The structure of GDP‐4‐keto‐6‐deoxy‐<scp>d</scp>‐mannose‐3‐dehydratase: A unique coenzyme B<sub>6</sub>‐dependent enzyme

Cook, P.D.; Thoden, James B.; Holden, Hazel M.

doi:10.1110/ps.062328306

Cited by 22 publications

(70 citation statements)

References 28 publications

(39 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In many examples, the PLP cofactor is involved in transamination reactions, which typically begin when glutamate or another amino donor reacts with the internal aldimine. A transient geminal diamine is first formed (Scheme 2), which subsequently collapses to form a Schiff base between the cofactor and glutamate, referred to as the external aldimine.A possible dehydration reaction mechanism for ColD, based on both biochemical and structural data, is presented in Scheme 3 (13,18). Consistent with all presently available data, it is thought that after the PLP has been converted to PMP, a Schiff base is then formed between the sugar C4′ and the PMP cofactor that is noncovalently bound to ColD.…”

supporting

confidence: 53%

“…Instead, ColD contains a histidine residue (His 188) at the homologous position, which does not form a covalent bond with the cofactor. Interestingly, the ColD active site is markedly devoid of potential catalytic bases other than His 188, suggesting that this residue functions as the sole proton donor/ acceptor in the catalytic mechanism (13). It is also noteworthy that ColD catalyzes the reaction using only PLP.…”

mentioning

confidence: 99%

See 1 more Smart Citation

A Structural Study of GDP-4-Keto-6-Deoxy-d-Mannose-3-Dehydratase: Caught in the Act of Geminal Diamine Formation^,

Cook

Holden

2007

Biochemistry

View full text Add to dashboard Cite

Di-and tri-deoxysugars are an important class of carbohydrates synthesized by certain plants, fungi, and bacteria. Colitose, for example, is a 3,6-dideoxysugar found in the O-antigens of Gram-negative bacteria such as Escherichia coli, Salmonella enterica, Yersinia pseudotuberculosis, and Vibrio cholerae, among others. These types of dideoxysugars are thought to serve as antigenic determinants and to play key roles in bacterial defense and survival. Four enzymes are required for the biochemical synthesis of colitose starting from mannose-1-phosphate. The focus of this investigation, GDP-4-keto-6-deoxy-D-mannose-3-dehydratase (ColD), catalyzes the third step in the pathway, namely the PLP-dependent removal of the C3′-hydroxyl group from GDP-4-keto-6-deoxymannose. Whereas most PLP-dependent enzymes contain an active site lysine, ColD utilizes a histidine as its catalytic acid/base. The ping-pong mechanism of the enzyme first involves the conversion of PLP to PMP followed by the dehydration step. Here we present the three-dimensional structure of a site-directed mutant form of ColD whereby the active site histidine has been replaced with a lysine. The electron density reveals that the geminal diamine, a tetrahedral intermediate in the formation of PMP from PLP, has been trapped within the active site region. Functional assays further demonstrate that this mutant form of ColD cannot catalyze the dehydration reaction.Di-and tri-deoxysugars are an intriguing class of carbohydrates that are synthesized by plants, fungi, and bacteria (1,2). The biosynthetic pathways for the production of these unusual sugars typically begin with simple monosaccharides such as glucose-1-phosphate or fructose-6-phosphate as starting materials. Via an impressive array of reactions including dehydrations, reductions, amino transfers, and methylations, the pathways result in an astonishing array of sugars with differing three-dimensional shapes and hydrophilicities. Many of these unusual sugars have been isolated from the O-antigens of a variety of Gram-negative bacteria, where they contribute to the structural variations observed in bacterial cell walls (3). It has been suggested that these sugars play a role in the virulence of a given pathogen (4). Other deoxysugars have been found in polyketide antibiotics including erythromycin, azithromycin, and clarithromycin, where they are known to enhance the biological activities of the respective drugs (5).The focus of this investigation is an enzyme involved in the biosynthesis of colitose, a 3,6-dideoxysugar found in the O-antigen of Gram-negative bacteria such as Escherichia coli (6), Yersinia pseudotuberculosis(7) , Salmonella enterica (8), Vibrio cholerae (9), and in marine bacteria such as Pseudoalteromonas tetraodonis (9) carrageenovora (10). The biosynthesis of the O-antigen requires nucleotide-linked sugars, which are transferred to the oligosaccharide chain by an array of glycosyltransferases. In the case of colitose, the sugar is linked to GDP 1 .As indicated in Scheme 1, four...

show abstract

supporting

confidence: 53%

mentioning

confidence: 99%

A Structural Study of GDP-4-Keto-6-Deoxy-d-Mannose-3-Dehydratase: Caught in the Act of Geminal Diamine Formation^,

Cook

Holden

2007

Biochemistry

View full text Add to dashboard Cite

show abstract

“…, determined by the ProtParam tool from the Expasy Proteomics Server). The wild-type enzyme required for functional studies was expressed and purified as previously reported (3).…”

Section: Methodsmentioning

confidence: 99%

“…Crystallization of H188N ColD-Crystallization conditions were first surveyed by the hanging drop method of vapor diffusion using a sparse matrix screen developed in the laboratory. Large single crystals were subsequently grown via batch methods as previously described (3). The concentrations of the protein solutions were typically 25 mg/ml, and they contained 25 mM Tris (pH 8.0) and 100 mM NaCl.…”

Section: Methodsmentioning

confidence: 99%

See 1 more Smart Citation

GDP-4-Keto-6-deoxy-D-mannose 3-Dehydratase, Accommodating a Sugar Substrate in the Active Site

Cook

Holden

2008

Journal of Biological Chemistry

View full text Add to dashboard Cite

Colitose is a dideoxysugar found in the O-antigen of the lipopolysaccharide that coats the outer membrane of some Gram-negative bacteria. Four enzymes are required for its production starting from D-mannose-1-phosphate and GTP. The focus of this investigation is GDP-4-keto-6-deoxy-D-mannose 3-dehydratase or ColD, which catalyzes the removal of the C3-hydroxyl group from GDP-4-keto-6-deoxymannose. The enzyme is pyridoxal 5-phosphate-dependent, but unlike most of these proteins, the conserved lysine residue that covalently holds the cofactor in the active site is replaced with a histidine residue. Here we describe the three-dimensional structure of ColD, determined to 1.7 Å resolution, whereby the active site histidine has been replaced with an asparagine residue. For this investigation, crystals of the site-directed mutant protein were grown in the presence of GDP-4-amino-4,6-dideoxy-D-mannose (GDP-perosamine). The electron density map clearly reveals the presence of the sugar analog trapped in the active site as an external aldimine. The active site is positioned between the two subunits of the dimer. Whereas the pyrophosphoryl groups of the ligand are anchored to the protein via Arg-219 and Arg-331, the hydroxyl groups of the hexose only lie within hydrogen bonding distance to ordered water molecules. Interestingly, the hexose moiety of the ligand adopts a boat rather than the typically observed chair conformation. Activity assays demonstrate that this mutant protein cannot catalyze the dehydration step. Additionally, we report data revealing that wild-type ColD is able to catalyze the production of GDP-4-keto-3,6-dideoxymannose using GDP-perosamine instead of GDP-4-keto-6-deoxymannose as a substrate.

show abstract

Structural and functional analysis of an l‐serine O‐phosphate decarboxylase involved in norcobamide biosynthesis

et al. 2019

View full text Add to dashboard Cite

Structural diversity of natural cobamides (Cbas, B12 vitamers) is limited to the nucleotide loop. The loop is connected to the cobalt‐containing corrin ring via an (R)‐1‐aminopropan‐2‐ol O‐2‐phosphate (AP‐P) linker moiety. AP‐P is produced by the l‐threonine O‐3‐phosphate (l‐Thr‐P) decarboxylase CobD. Here, the CobD homolog SMUL_1544 of the organohalide‐respiring epsilonproteobacterium Sulfurospirillum multivorans was characterized as a decarboxylase that produces ethanolamine O‐phosphate (EA‐P) from l‐serine O‐phosphate (l‐Ser‐P). EA‐P is assumed to serve as precursor of the linker moiety of norcobamides that function as cofactors in the respiratory reductive dehalogenase. SMUL_1544 (SmCobD) is a pyridoxal‐5′‐phosphate (PLP)‐containing enzyme. The structural analysis of the SmCobD apoprotein combined with the characterization of truncated mutant proteins uncovered a role of the SmCobD N‐terminus in efficient l‐Ser‐P conversion.

show abstract

The structure of GDP‐4‐keto‐6‐deoxy‐d‐mannose‐3‐dehydratase: A unique coenzyme B₆‐dependent enzyme

Cited by 22 publications

References 28 publications

A Structural Study of GDP-4-Keto-6-Deoxy-d-Mannose-3-Dehydratase: Caught in the Act of Geminal Diamine Formation^,

A Structural Study of GDP-4-Keto-6-Deoxy-d-Mannose-3-Dehydratase: Caught in the Act of Geminal Diamine Formation^,

GDP-4-Keto-6-deoxy-D-mannose 3-Dehydratase, Accommodating a Sugar Substrate in the Active Site

Structural and functional analysis of an l‐serine O‐phosphate decarboxylase involved in norcobamide biosynthesis

Contact Info

Product

Resources

About

The structure of GDP‐4‐keto‐6‐deoxy‐d‐mannose‐3‐dehydratase: A unique coenzyme B6‐dependent enzyme

Cited by 22 publications

References 28 publications

A Structural Study of GDP-4-Keto-6-Deoxy-d-Mannose-3-Dehydratase: Caught in the Act of Geminal Diamine Formation,

A Structural Study of GDP-4-Keto-6-Deoxy-d-Mannose-3-Dehydratase: Caught in the Act of Geminal Diamine Formation,

GDP-4-Keto-6-deoxy-D-mannose 3-Dehydratase, Accommodating a Sugar Substrate in the Active Site

Structural and functional analysis of an l‐serine O‐phosphate decarboxylase involved in norcobamide biosynthesis

Contact Info

Product

Resources

About

The structure of GDP‐4‐keto‐6‐deoxy‐d‐mannose‐3‐dehydratase: A unique coenzyme B₆‐dependent enzyme

A Structural Study of GDP-4-Keto-6-Deoxy-d-Mannose-3-Dehydratase: Caught in the Act of Geminal Diamine Formation^,

A Structural Study of GDP-4-Keto-6-Deoxy-d-Mannose-3-Dehydratase: Caught in the Act of Geminal Diamine Formation^,