Structural and Mutational Studies on the Unusual Substrate Specificity of <i>meso</i>‐Diaminopimelate Dehydrogenase from <i>Symbiobacterium thermophilum</i>

Liu, Weidong; Li, Zhe; Huang, Chun‐Hsiang; Guo, Rey‐Ting; Zhao, Leiming; Zhang, Dalong; Chen, Xi; Wu, Qingping; Zhu, Dunming

doi:10.1002/cbic.201300691

Cited by 32 publications

(40 citation statements)

References 35 publications

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“…The indels were conserved within each type. According to previous crystal structural studies (14,18,19), StDAPDH aggregates as a hexamer, whereas CgDAPDH forms a dimer, and indels are located at ␣2, ␣9, and some linkers of CgDAPDH but not in the catalytic pocket. Quaternary structures indicated that, as shown in Fig.…”

Section: Resultsmentioning

confidence: 89%

“…Subsequently, the conserved positions in CgDAPDH and StDAPDH were compared. Although interaction models for proteins and meso-DAP or NADP ϩ have been reported (14,18,19), there are no obvious definitions of the substrate/NADP ϩ -binding residues for CgDAPDH and StDAPDH. Therefore, MSDsite (28) was used to predict substrate/ NADP ϩ -binding residues for the two enzymes.…”

Section: Resultsmentioning

confidence: 99%

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A Newly Determined Member of the meso -Diaminopimelate Dehydrogenase Family with a Broad Substrate Spectrum

Gao

Zheng

Zhang

et al. 2017

Appl Environ Microbiol

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meso-Diaminopimelate dehydrogenase (meso-DAPDH) from Symbiobacterium thermophilum (StDAPDH) is the first member of the meso-DAPDH family known to catalyze the asymmetric reductive amination of 2-keto acids to produce D-amino acids. It is important to understand the catalytic mechanisms of StDAPDH and other enzymes in this family. In this study, based on an evolutionary analysis and examination of catalytic activity, the meso-DAPDH enzymes can be divided into two types. Type I showed highly preferable activity toward meso-diaminopimelate (meso-DAP), and type II exhibited obviously reversible amination activity with a broad substrate spectrum. StDAPDH belongs to type II. A quaternary structure analysis revealed that insertions/deletions (indels) and a loss of quaternary structure resulted in divergence among members of the meso-DAPDH family. A structure alignment of StDAPDH with a representative of type I, the meso-DAPDH from Corynebacterium glutamicum (CgDAPDH), indicated that they had the same folding. Based on sequence and conservation analyses, two amino acid residues of StDAPDH, R35 and R71, were found to be highly conserved within type II while also distinct from each other between the subtypes. Site mutagenesis studies identified R71 as a substrate preference-related residue of StDAPDH, which may serve as an indicator of the amination preference of type II. These results deepen the present understanding of the meso-DAPDH family and provide a solid foundation for the discovery and engineering of meso-DAPDH for D-amino acid biosynthesis.IMPORTANCE The L-form of amino acids is typically more abundant than the D-form. However, the D-form has many important pharmaceutical applications. mesoDiaminopimelate dehydrogenase (meso-DAPDH) from Symbiobacterium thermophilum (StDAPDH) was the first member of meso-DAPDH known to catalyze the amination of 2-keto acids to produce D-amino acids. Accordingly, we analyzed the evolution of meso-DAPDH proteins and found that they form two groups, i.e., type I proteins, which show high preference toward meso-diaminopimelate (meso-DAP), and type II proteins, which show a broad substrate spectrum. We examined the differences in sequence, ternary structure, and quaternary structure to determine the mechanisms underlying the functional differences between the type I and type II lineages. These results will facilitate the identification of additional meso-DAPDHs and may provide guidance to protein engineering studies for D-amino acid biosynthesis.

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Section: Resultsmentioning

confidence: 89%

Section: Resultsmentioning

confidence: 99%

A Newly Determined Member of the meso -Diaminopimelate Dehydrogenase Family with a Broad Substrate Spectrum

Gao

Zheng

Zhang

et al. 2017

Appl Environ Microbiol

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“…The U. thermosphaericus DAPDH monomer also showed high structural similarity to DAPDH from S. thermophilum (PDB entries 3wb9, 3wbb and 3wbf, with r.m.s.d.s between 1.6 and 3.1 Å ; Liu et al, 2014), but 9 and 10 in the structure of the former were replaced by a short loop in the latter (Fig. 3).…”

Section: Overall Structure and Structural Homologuesmentioning

confidence: 92%

“…In addition, structures of S. thermophilum DAPDH in its apo form, in complex with NADP + and in complex with both NADPH and meso-DAP have been determined (Liu et al, 2014). Although extensive analysis of these structures has shed light on the structure of the substrate-binding site and has enabled the elucidation of the substrate-recognition mechanism of these enzymes, the structural features responsible for the high thermostability of thermophilic DAPDHs have not yet been determined.…”

Section: Introductionmentioning

confidence: 99%

Structural insight into the thermostable NADP⁺-dependentmeso-diaminopimelate dehydrogenase fromUreibacillus thermosphaericus

Akita

Seto

Ohshima

et al. 2015

Acta Cryst D Biol Crystallogr

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Crystal structures of the thermostable meso-diaminopimelate dehydrogenase (DAPDH) from Ureibacillus thermosphaericus were determined for the enzyme in the apo form and in complex with NADP(+) and N-tris(hydroxymethyl)methyl-2-aminoethanesulfonic acid. The main-chain coordinates of the enzyme showed notable similarity to those of Symbiobacterium thermophilum DAPDH. However, the subunit arrangement of U. thermosphaericus DAPDH (a dimer) was totally different from that of the S. thermophilum enzyme (a hexamer). Structural comparison with the dimeric enzyme from the mesophile Corynebacterium glutamicum revealed that the presence of large numbers of intrasubunit and intersubunit hydrophobic interactions, as well as the extensive formation of intersubunit ion-pair networks, were likely to be the main factors contributing to the higher thermostability of U. thermosphaericus DAPDH. This differs from S. thermophilum DAPDH, within which the unique hexameric assembly is likely to be responsible for its high thermostability. Analysis of the active site of U. thermosphaericus DAPDH revealed the key factors responsible for the marked difference in substrate specificity between DAPDH and the D-amino acid dehydrogenase recently created from DAPDH by introducing five point mutations [Akita et al. (2012). Biotechnol. Lett. 34, 1693-1699; 1701-1702].

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“…The six Gfo/Idh/MocA family proteins did not form a single structural cluster. Meso-diaminopimelate dehydrogenase from Symbiobacterium thermophilum 24 was included in the dihydrodipicolinate reductase domain superfamily and could be considered as a member of the Gfo/Idh/MocA protein family, but it had a six-stranded completely antiparallel bsheet without the ba-motif described before. Furthermore, aspartate dehydrogenase from Thermotoga maritima 25 could be considered a candidate for the Gfo/Idh/MocA family, but it did not have the central ahelix after the first b-strand in the a/b-domain, and the b-sheet was smaller and only five-stranded.…”

Section: Topological Conservationmentioning

confidence: 99%

Structural and functional features of the NAD(P) dependent Gfo/Idh/MocA protein family oxidoreductases

2016

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The Gfo/Idh/MocA protein family contains a number of different proteins, which almost exclusively consist of NAD(P)-dependent oxidoreductases that have a diverse set of substrates, typically pyranoses. In this study, to clarify common structural features that would contribute to their function, the available crystal structures of the members of this family have been analyzed. Despite a very low sequence identity, the central features of the three-dimensional structures of the proteins are surprisingly similar. The members of the protein family have a two-domain structure consisting of a N-terminal nucleotide-binding domain and a C-terminal a/b-domain. The C-terminal domain contributes to the substrate binding and catalysis, and contains a ba-motif with a central a-helix carrying common essential amino acid residues. The b-sheet of the a/b-domain contributes to the oligomerization in most of the proteins in the family.

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Structural and Mutational Studies on the Unusual Substrate Specificity of meso‐Diaminopimelate Dehydrogenase from Symbiobacterium thermophilum

Cited by 32 publications

References 35 publications

A Newly Determined Member of the meso -Diaminopimelate Dehydrogenase Family with a Broad Substrate Spectrum

A Newly Determined Member of the meso -Diaminopimelate Dehydrogenase Family with a Broad Substrate Spectrum

Structural insight into the thermostable NADP⁺-dependentmeso-diaminopimelate dehydrogenase fromUreibacillus thermosphaericus

Structural and functional features of the NAD(P) dependent Gfo/Idh/MocA protein family oxidoreductases

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Structural and Mutational Studies on the Unusual Substrate Specificity of meso‐Diaminopimelate Dehydrogenase from Symbiobacterium thermophilum

Cited by 32 publications

References 35 publications

A Newly Determined Member of the meso -Diaminopimelate Dehydrogenase Family with a Broad Substrate Spectrum

A Newly Determined Member of the meso -Diaminopimelate Dehydrogenase Family with a Broad Substrate Spectrum

Structural insight into the thermostable NADP+-dependentmeso-diaminopimelate dehydrogenase fromUreibacillus thermosphaericus

Structural and functional features of the NAD(P) dependent Gfo/Idh/MocA protein family oxidoreductases

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Structural insight into the thermostable NADP⁺-dependentmeso-diaminopimelate dehydrogenase fromUreibacillus thermosphaericus