PDBsum entry: 1zs9

Hydrolase

PDB id: 1zs9

Contents

Protein chain

253 a.a. *

Metals

_MG ×3

Waters ×264

* Residue conservation analysis

PDB id:

1zs9

Name:

Hydrolase

Title:

Crystal structure of human enolase-phosphatase e1

Structure:

E-1 enzyme. Chain: a. Synonym: enolase-phosphatase e1. Engineered: yes

Source:

Homo sapiens. Human. Organism_taxid: 9606. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008.

Resolution:

1.70Å R-factor: 0.208 R-free: 0.241

Authors:

H.Wang,H.Pang,M.Bartlam,Z.Rao

Key ref:

H.Wang et al. (2005). Crystal structure of human E1 enzyme and its complex with a substrate analog reveals the mechanism of its phosphatase/enolase activity. J Mol Biol, 348, 917-926. PubMed id: 15843022 DOI: 10.1016/j.jmb.2005.01.072

Date:

23-May-05 Release date: 21-Jun-05

Supersedes:

1wdh

Protein chain

Q9UHY7  (ENOPH_HUMAN) -  Enolase-phosphatase E1

Seq: 261 a.a.

Struc: 253 a.a.

Enzyme reactions

• Enzyme class: E.C.3.1.3.77 - Acireductone synthase.
• Reaction: 5-(methylthio)-2,3-dioxopentyl phosphate + H₂O = 1,2-dihydroxy-5- (methylthio)pent-1-en-3-one + phosphate

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

 Gene Ontology (GO) functional annotation 

• Cellular component: cellular_component (3 terms)
• Biological process: metabolic process (4 terms)
• Biochemical function: catalytic activity (5 terms)

reference

DOI no: 10.1016/j.jmb.2005.01.072

J Mol Biol 348:917-926 (2005)

PubMed id: 15843022

Crystal structure of human E1 enzyme and its complex with a substrate analog reveals the mechanism of its phosphatase/enolase activity.

H.Wang, H.Pang, M.Bartlam, Z.Rao.

ABSTRACT

Enolase-phosphatase E1 (MASA) is a bifunctional enzyme in the ubiquitous methionine salvage pathway that catalyzes the continuous reactions of 2,3-diketo-5-methylthio-1-phosphopentane to yield the aci-reductone metabolite using Mg2+ as cofactor. In this study, we have determined the crystal structure of MASA and its complex with a substrate analog to 1.7A resolution by multi-wavelength anomalous diffraction and molecular replacement techniques, respectively. The structures support the proposed mechanism of phosphatase activity and further suggest the probable mechanism of enolization. We establish a model for substrate binding to describe in detail the enzymatic reaction and the formation of the transition state, which will provide insight into the reaction mechanisms of other enzymes in the same family.

Selected figure(s)

Figure 1.
Figure 1. Structure of MASA and its active site. (a) The tertiary monomer structure is represented as a ribbon diagram. The core domain is shown in light blue and the cap domain shown in red. The three magnesium ions are shown as gray spheres. The Figure was generated using the program MOLSCRIPT.36 (b) The active site of MASA. The magnesium ion is shown as a gray sphere and the enzyme active-site residues are shown in yellow as ball-and-stick representations. The Figure was generated using the program MOLSCRIPT.36

Figure 3.
Figure 3. (a) Stereoview of the substrate analog (shown as ball-and-stick in green) binding in the active site of MASA (shown as ball-and-stick) with the corresponding electron density map (omit map contoured at 2.4 s shown in cyan) covering the analog. The Mg2+ is shown as a gray sphere and the water molecules are shown as red spheres. Hydrogen bonds are represented by broken lines in pink and the hexa-coordinated bonds of the Mg2+ are represented by broken brown lines. The Figure was rendered using the program MOLSCRIPT.36 (b) A model of the substrate binding implies the enzymatic mechanism. The model was based on superposition of the active sites of MASA and PSP, which indicates the position of the intermediate phosphate group. The actual binding of the substrate analog also provides clues for the substrate model location. We combine these two pieces of evidence and propose the model as follows. The substrate model is shown as ball-and-stick in green and the important enzymatic residues are shown as ball-and-stick. The Mg2+ is shown as a gray sphere and the water molecules are shown as red spheres. The hydrogen bonds are represented by broken lines and the hexa-coordinated bonds of Mg2+ are represented by broken brown lines. The probable nucleophilic attack of Asp16 is shown as a broken blue line. The Figure was rendered using the program MOLSCRIPT.36

The above figures are reprinted by permission from Elsevier: J Mol Biol (2005, 348, 917-926) copyright 2005.

Figures were selected by an automated process.