PDBsum entry 2pan

Lyase

PDB id: 2pan

Contents

Protein chains

(+ 0 more) 592 a.a. *

Ligands

FAD ×6

TPP ×6

DTT ×6

1PE

Metals

_MG ×10

Waters ×363

* Residue conservation analysis

PDB id:

2pan

Name:

Lyase

Title:

Crystal structure of e. Coli glyoxylate carboligase

Structure:

Glyoxylate carboligase. Chain: a, b, c, d, e, f. Synonym: tartronate-semialdehyde synthase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 562. Strain: xl1. Gene: gcl. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

2.70Å R-factor: 0.220 R-free: 0.253

Authors:

A.Kaplun,D.M.Chipman,Z.Barak,M.Vyazmensky,B.Shaanan

Key ref:

A.Kaplun et al. (2008). Glyoxylate carboligase lacks the canonical active site glutamate of thiamine-dependent enzymes. Nat Chem Biol, 4, 113-118. PubMed id: 18176558 DOI: 10.1038/nchembio.62

Date:

27-Mar-07 Release date: 01-Jan-08

Protein chains

P0AEP7  (GCL_ECOLI) -  Glyoxylate carboligase from Escherichia coli (strain K12)

Seq: 593 a.a.

Struc: 592 a.a.

Enzyme reactions

• Enzyme class: E.C.4.1.1.47 - tartronate-semialdehyde synthase.
• Reaction: 2 glyoxylate + H⁺ = 2-hydroxy-3-oxopropanoate + CO2

2 × glyoxylate + H(+) (Bound ligand (Het Group name = DTT) matches with 50.00% similarity) = 2-hydroxy-3-oxopropanoate + CO2

• Cofactor: Thiamine diphosphate

Thiamine diphosphate (Bound ligand (Het Group name = TPP) corresponds exactly)

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

reference

DOI no: 10.1038/nchembio.62

Nat Chem Biol 4:113-118 (2008)

PubMed id: 18176558

Glyoxylate carboligase lacks the canonical active site glutamate of thiamine-dependent enzymes.

A.Kaplun, E.Binshtein, M.Vyazmensky, A.Steinmetz, Z.Barak, D.M.Chipman, K.Tittmann, B.Shaanan.

ABSTRACT

Thiamine diphosphate (ThDP), a derivative of vitamin B1, is an enzymatic cofactor whose special chemical properties allow it to play critical mechanistic roles in a number of essential metabolic enzymes. It has been assumed that all ThDP-dependent enzymes exploit a polar interaction between a strictly conserved glutamate and the N1' of the ThDP moiety. The crystal structure of glyoxylate carboligase challenges this paradigm by revealing that valine replaces the conserved glutamate. Through kinetic, spectroscopic and site-directed mutagenesis studies, we show that although this extreme change lowers the rate of the initial step of the enzymatic reaction, it ensures efficient progress through subsequent steps. Glyoxylate carboligase thus provides a unique illustration of the fine tuning between catalytic stages imposed during evolution on enzymes catalyzing multistep processes.

Selected figure(s)

Figure 1.
(a) Conserved glutamate residue in other ThDP-dependent enzymes interacts with N1' of bound ThDP. Shown are the glutamate and ThDP after superposition of pyruvate oxidase (PDB code 1POX, green), pyruvate dehydrogenase (PDB code 1NI4, gray), transketolase (PDB code 1TRK, magenta) and pyruvate decarboxylase (PDB code 1PVD, yellow). ThDP adopts the typical V-shaped conformation juxtaposing the 4'-amino group and the reactive C2. (b) The conserved glutamate participates in the aminopyrimidine-iminopyrimidine tautomerization of ThDP. The iminopyrimidine acts as the general base that removes the proton from C2 of the thiazol moiety. (c) The reaction catalyzed by GCL.

Figure 2.
(a) Structure of GCL protomer (ribbons) with cofactors (stick). The three domains are the PYR domain (residues 1–185, magenta), contacting the ThDP aminopyrimidine group; the FAD domain (residues 186–357, blue), surrounding the FAD group; and the PP domain (residues 358–592, yellow), providing polar interactions with the ThDP diphosphate moiety. (b) Electron density around Val51 and ThDP. 2F[o] – F[c] [a]-weighted, contoured at 1 level around Val51 (magenta) and neighboring residues. (c) Similarity between the loop containing Val51 in GCL and other ThDP-dependent enzymes. GCL and seven other enzymes with top Z similarity scores according to the Dali^42 server were superimposed. (d) Hydrophobic environment of the thiazol in GCL: Residues are colored according a hydrophobicity scale (aquamarine - hydrophilic, gold - hydrophobic). Hydrophobic residues in contact with the thiazol and pyrimidine of ThDP are depicted as space-filling models. Note that the thiazol is sandwiched between those residues. The labels of residues contributed by the neighboring subunit are in pink.

The above figures are reprinted by permission from Macmillan Publishers Ltd: Nat Chem Biol (2008, 4, 113-118) copyright 2008.

Figures were selected by the author.