Crystal Structure of Urea Carboxylase Provides Insights into the Carboxyltransfer Reaction

Chen, Fan; Chou, Chi-Yuan; Tong, Liang; Xiang, Song

doi:10.1074/jbc.m111.319475

Cited by 32 publications

(49 citation statements)

References 50 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…An x-ray structural model of the carboxylase domain of the urea amidolyase from the eukaryote Kluyveromyces lactis has been solved previously (Fan et al, 2012). Based on this structure, it is hypothesized that a protonated aspartic acid residue near the active site, which is conserved in the O. sagaranensis carboxylase, forms a hydrogen bond with the oxygen atom of urea.…”

Section: Resultsmentioning

confidence: 99%

Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class

et al. 2017

View full text Add to dashboard Cite

SUMMARY The guanidyl moiety is a component of fundamental metabolites including the amino acid arginine, the energy carrier creatine, and the nucleobase guanine. Curiously, reports regarding the importance of free guanidine in biology are sparse and no biological receptors that specifically recognize this compound have been previously identified. We report that many members of the ykkC motif RNA, the longest-unresolved riboswitch candidate, naturally sense and respond to guanidine. This RNA is found throughout much of the bacterial domain of life, where it commonly controls the expression of proteins annotated as urea carboxylases and multidrug efflux pumps. Our analyses reveal that these proteins likely function as guanidine carboxylases and guanidine transporters, respectively. Furthermore, we demonstrate that bacteria are capable of endogenously producing guanidine. These and related findings demonstrate that free guanidine is a biologically relevant compound and several gene families exists that can alleviate guanidine toxicity.

show abstract

Section: Resultsmentioning

confidence: 99%

Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class

et al. 2017

View full text Add to dashboard Cite

show abstract

“…As such the exact mechanism by which the keto acid enolate is stabilized is unclear at the present time. 10,20,21,91,92 It is possible that stabilization of the keto acid enolate is achieved through a combination of metal ion coordination and/or interaction with an Arg/Gln side chain pair. It is also possible that these enzymes stabilize the biotin enolate through tetrahedral coordination of the ureido oxygen.…”

Section: Carboxyltransferase Domains Without a Crotonase Foldmentioning

confidence: 99%

“…This sequence is not absolutely invariant, however, because in some of the urea amidolyases the lysine is contained within the following sequences: Ser-Met-Lys-Met or AlaMet-Lys-Ala or Ala-Met-Lys-Thr. 10 At present there are more than 70 X-ray coordinate files deposited in the Protein Data Bank for structures of biotin-dependent enzymes. An elegant review focusing on the holoenzyme structures of various biotin-dependent carboxylases has recently been published.…”

Section: Introductionmentioning

confidence: 99%

The enzymes of biotin dependent CO₂ metabolism: What structures reveal about their reaction mechanisms

2012

View full text Add to dashboard Cite

Biotin is the major cofactor involved in carbon dioxide metabolism. Indeed, biotindependent enzymes are ubiquitous in nature and are involved in a myriad of metabolic processes including fatty acid synthesis and gluconeogenesis. The cofactor, itself, is composed of a ureido ring, a tetrahydrothiophene ring, and a valeric acid side chain. It is the ureido ring that functions as the CO 2 carrier. A complete understanding of biotin-dependent enzymes is critically important for translational research in light of the fact that some of these enzymes serve as targets for antiobesity agents, antibiotics, and herbicides. Prior to 1990, however, there was a dearth of information regarding the molecular architectures of biotin-dependent enzymes. In recent years there has been an explosion in the number of three-dimensional structures reported for these proteins. Here we review our current understanding of the structures and functions of biotindependent enzymes. In addition, we provide a critical analysis of what these structures have and have not revealed about biotin-dependent catalysis.

show abstract

“…These proteins and complexes show no sequence homology to the allophanate hydrolases discussed here, and attempts to demonstrate the AH activity of TTHA0988 were not successful (21). They are instead homologous to the KipIKipA complex involved in the Bacillus subtilis sporulation regulation (21) and the urea carboxylase carboxyltransferase domain (22) and are probably not true allophanate hydrolases.…”

mentioning

confidence: 99%

“…We have previously reported the crystal structure of the urea carboxylase component of UA (22). However, the structure and catalytic mechanism of its AH component are not clear.…”

mentioning

confidence: 99%

Structure and Function of Allophanate Hydrolase

Chen

Yin

et al. 2013

Journal of Biological Chemistry

Self Cite

View full text Add to dashboard Cite

Background: Allophanate hydrolase (AH) is essential for urea utilization in many organisms. Results: We determined the crystal structure of the Kluyveromyces lactis AH and performed mechanistic studies. Conclusion: Our work revealed that the AH N and C domains catalyze sequential reactions and provided insights into their catalysis. Significance: The catalytic mechanism of the C domain might expand the knowledge of decarboxylation reactions.

show abstract

Crystal Structure of Urea Carboxylase Provides Insights into the Carboxyltransfer Reaction

Cited by 32 publications

References 50 publications

Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class

Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class

The enzymes of biotin dependent CO₂ metabolism: What structures reveal about their reaction mechanisms

Structure and Function of Allophanate Hydrolase

Contact Info

Product

Resources

About

Crystal Structure of Urea Carboxylase Provides Insights into the Carboxyltransfer Reaction

Cited by 32 publications

References 50 publications

Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class

Metabolism of Free Guanidine in Bacteria Is Regulated by a Widespread Riboswitch Class

The enzymes of biotin dependent CO2 metabolism: What structures reveal about their reaction mechanisms

Structure and Function of Allophanate Hydrolase

Contact Info

Product

Resources

About

The enzymes of biotin dependent CO₂ metabolism: What structures reveal about their reaction mechanisms