PDBsum entry 4eay

Lyase

PDB id: 4eay

Contents

Protein chains

395 a.a.

Ligands

CS2 ×2

Metals

_MN ×4

_CL ×4

Waters ×795

PDB id:

4eay

Name:

Lyase

Title:

Crystal structures of mannonate dehydratase from escherichia coli strain k12 complexed with d-mannonate

Structure:

Mannonate dehydratase. Chain: a, b, c, d. Synonym: d-mannonate hydrolase. Engineered: yes

Source:

Escherichia coli. Organism_taxid: 83333. Strain: k12. Gene: uxua, b4322, jw4285. Expressed in: escherichia coli. Expression_system_taxid: 562

Resolution:

2.35Å R-factor: 0.191 R-free: 0.236

Authors:

X.Qiu,Y.Zhu,Y.Yuan,Y.Zhang,H.Liu,Y.Gao,M.Teng,L.Niu

Key ref:

X.Qiu et al. (2012). Structural insights into decreased enzymatic activity induced by an insert sequence in mannonate dehydratase from Gram negative bacterium. J Struct Biol, 180, 327-334. PubMed id: 22796868 DOI: 10.1016/j.jsb.2012.06.013

Date:

23-Mar-12 Release date: 27-Mar-13

Protein chains

P24215  (UXUA_ECOLI) -  Mannonate dehydratase from Escherichia coli (strain K12)

Seq: 394 a.a.

Struc: 395 a.a.

Enzyme reactions

• Enzyme class: E.C.4.2.1.8 - mannonate dehydratase.
• Pathway: Altronate Dehydratase; Mannonate Dehydratase
• Reaction: D-mannonate = 2-dehydro-3-deoxy-D-gluconate + H2O

D-mannonate (Bound ligand (Het Group name = CS2) corresponds exactly) = 2-dehydro-3-deoxy-D-gluconate + H2O

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

Added reference

DOI no: 10.1016/j.jsb.2012.06.013

J Struct Biol 180:327-334 (2012)

PubMed id: 22796868

Structural insights into decreased enzymatic activity induced by an insert sequence in mannonate dehydratase from Gram negative bacterium.

X.Qiu, Y.Tao, Y.Zhu, Y.Yuan, Y.Zhang, H.Liu, Y.Gao, M.Teng, L.Niu.

ABSTRACT

Mannonate dehydratase (ManD; EC4.2.1.8) catalyzes the dehydration of D-mannonate to 2-keto-3-deoxygluconate. It is the third enzyme in the pathway for dissimilation of D-glucuronate to 2-keto-3-deoxygluconate involving in the Entner-Doudoroff pathway in certain bacterial and archaeal species. ManD from Gram negative bacteria has an insert sequence as compared to those from Gram positives revealed by sequence analysis. To evaluate the impact of this insert sequence on the catalytic efficiency, we solved the crystal structures of ManD from Escherichia coli strain K12 and its complex with D-mannonate, which reveal that this insert sequence forms two α helices locating above the active site. The two insert α helices introduce a loop that forms a cap covering the substrate binding pocket, which restricts the tunnels of substrate entering and product releasing from the active site. Site-directed mutations and enzymatic activity assays confirm that the catalytic rate is decreased by this loop. These features are conserved among Gram negative bacteria. Thus, the insert sequence of ManD from Gram negative bacteria acts as a common inducer to decrease the catalytic rate and consequently the glucuronate metabolic rate as compared to those from Gram positives. Moreover, residues essential for substrate to enter the active site were characterized via structural analysis and enzymatic activity assays.