PDBsum entry 2uyu

Lyase

PDB id: 2uyu

Contents

Protein chains

274 a.a. *

Metals

_FE ×2

_ZN ×2

Waters ×341

* Residue conservation analysis

PDB id:

2uyu

Name:

Lyase

Title:

L-rhamnulose-1-phosphate aldolase from escherichia coli (mutant a88f- e192a)

Structure:

Rhamnulose-1-phosphate aldolase. Chain: a, e. Engineered: yes. Mutation: yes

Source:

Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.96Å R-factor: 0.204 R-free: 0.245

Authors:

D.Grueninger,G.E.Schulz

Key ref:

D.Grueninger et al. (2008). Designed protein-protein association. Science, 319, 206-209. PubMed id: 18187656 DOI: 10.1126/science.1150421

Date:

20-Apr-07 Release date: 15-Jan-08

Protein chains

P32169  (RHAD_ECOLI) -  Rhamnulose-1-phosphate aldolase from Escherichia coli (strain K12)

Seq: 274 a.a.

Struc: 274 a.a.*

* PDB and UniProt seqs differ at 2 residue positions (black crosses)

Enzyme reactions

• Enzyme class: E.C.4.1.2.19 - rhamnulose-1-phosphate aldolase.
• Reaction: L-rhamnulose 1-phosphate = (S)-lactaldehyde + dihydroxyacetone phosphate

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

reference

DOI no: 10.1126/science.1150421

Science 319:206-209 (2008)

PubMed id: 18187656

Designed protein-protein association.

D.Grueninger, N.Treiber, M.O.Ziegler, J.W.Koetter, M.S.Schulze, G.E.Schulz.

ABSTRACT

The analysis of natural contact interfaces between protein subunits and between proteins has disclosed some general rules governing their association. We have applied these rules to produce a number of novel assemblies, demonstrating that a given protein can be engineered to form contacts at various points of its surface. Symmetry plays an important role because it defines the multiplicity of a designed contact and therefore the number of required mutations. Some of the proteins needed only a single side-chain alteration in order to associate to a higher-order complex. The mobility of the buried side chains has to be taken into account. Four assemblies have been structurally elucidated. Comparisons between the designed contacts and the results will provide useful guidelines for the development of future architectures.

Selected figure(s)

Figure 1.
Fig. 1. Design of protein assemblies (24). The proteins in (C) to (H) are depicted as thick-lined C plots at various scales with mutated residues as colored spheres. (A) Sketch of an asymmetric interface between patches a and b, which, in general, gives rise to an infinite helix (top). A C[2]-symmetric interface also between patches a and b doubles the numbers of contacts and forms a globular complex (bottom). Along the same lines, the reported D[2], D[4], and D[8] oligomers have 4-, 8-, and 16-fold contacts, respectively (fig. S4). (B) Side-chain mobility of the C[4]-symmetric Rua, color-coded from 0° (blue) to 90° (red) angular spread in the torsion angles [1] and [2] (24). The C- and N-terminal domains are at the top and bottom, respectively. (C) Pga-A and -B designed in crystal contact a-a(25). (D) Pga-C and-D designed in crystal contact f-f (25). (E) Oas-A and-B planned as a D[2] tetramer at a rotation angle of 86° around a common molecular twofold axis (vertical). (F) Oas-C designed as a D[2] tetramer at an alternative rotation angle of 29°. (G) Designed D[2] tetramer of Uro-A around a common molecular twofold axis (vertical). The designed contact is between the NAD^+-binding domains (residues 142 to 343), which are given in lighter hues. (H) Designed octameric Rua-D with a head-head contact.

Figure 3.
Fig. 3. Established oligomer structures (24). All mutations are marked by purple spheres. (A) Crystal structure of C[2]-symmetric Uro-A showing the twofold molecular symmetry axis (red) and four local twofold axes relating the cores (darker colors) and the NAD^+ domains (light colors) to their counterparts. The interface between core and NAD^+ domains was broken in the lower left and upper right chains. (B) D[4]-symmetric octamer Rua-A. (C) C[2]-symmetric octamer Rua-B. (D) Negatively stained electron micrograph of Rua-E showing the fiber association and a Rua-A octamer (B) at the scale defined by the box edge. (E) Native mycobacterial porin (28). The encircled membrane-immersed part was deleted, giving rise to Myp-A. (F) D[8]-symmetric association of two Myp-A molecules (top and bottom ring). The positions of the 52-residue deletions are marked by red spheres (fig. S1D).

The above figures are reprinted by permission from the AAAs: Science (2008, 319, 206-209) copyright 2008.

Figures were selected by the author.