PDBsum entry 5g5x

Hydrolase

PDB id: 5g5x

Contents

Protein chains

119 a.a.

118 a.a.

Ligands

AMP

ATP

PDB id:

5g5x

Name:

Hydrolase

Title:

Cbs domain tandem of site-2 protease from archaeoglobus fulgidus in complex with llama nanobody - nucleotide-bound 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, c-terminal 6xhis- tag

Source:

Archaeoglobus fulgidus. Organism_taxid: 2234. Atcc: 49558. Expressed in: escherichia coli. Expression_system_taxid: 469008. Expression_system_variant: plyss. Other_details: dsm 4304 genomic DNA. Lama glama. Llama.

Resolution:

2.80Å R-factor: 0.248 R-free: 0.269

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:

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

Protein chain

A0A0H2URD6  (FUSA_STRPN) -  Fructooligosaccharide ABC transporter substrate-binding protein FusA from Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4)

Seq: 538 a.a.

Struc: 119 a.a.*

Protein chain

No UniProt id for this chain

Struc: 118 a.a.

* PDB and UniProt seqs differ at 96 residue positions (black crosses)

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.