PDBsum entry 1g4u

Signaling protein

PDB id: 1g4u

Contents

Protein chains

360 a.a. *

180 a.a. *

Ligands

GDP-AF3

Metals

_MG

Waters ×334

* Residue conservation analysis

PDB id:

1g4u

Name:

Signaling protein

Title:

Crystal structure of the salmonella tyrosine phosphatase and gtpase activating protein sptp bound to rac1

Structure:

Protein tyrosine phosphatase sptp. Chain: s. Fragment: sptp residues 161-543. Engineered: yes. Ras-related c3 botulinum toxin substrate 1. Chain: r. Fragment: rac1 residues 1-184. Engineered: yes. Mutation: yes

Source:

Salmonella typhimurium. Organism_taxid: 602. Gene: sptp. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693. Homo sapiens. Human. Organism_taxid: 9606. Gene: rac1.

Biol. unit:

Dimer (from PQS)

Resolution:

2.30Å R-factor: 0.204 R-free: 0.258

Authors:

C.E.Stebbins,J.E.Galan

Key ref:

C.E.Stebbins and J.E.Galán (2000). Modulation of host signaling by a bacterial mimic: structure of the Salmonella effector SptP bound to Rac1. Mol Cell, 6, 1449-1460. PubMed id: 11163217 DOI: 10.1016/S1097-2765(00)00141-6

Date:

28-Oct-00 Release date: 24-Jan-01

Protein chain

P74873  (SPTP_SALTY) -  Secreted effector protein SptP from Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)

Seq: 543 a.a.

Struc: 360 a.a.

Protein chain

P63000  (RAC1_HUMAN) -  Ras-related C3 botulinum toxin substrate 1 from Homo sapiens

Seq: 192 a.a.

Struc: 180 a.a.*

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

Enzyme reactions

• Enzyme class 2: Chain R: E.C.3.6.5.2 - small monomeric GTPase.
• Reaction: GTP + H2O = GDP + phosphate + H⁺

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

• Enzyme class 3: Chain S: E.C.3.1.3.48 - protein-tyrosine-phosphatase.
• Reaction: O-phospho-L-tyrosyl-[protein] + H2O = L-tyrosyl-[protein] + phosphate

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/S1097-2765(00)00141-6

Mol Cell 6:1449-1460 (2000)

PubMed id: 11163217

Modulation of host signaling by a bacterial mimic: structure of the Salmonella effector SptP bound to Rac1.

C.E.Stebbins, J.E.Galán.

ABSTRACT

Salmonella spp. utilize a specialized protein secretion system to deliver a battery of effector proteins into host cells. Several of these effectors stimulate Cdc42- and Rac1-dependent cytoskeletal changes that promote bacterial internalization. These potentially cytotoxic alterations are rapidly reversed by the effector SptP, a tyrosine phosphatase and GTPase activating protein (GAP) that targets Cdc42 and Rac1. The 2.3 A resolution crystal structure of an SptP-Rac1 transition state complex reveals an unusual GAP architecture that mimics host functional homologs. The phosphatase domain possesses a conserved active site but distinct surface properties. Binding to Rac1 induces a dramatic stabilization in SptP of a four-helix bundle that makes extensive contacts with the Switch I and Switch II regions of the GTPase.

Selected figure(s)

Figure 4.
Figure 4. The Interface with Rac1 Is Extensive and Highly Complementary to the Switch I, Switch II, and Nucleotide Regions of the GTPase(A) The extensive surface charge complementarity between the GAP domain and Rac1 is illustrated with a molecular surface colored by electrostatic potential such that red is negative (acidic) and blue is positive (basic). Arrows indicate regions of charge complementarity between the Rac1 and SptP surfaces. (B and C) The SptP GAP domain (secondary structure shown in blue and side chains in cyan) interact with the Switch I (yellow) and Switch II (red) regulatory elements of Rac1 (with yellow side chains). Hydrogen bonds are indicated by white dotted lines, and the atoms of nitrogen and oxygen are show in blue and red, respectively. Water molecules are shown as large magenta spheres. A large “W” indicates the nucleophilic water molecule positioned by Gln-61 of Rac. (D) SptP positions Gln-61 of Rac1 through molecular contacts and inserts Arg-209 into the active site to stabilize the transition state. Hydrogen bonds are indicated by white dotted lines or as smaller gray dotted lines for weak bonds. AlF[3] is shown with the fluorides colored brown and the aluminum gray. The magnesium ion and water molecules are shown as large blue or magenta spheres, respectively. GDP carbon bonds are shown in yellow. A large “W” indicates the nucleophilic water molecule positioned by Gln-61 of Rac1. The phosphate binding (P loop) and guanine binding loops (G loops) of Rac1 are shown in purple. The bonds proposed to form during the phosphoryl transfer are shown as solid white lines. (E) The interface between the GAP (blue) and tyrosine phosphatase (purple) domains of SptP consists of several direct and water-mediated hydrogen bonds as well as a small hydrophobic interface.

Figure 5.
Figure 5. The GAP Domain of SptP Undergoes Marked Structural Changes upon Binding Rac1A comparison of the atomic B factors between the SptP monomer and the SptP–Rac1 heterodimeric transition state complex is shown. The ribbon diagrams are colored according to an absolute gradient in the B factor from blue (ordered with a low B factor) through red (disordered with a high B factor). Connectivity missing due to disorder in the monomer is represented by black dotted lines based on their conformation in the heterodimer.

The above figures are reprinted by permission from Cell Press: Mol Cell (2000, 6, 1449-1460) copyright 2000.

Figures were selected by an automated process.