InChI=1S/C5H10O6/c6-1-2(7)3(8)4(9)5(10)11/h2-4,6-9H,1H2,(H,10,11)/t2-,3+,4+/m0/s1 |
QXKAIJAYHKCRRA-PZGQECOJSA-N |
OC[C@@H]([C@H]([C@H](C(O)=O)O)O)O |
|
Rattus norvegicus
(NCBI:txid10116)
|
Found in
kidney
(BTO:0000671).
See:
PubMed
|
Homo sapiens
(NCBI:txid9606)
|
Found in
urine
(BTO:0001419).
See:
PubMed
|
Bronsted acid
A molecular entity capable of donating a hydron to an acceptor (Bronsted base).
(via oxoacid )
|
|
human urinary metabolite
Any metabolite (endogenous or exogenous) found in human urine samples.
rat metabolite
Any mammalian metabolite produced during a metabolic reaction in rat (Rattus norvegicus).
|
|
View more via ChEBI Ontology
(2R,3R,4S)-2,3,4,5-tetrahydroxypentanoic acid
|
IUPAC
|
4172-43-4
|
CAS Registry Number
|
ChEBI
|
Luo S, Huang H (2018) Discovering a new catabolic pathway of D-ribonate in Mycobacterium smegmatis. Biochemical and biophysical research communications 505, 1107-1111 [PubMed:30316512] [show Abstract] In vivo growth study indicates that Mycobacterium smegmatis could utilize D-ribonate as sole carbon source under an unknown pathway. To clarify this pathway, we start with the statistical analysis of genome neighborhood networks(GNNs) of erythrulose kinase which has been approved to participate in several sugars' degradation. In M. smegmatis, two novel dehydrogenases (3HCDH & ADH_short) and one unknown isomerase (AP_endonuc) are targeted and characterized, for the catabolism of D-ribonate in this organism, this acid sugar is firstly oxidized into 2-keto-D-ribonate by a dehydrogenase, and then sequentially isomerized to 3-keto D-ribonate by an AP_endonuc isomerase; afterward, through decarboxylation, this 3-keto sugar acid is degraded into D-erythrulose which enters a known pathway through erythrulose kinase. Additionally, several other acid sugars (L-ribonate, D/L-lyxonate, L-threonate and D-erythronate) have been proved to be catalyzed by same enzymes and proceed with a similar catabolic pathway. | Ghasempur S, Eswaramoorthy S, Hillerich BS, Seidel RD, Swaminathan S, Almo SC, Gerlt JA (2014) Discovery of a novel L-lyxonate degradation pathway in Pseudomonas aeruginosa PAO1. Biochemistry 53, 3357-3366 [PubMed:24831290] [show Abstract] The l-lyxonate dehydratase (LyxD) in vitro enzymatic activity and in vivo metabolic function were assigned to members of an isofunctional family within the mandelate racemase (MR) subgroup of the enolase superfamily. This study combined in vitro and in vivo data to confirm that the dehydration of l-lyxonate is the biological role of the members of this family. In vitro kinetic experiments revealed catalytic efficiencies of ∼10(4) M(-1) s(-1) as previously observed for members of other families in the MR subgroup. Growth studies revealed that l-lyxonate is a carbon source for Pseudomonas aeruginosa PAO1; transcriptomics using qRT-PCR established that the gene encoding LyxD as well as several other conserved proximal genes were upregulated in cells grown on l-lyxonate. The proximal genes were shown to be involved in a pathway for the degradation of l-lyxonate, in which the first step is dehydration by LyxD followed by dehydration of the 2-keto-3-deoxy-l-lyxonate product by 2-keto-3-deoxy-l-lyxonate dehydratase to yield α-ketoglutarate semialdehyde. In the final step, α-ketoglutarate semialdehyde is oxidized by a dehydrogenase to α-ketoglutarate, an intermediate in the citric acid cycle. An X-ray structure for the LyxD from Labrenzia aggregata IAM 12614 with Mg(2+) in the active site was determined that confirmed the expectation based on sequence alignments that LyxDs possess a conserved catalytic His-Asp dyad at the end of seventh and sixth β-strands of the (β/α)7β-barrel domain as well as a conserved KxR motif at the end of second β-strand; substitutions for His 316 or Arg 179 inactivated the enzyme. This is the first example of both the LyxD function in the enolase superfamily and a pathway for the catabolism of l-lyxonate. | Rakus JF, Fedorov AA, Fedorov EV, Glasner ME, Hubbard BK, Delli JD, Babbitt PC, Almo SC, Gerlt JA (2008) Evolution of enzymatic activities in the enolase superfamily: L-rhamnonate dehydratase. Biochemistry 47, 9944-9954 [PubMed:18754693] [show Abstract] The l-rhamnonate dehydratase (RhamD) function was assigned to a previously uncharacterized family in the mechanistically diverse enolase superfamily that is encoded by the genome of Escherichia coli K-12. We screened a library of acid sugars to discover that the enzyme displays a promiscuous substrate specificity: l-rhamnonate (6-deoxy- l-mannonate) has the "best" kinetic constants, with l-mannonate, l-lyxonate, and d-gulonate dehydrated less efficiently. Crystal structures of the RhamDs from both E. coli K-12 and Salmonella typhimurium LT2 (95% sequence identity) were obtained in the presence of Mg (2+); the structure of the RhamD from S. typhimurium was also obtained in the presence of 3-deoxy- l-rhamnonate (obtained by reduction of the product with NaBH 4). Like other members of the enolase superfamily, RhamD contains an N-terminal alpha + beta capping domain and a C-terminal (beta/alpha) 7beta-barrel (modified TIM-barrel) catalytic domain with the active site located at the interface between the two domains. In contrast to other members, the specificity-determining "20s loop" in the capping domain is extended in length and the "50s loop" is truncated. The ligands for the Mg (2+) are Asp 226, Glu 252 and Glu 280 located at the ends of the third, fourth and fifth beta-strands, respectively. The active site of RhamD contains a His 329-Asp 302 dyad at the ends of the seventh and sixth beta-strands, respectively, with His 329 positioned to function as the general base responsible for abstraction of the C2 proton of l-rhamnonate to form a Mg (2+)-stabilized enediolate intermediate. However, the active site does not contain other acid/base catalysts that have been implicated in the reactions catalyzed by other members of the MR subgroup of the enolase superfamily. Based on the structure of the liganded complex, His 329 also is expected to function as the general acid that both facilitates departure of the 3-OH group in a syn-dehydration reaction and delivers a proton to carbon-3 to replace the 3-OH group with retention of configuration. | Lawson AM, Chalmers RA, Watts RW (1976) Urinary organic acids in man. I. Normal patterns. Clinical chemistry 22, 1283-1287 [PubMed:949837] [show Abstract] We studied qualitative pattern of urinary acidic metabolites excreted by normal persons. The results provide a basis on which to compare results for patients with potentially abnormal organic acidurias. A series of urinary polyhydroxy (aldonic and deoxyaldonic) acids has been identified. Most of these compounds have not been previously reported in human urine, except in connection with the present work, and are additional to the previously recognized urinary organic acids, which were also observed. Possible metabolic origins of some of the acids are briefly discussed. | KANFER J, ASHWELL G, BURNS JJ (1960) Formation of L-lyxonic and L-xylonic acids from L-ascorbic acid in rat kidney. The Journal of biological chemistry 235, 2518-2521 [PubMed:14404302] |
|