PDBsum entry 5g5r

Hydrolase

PDB id: 5g5r

Contents

Protein chains

122 a.a.

120 a.a.

Ligands

SO4 ×2

Waters ×31

PDB id:

5g5r

Name:

Hydrolase

Title:

Cbs domain tandem of site-2 protease from archaeoglobus fulgidus in complex with llama nanobody - apo form

Structure:

Site-2 protease. Chain: a. Fragment: regulatory domain, residues 236-362. Engineered: yes. Other_details: c-terminal strepii-tag. Nanobody. Chain: b. Engineered: yes. Other_details: nb330 selected from llama glama

Source:

Archaeoglobus fulgidus. Organism_taxid: 2234. Atcc: 49558. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: plyss. Other_details: dsm4304 genomic DNA. Lama glama. Llama.

Resolution:

2.40Å R-factor: 0.209 R-free: 0.250

Authors:

M.Schacherl,U.Baumann

Key ref:

M.Schacherl et al. (2017). Crystallographic and biochemical characterization of the dimeric architecture of site-2 protease. Biochim Biophys Acta, 1859, 1859-1871. PubMed id: 28502790 DOI: 10.1016/j.bbamem.2017.05.006

Date:

02-Jun-16 Release date: 24-May-17

Protein chain

O29915  (O29915_ARCFU) -  Zinc metalloprotease from Archaeoglobus fulgidus (strain ATCC 49558 / DSM 4304 / JCM 9628 / NBRC 100126 / VC-16)

Seq: 362 a.a.

Struc: 122 a.a.*

Protein chain

No UniProt id for this chain

Struc: 120 a.a.

* PDB and UniProt seqs differ at 1 residue position (black cross)

Enzyme reactions

• Enzyme class: Chain A: E.C.3.4.24.85 - S2P endopeptidase.
• Cofactor: Zn(2+)

DOI no: 10.1016/j.bbamem.2017.05.006

Biochim Biophys Acta 1859:1859-1871 (2017)

PubMed id: 28502790

Crystallographic and biochemical characterization of the dimeric architecture of site-2 protease.

M.Schacherl, M.Gompert, E.Pardon, T.Lamkemeyer, J.Steyaert, U.Baumann.

ABSTRACT

Regulated intramembrane proteolysis by members of the site-2 protease family (S2P) is an essential signal transduction mechanism conserved from bacteria to humans. There is some evidence that extra-membranous domains, like PDZ and CBS domains, regulate the proteolytic activity of S2Ps and that some members act as dimers. Here we report the crystal structure of the regulatory CBS domain pair of S2P from Archaeoglobus fulgidus, AfS2P, in the apo and nucleotide-bound form in complex with a specific nanobody from llama. Cross-linking and SEC-MALS analyses show for the first time the dimeric architecture of AfS2P both in the membrane and in detergent micelles. The CBS domain pair dimer (CBS module) displays an unusual head-to-tail configuration and nucleotide binding triggers no major conformational changes in the magnesium-free state. In solution, MgATP drives monomerization of the CBS module. We propose a model of the so far unknown architecture of the transmembrane domain dimer and for a regulatory mechanism of AfS2P that involves the interaction of positively charged arginine residues located at the cytoplasmic face of the transmembrane domain with the negatively charged phosphate groups of ATP moieties bound to the CBS domain pairs. Binding of MgATP could promote opening of the CBS module to allow lateral access of the globular cytoplasmic part of the substrate.