PDBsum entry 1v7l

Lyase

PDB id: 1v7l

Contents

Protein chains

162 a.a. *

Waters ×294

* Residue conservation analysis

PDB id:

1v7l

Name:

Lyase

Title:

Structure of 3-isopropylmalate isomerase small subunit from pyrococcus horikoshii

Structure:

3-isopropylmalate dehydratase small subunit. Chain: a, b. Synonym: 3-isopropylmalate isomerase small subunit, isopropylmalate isomerase, alpha-ipm isomerase, ipmi. Engineered: yes

Source:

Pyrococcus horikoshii. Organism_taxid: 70601. Strain: ot3. Gene: ph1724. Expressed in: escherichia coli. Expression_system_taxid: 562.

Resolution:

1.98Å R-factor: 0.206 R-free: 0.247

Authors:

M.Yao,T.Kirita,N.Sakai,I.Tanaka

Key ref:

Y.Yasutake et al. (2004). Crystal structure of the Pyrococcus horikoshii isopropylmalate isomerase small subunit provides insight into the dual substrate specificity of the enzyme. J Mol Biol, 344, 325-333. PubMed id: 15522288 DOI: 10.1016/j.jmb.2004.09.035

Date:

18-Dec-03 Release date: 16-Nov-04

Protein chains

O59393  (LEUD_PYRHO) -  3-isopropylmalate dehydratase small subunit from Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)

Seq: 163 a.a.

Struc: 162 a.a.

Enzyme reactions

• Enzyme class: E.C.4.2.1.33 - 3-isopropylmalate dehydratase.
• Pathway: Leucine Biosynthesis
• Reaction: (2R,3S)-3-isopropylmalate = (2S)-2-isopropylmalate
• Cofactor: Iron-sulfur

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

reference

DOI no: 10.1016/j.jmb.2004.09.035

J Mol Biol 344:325-333 (2004)

PubMed id: 15522288

Crystal structure of the Pyrococcus horikoshii isopropylmalate isomerase small subunit provides insight into the dual substrate specificity of the enzyme.

Y.Yasutake, M.Yao, N.Sakai, T.Kirita, I.Tanaka.

ABSTRACT

Recent studies have implied that the isopropylmalate isomerase small subunit of the hyperthermophilic archaea Pyrococcus horikoshii (PhIPMI-s) functions as isopropylmalate isomerase in the leucine biosynthesis pathway, and as homoaconitase (HACN) in the lysine biosynthesis pathway via alpha-aminoadipic acid. PhIPMI is thus considered a key to understanding the fundamental metabolism of the earliest organisms. We describe for the first time the crystal structure of PhIPMI-s, which displays dual substrate specificity. The crystal structure unexpectedly shows that four molecules create an interlocked assembly with intermolecular disulfide linkages having a skewed 222 point-group symmetry. Although the overall fold of the PhIPMI-s monomer is related closely to domain 4 of the aconitase (ACN), one alpha-helix in the ACN structure is replaced by a short loop with relatively high temperature factor values. Because this region is essential for discriminating the structurally similar substrate based on interactions with its diversified gamma-moiety, the loop structure in the PhIPMI-s must be dependent on the presence of a substrate. The flexibility of the loop region might be a structural basis for recognizing both hydrophobic and hydrophilic gamma-moieties of two distinct substrates, isopropylmalate and homocitrate.

Selected figure(s)

Figure 1.
Figure 1. Crystal structure of the PhIPMI-s. (a) Stereoview ribbon diagram of the PhIPMI-s monomer. The model is colored according to sequence by a rainbow color ramp from blue at the N terminus to red at the C terminus. The secondary structures and the flexible loop moiety are labeled. (b) Superimposition of the bovine mACN (PDB code, 1ACO) and PhIPMI-s structures. The PhIPMI-s is colored in green, and the mACN in blue. The structure of PhIPMI-s is similar to domain 4 of the mACN. The g-moiety recognition loop of the PhIPMI-s and the corresponding part of mACN is colored in red. The active-site cleft of mACN is shown. The superimposition is performed using the program LSQKAB.33 (c) C^a trace and a diagram of the interlocked tetramer. The side-chains of the Cys162 forming the intermolecular disulfide linkages are represented as a ball-and-stick model. The chains A and B correspond to two molecules in the asymmetric unit, and chains A' and B' are generated by the crystallographic 2-fold symmetry. The Figures were prepared using the programs MOLSCRIPT34 and Raster3D.35

Figure 4.
Figure 4. Stereoview of the g-moiety recognition site of the mACN and PhIPMI-s. (a) Bovine mACN (PDB code, 1ACO). The structure shows that the Arg580 forms double hydrogen bonds with the g-carboxylate group of the substrate (aconitate in this structure). In this diagram, only the residues belonging to domain 4 are shown. (b) PhIPMI-s. The structure of the mACN in diagram (a) is shown in gray for comparison. The loop including Ser65-Arg67 is very well superimposed on the mACN structure, while the region that would interact with the g-moiety of the substrate (Tyr24-Lys28) is dissimilar. The helix is replaced by the loop structure in the PhIPMI-s, and the residues in this region are absolutely not conserved. The Figures were prepared using the programs MOLSCRIPT34 and Raster3D.35

The above figures are reprinted by permission from Elsevier: J Mol Biol (2004, 344, 325-333) copyright 2004.

Figures were selected by an automated process.