The crystal structure of maleylacetate reductase from Rhizobium sp. strain MTP-10005 provides insights into the reaction mechanism of enzymes in its original family

• Published in: Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2016-08, Vol.84 (8), p.1029-1042
• Main Authors: Fujii, Tomomi, Sato, Ai, Okamoto, Yuko, Yamauchi, Takae, Kato, Shiro, Yoshida, Masahiro, Oikawa, Tadao, Hata, Yasuo
• Format: Article
• Language: English
• Subjects: Adipates - chemistry; Adipates - metabolism; Agrobacterium tumefaciens - chemistry; Agrobacterium tumefaciens - enzymology; aromatic compound metabolism; Bacterial Proteins - chemistry; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Catalytic Domain; Cloning, Molecular; Crystallography, X-Ray; domain movement; double-bond reduction; Escherichia coli - genetics; Escherichia coli - metabolism; Gene Expression; Maleates - chemistry; Maleates - metabolism; Models, Molecular; Mutation; NAD - chemistry; NAD - metabolism; NADH; Oxidoreductases Acting on CH-CH Group Donors - chemistry; Oxidoreductases Acting on CH-CH Group Donors - genetics; Oxidoreductases Acting on CH-CH Group Donors - metabolism; Protein Multimerization; Protein Structure, Secondary; Protein Subunits - chemistry; Protein Subunits - genetics; Protein Subunits - metabolism; Recombinant Proteins - chemistry; Recombinant Proteins - genetics; Recombinant Proteins - metabolism; resorcinol catabolism; Rhizobium; Rhizobium - chemistry; Rhizobium - enzymology; Structural Homology, Protein; x-ray structure
• ISSN: 0887-3585; 1097-0134
• DOI: 10.1002/prot.25046

ABSTRACT Maleylacetate reductase plays a crucial role in catabolism of resorcinol by catalyzing the NAD(P)H‐dependent reduction of maleylacetate, at a carbon–carbon double bond, to 3‐oxoadipate. The crystal structure of maleylacetate reductase from Rhizobium sp. strain MTP‐10005, GraC, has been elucidated by the X‐ray diffraction method at 1.5 Å resolution. GraC is a homodimer, and each subunit consists of two domains: an N‐terminal NADH‐binding domain adopting an α/β structure and a C‐terminal functional domain adopting an α‐helical structure. Such structural features show similarity to those of the two existing families of enzymes in dehydroquinate synthase‐like superfamily. However, GraC is distinct in dimer formation and activity expression mechanism from the families of enzymes. Two subunits in GraC have different structures from each other in the present crystal. One subunit has several ligands mimicking NADH and the substrate in the cleft and adopts a closed domain arrangement. In contrast, the other subunit does not contain any ligand causing structural changes and adopts an open domain arrangement. The structure of GraC reveals those of maleylacetate reductase both in the coenzyme, substrate‐binding state and in the ligand‐free state. The comparison of both subunit structures reveals a conformational change of the Tyr326 loop for interaction with His243 on ligand binding. Structures of related enzymes suggest that His243 is likely a catalytic residue of GraC. Mutational analyses of His243 and Tyr326 support the catalytic roles proposed from structural information. The crystal structure of GraC characterizes the maleylacetate reductase family as a third family in the dehydroquinate synthase‐like superfamily. Proteins 2016; 84:1029–1042. © 2016 Wiley Periodicals, Inc.