3R4Z

Crystal structure of alpha-neoagarobiose hydrolase (ALPHA-NABH) in complex with alpha-d-galactopyranose from Saccharophagus degradans 2-40

Summary for 3R4Z

• Entry DOI: 10.2210/pdb3r4z/pdb
• Related: 3R4Y
• Descriptor: Glycosyl hydrolase family 32, N terminal, alpha-D-galactopyranose (3 entities in total)
• Functional Keywords: agar metabolism, neoagarobiose, 3, 6-anhydro-l-galactose, alpha-d-galactopyranose, bioenergy, hydrolase
• Biological source: Saccharophagus degradans
• Total number of polymer chains: 2
• Total formula weight: 85240.18

Authors

Lee, S.,Lee, J.Y.,Ha, S.C.,Shin, D.H.,Kim, K.H.,Bang, W.G.,Kim, S.H.,Choi, I.G. (deposition date: 2011-03-18, release date: 2012-02-01, Last modification date: 2024-03-20)

Primary citation

Ha, S.C.,Lee, S.,Lee, J.,Kim, H.T.,Ko, H.J.,Kim, K.H.,Choi, I.G.
Crystal structure of a key enzyme in the agarolytic pathway, alpha-neoagarobiose hydrolase from Saccharophagus degradans 2-40
Biochem.Biophys.Res.Commun., 412:238-244, 2011

PubMed Abstract: In agarolytic microorganisms, α-neoagarobiose hydrolase (NABH) is an essential enzyme to metabolize agar because it converts α-neoagarobiose (O-3,6-anhydro-alpha-l-galactopyranosyl-(1,3)-d-galactose) into fermentable monosaccharides (d-galactose and 3,6-anhydro-l-galactose) in the agarolytic pathway. NABH can be divided into two biological classes by its cellular location. Here, we describe a structure and function of cytosolic NABH from Saccharophagus degradans 2-40 in a native protein and d-galactose complex determined at 2.0 and 1.55 Å, respectively. The overall fold is organized in an N-terminal helical extension and a C-terminal five-bladed β-propeller catalytic domain. The structure of the enzyme-ligand (d-galactose) complex predicts a +1 subsite in the substrate binding pocket. The structural features may provide insights for the evolution and classification of NABH in agarolytic pathways.

PubMed: 21810409
DOI: 10.1016/j.bbrc.2011.07.073

Experimental method

X-RAY DIFFRACTION (1.55 Å)