The Structures of l-Rhamnose Isomerase from Pseudomonas stutzeri in Complexes with l-Rhamnose and d-Allose Provide Insights into Broad Substrate Specificity

Yoshida, Hiromi; Yamada, Michihiro; Ohyama, Yuya; Takada, Goro; Izumori, Ken; Kamitori, Shigehiro

doi:10.1016/j.jmb.2006.11.004

Cited by 33 publications

(60 citation statements)

References 39 publications

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“…Also, three-dimensional structures of enzyme/substrate complexes could give insights into substrate-recognition and catalytic mechanisms of the enzyme, which comprise important information for rare sugar production. 12 Crystallization and preliminary X-ray analyses of P. cichorii D-TE were already reported. 13 Here we report the crystal structures of P. cichorii D-TE alone and in complexes with D-tagatose (P. cichorii D-TE/D-tagatose) and D-fructose (P. cichorii D-TE/ D-fructose).…”

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confidence: 99%

Crystal Structures of d-Tagatose 3-Epimerase from Pseudomonas cichorii and Its Complexes with d-Tagatose and d-Fructose

Yoshida

Yamada

Nishitani

et al. 2007

Journal of Molecular Biology

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confidence: 99%

Crystal Structures of d-Tagatose 3-Epimerase from Pseudomonas cichorii and Its Complexes with d-Tagatose and d-Fructose

Yoshida

Yamada

Nishitani

et al. 2007

Journal of Molecular Biology

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“…10) The AARs of M. loti L-RhI (Glu219, Lys221, Asp254, His257, His281, Asp289, Asp291, Asp327), which interacted with C1, C2, and C3 positions of the sugar substrate, were conserved. 11) This confirms a similarity of substrate specificity between M. loti L-RhI and P. stutzeri L-RhI, but X-ray crystallography determination is necessary to provide further evidence of this.…”

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confidence: 54%

“…There was no significant difference between the structure of P. stutzeri L-RhI and the modeled structure of M. loti L-RhI (data not shown). 11) The BamHI-and BglII-digested rhi fragments derived from pLM1 were ligated into pQE60, which had been digested with BamHI and BglII (designated pLM2) and then transformed into E. coli JM109. E. coli JM109 harboring pLM2 was cultivated at 30 C in 400 mL of SB medium supplemented with ampicillin until the OD 600 was 0.5.…”

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confidence: 99%

Characterization ofMesorhizobium lotiL-Rhamnose Isomerase and Its Application toL-Talose Production

Takata

Uechi

Taniguchi

et al. 2011

Bioscience, Biotechnology, and Biochemistry

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“…These side chains allow access to the Zn 2ϩ ion from one side, and we found a weakly bound water molecule in this location, potentially corresponding to the position of an oxygen atom (O-2 or O-3) of the substrate. Similar coordination of the substrate oxygen was observed in D-psicose 3-epimerase (18) and in L-rhamnose isomerase (42). There are also similar metalbinding sites in the structural homologs IolI (PDB code 1I6N) (43) and endonuclease IV (16).…”

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confidence: 65%

Structure of l -Xylulose-5-Phosphate 3-Epimerase (UlaE) from the Anaerobic l -Ascorbate Utilization Pathway of Escherichia coli : Identification of a Novel Phosphate Binding Motif within a TIM Barrel Fold

et al. 2008

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Three catabolic enzymes, UlaD, UlaE, and UlaF, are involved in a pathway leading to fermentation of L-ascorbate under anaerobic conditions. UlaD catalyzes a ␤-keto acid decarboxylation reaction to produce L-xylulose-5-phosphate, which undergoes successive epimerization reactions with UlaE (L-xylulose-5-phosphate 3-epimerase) and UlaF (L-ribulose-5-phosphate 4-epimerase), yielding D-xylulose-5-phosphate, an intermediate in the pentose phosphate pathway. We describe here crystallographic studies of UlaE from Escherichia coli O157:H7 that complete the structural characterization of this pathway. UlaE has a triosephosphate isomerase (TIM) barrel fold and forms dimers. The active site is located at the C-terminal ends of the parallel ␤-strands. The enzyme binds Zn 2؉ , which is coordinated by Glu155, Asp185, His211, and Glu251. We identified a phosphate-binding site formed by residues from the ␤1/␣1 loop and ␣3 helix in the N-terminal region. This site differs from the well-characterized phosphate-binding motif found in several TIM barrel superfamilies that is located at strands ␤7 and ␤8. The intrinsic flexibility of the active site region is reflected by two different conformations of loops forming part of the substrate-binding site. Based on computational docking of the L-xylulose 5-phosphate substrate to UlaE and structural similarities of the active site of this enzyme to the active sites of other epimerases, a metal-dependent epimerization mechanism for UlaE is proposed, and Glu155 and Glu251 are implicated as catalytic residues. Mutation and activity measurements for structurally equivalent residues in related epimerases supported this mechanistic proposal.It has been known for nearly 70 years that various bacteria, including Escherichia coli, can ferment L-ascorbate (vitamin C) under anaerobic conditions (2,10,30,40). This process has been demonstrated to involve proteins encoded by two divergently transcribed operons, the ulaGR and ulaABCDEF operons (3,40,44). The ulaG gene encodes L-ascorbate-6-phosphate lactonase. The ulaABCDEF operon encodes an L-ascorbate phosphotransferase transport system (UlaABC, formerly designated SgaTBA) responsible for the uptake and phosphorylation of L-ascorbate, and the ulaDEF genes encode three enzymes that catalyze the conversion of the phosphorylated, hydrolytic product of L-ascorbate, 3-keto-L-gulonate-6-phosphate, to D-xylulose-5-phosphate, which is subsequently metabolized by the pentose phosphate pathway. UlaD (formerly SgaH) decarboxylates 3-keto-L-gulonate-6-phosphate, yielding L-xylulose-5-phosphate, which is subsequently epimerized by UlaE (formerly SgaU) at C-3 to L-ribulose-5-phosphate and then epimerized by UlaF (formerly SgaE) at C-4 to D-xylulose-5-phosphate (Fig.

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The Structures of l-Rhamnose Isomerase from Pseudomonas stutzeri in Complexes with l-Rhamnose and d-Allose Provide Insights into Broad Substrate Specificity

Cited by 33 publications

References 39 publications

Crystal Structures of d-Tagatose 3-Epimerase from Pseudomonas cichorii and Its Complexes with d-Tagatose and d-Fructose

Crystal Structures of d-Tagatose 3-Epimerase from Pseudomonas cichorii and Its Complexes with d-Tagatose and d-Fructose

Characterization ofMesorhizobium lotiL-Rhamnose Isomerase and Its Application toL-Talose Production

Structure of l -Xylulose-5-Phosphate 3-Epimerase (UlaE) from the Anaerobic l -Ascorbate Utilization Pathway of Escherichia coli : Identification of a Novel Phosphate Binding Motif within a TIM Barrel Fold

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