is distinct from the predicted adaptor-binding site for the p97/VCP homologue N-ethylmaleimide sensitive factor (NSF). Together, our data suggest that UBX domains may act as general p97/VCP/CDC48 binding modules and that adaptor binding for NSF and p97 might involve different binding sites. We also propose a classification for ubiquitin-like domains containing or lacking a longer S3/S4 loop.

Selected figure(s)

Figure 2.
Figure 2 Comparison of p47 UBX with other UBX domains/ubiquitin and p97 N domain with NSF. (A) Superpositions of p47 C (red) with p47 UBX solution structure (grey, pdb-code 1JRU), FAF1 UBX (blue, pdb-code 1H8C) and ubiquitin (yellow, pdb-code 1UBI). Note the shorter turn between S3 and S4 for ubiquitin and the additional helix H1 in p47 C. (B) Top view of a superposition of p97 ND1 and NSF N domain. The p97 N domain has 9% sequence identity with NSF (1.9 Å rmsd over 117 residues). The p97 N domain is coloured blue, p97 D1 grey and NSF N domain gold. Residues at the p97 N -p47 C complex interface are shown in ball-and-stick representation (red). Residues implicated in -SNAP binding by NSF N are coloured magenta and are located on the opposite side of the p47-binding site.

Figure 3.
Figure 3 Binding of p47 C to p97 N domain. (A) Electrostatic surface representation of p97 N domain interacting with p47 C (ribbon coloured red). Key residues of p47 C at the N-domain interface are shown in ball-and-stick representation. D1 is depicted in blue. (B) Detailed view of specific interactions at the p47 C -p97 N interface. p47 C is shown as a ribbon representation (red) with key residues in ball-and-stick, p97 N is depicted in blue. Hydrogen-bonding interactions (p47 C Arg301NH2 and p97 N Val108O as well as p47 C Asn345ND2 and p97 N Glu141O) are indicated by a dotted line. Key residues conserved within UBX domains are labelled in red.

The above figures are reprinted from an Open Access publication published by Macmillan Publishers Ltd: EMBO J (2004, 23, 1030-1039) copyright 2004.

Figures were selected by an automated process.