4EAC

Crystal structure of mannonate dehydratase from Escherichia coli strain K12

Summary for 4EAC

• Entry DOI: 10.2210/pdb4eac/pdb
• Related: 1TZ9 3DBN 3FVM 4EAY
• Descriptor: Mannonate dehydratase, CHLORIDE ION, MANGANESE (II) ION, ... (4 entities in total)
• Functional Keywords: tim barrel, dehydratase, lyase
• Biological source: Escherichia coli
• Total number of polymer chains: 4
• Total formula weight: 188638.78

Authors

Qiu, X.,Zhu, Y.,Yuan, Y.,Zhang, Y.,Liu, H.,Gao, Y.,Teng, M.,Niu, L. (deposition date: 2012-03-22, release date: 2013-03-27, Last modification date: 2023-11-08)

Primary citation

Qiu, X.,Tao, Y.,Zhu, Y.,Yuan, Y.,Zhang, Y.,Liu, H.,Gao, Y.,Teng, M.,Niu, L.
Structural insights into decreased enzymatic activity induced by an insert sequence in mannonate dehydratase from Gram negative bacterium.
J.Struct.Biol., 180:327-334, 2012

PubMed 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.

PubMed: 22796868
DOI: 10.1016/j.jsb.2012.06.013

Experimental method

X-RAY DIFFRACTION (2.3 Å)