MiMeDB: Showing metabocard for 2,3,4,5-Tetrahydrodipicolinate (MMDBc0049956)

Record Information

Version

1.0

Status

Detected and Quantified

Creation Date

2022-04-29 22:47:03 UTC

Update Date

2025-01-15 23:37:24 UTC

Metabolite ID

MMDBc0049956

Metabolite Identification

Common Name

2,3,4,5-Tetrahydrodipicolinate

Description

Tetrahydrodipicolinate (CAS: 2353-17-5), converted from L-aspartate, is an important intermediate in the lysine biosynthesis pathway. Several pathways are now recognized in bacteria, most algae, fungi, and higher plants for the biosynthesis of lysine. They are divided into two groups: (1) the diaminopimelate (DAP) pathways, and (2) the alpha-aminoadipate (AAA) pathways. In the pathways that belong to the DAP group, lysine is produced from aspartate (along with methionine, threonine, and isoleucine). All of these pathways share the upper segments, which include the four steps required for the conversion of L-aspartate into tetrahydrodipicolinate. They also share the last step, which is the conversion of the intermediate meso-diaminopimelate (D,L-DAP, or meso-DAP) into lysine. However, these pathways differ in the routes leading from tetrahydrodipicolinate to meso-diaminopimelate. The four variations include: (I) the succinylase variant, which involves succinylated intermediates, where tetrahydrodipicolinate is converted into meso-diaminopimelate in four enzymatic steps; (II) the acetylase variant, which involves acetylated intermediates, where tetrahydrodipicolinate is converted into meso-diaminopimelate in four enzymatic steps; (III) the dehydrogenase variant, in which tetrahydrodipicolinate is converted into meso-diaminopimelate in a single enzymatic step; and (IV) the diaminopimelate-aminotransferase variant, in which tetrahydrodipicolinate is converted into meso-diaminopimelate in two steps. In addition to lysine, the pathways in this group also produce meso-DAP, which is an important metabolite on its own.

Structure

MOL SDF PDB SMILES InChI

Synonyms

Not Available

Molecular Formula

C₇H₉NO₄

Average Mass

171.1507

Monoisotopic Mass

171.0531578

IUPAC Name

Not Available

Traditional Name

Not Available

CAS Registry Number

Not Available

SMILES

Not Available

InChI Identifier

InChI=1S/C7H9NO4/c9-6(10)4-2-1-3-5(8-4)7(11)12/h4H,1-3H2,(H,9,10)(H,11,12)/t4-/m0/s1

InChI Key

CXMBCXQHOXUCEO-BYPYZUCNSA-N

Chemical Taxonomy

Functional Ontology

Not Available

Physical Properties

State

Solid

Predicted Properties

Not Available

Spectra

Not Available

Biological Properties

Cellular Locations

Not Available

Biospecimen Locations

Feces

Tissue Locations

Not Available

Associated OMIM IDs

114500 (Colorectal cancer)
610247 (Eosinophilic esophagitis)

Human Proteins and Enzymes

Protein ID	Protein Name	Protein Type	Uniprot ID	Species

Human Pathways

Pathways

Name	SMPDB/PathBank

Metabolic Reactions

Reactions

Reaction ID	Precursor	Product	Enzyme	Data Source	Reference
MMDBr0006985	LL-2,6-Diaminoheptanedioate	L-Glutamic acid	Not Available	VMH	30371894
MMDBr0006986	2,3-Dihydrodipicolinate	2,3,4,5-Tetrahydrodipicolinate	Not Available	VMH	30371894
MMDBr0007307	2,3-Dihydrodipicolinate	2,3,4,5-Tetrahydrodipicolinate	Not Available	VMH	30371894
MMDBr0007575	Succinyl-CoA	N-Succinyl-2-L-amino-6-oxoheptanedioate	Not Available	VMH	30371894
MMDBr0008087	2,3,4,5-Tetrahydrodipicolinate	N_Acetyl_L_2_amino_6_oxopimelate	Not Available	VMH	30371894
MMDBr0008516	L-Glutamic acid	LL-2,6-Diaminoheptanedioate	Not Available	VMH	30371894
MMDBr0011006	2,3,4,5-Tetrahydrodipicolinate	Meso-2,6-Diaminoheptanedioate	Not Available	VMH	30371894

Health Effects and Bioactivity

Health Outcome/Bioactivity	Metabolite Response/Effect	Evidence Type	Host and Biospecimen	Data Source	Reference

Microbial Sources

Superkingdom/Kingdom	Phylum	Total species	Hosts and Body Sites	Microbial Links
Bacteria	Firmicutes	370	Human feces; Human pleural fluid plaque; Pig ; Human ; Human supragingival plaque; Human saliva; Cattle ; Human stool; Human subgingival plaque	Metabolic reconstruction
Bacteria	Proteobacteria	177	Human ; Human feces; Human sputum; Human unknown; Pig ; Human pleural fluid plaque; Human stool; Human dental plaque; Human nasal swab; Human feces; pleural fluid plaque; bal	Metabolic reconstruction
Bacteria	Actinobacteria	124	Human feces; Human sputum; Human pleural fluid plaque; Human dental plaque; Human ; Human nasopharyngeal swab; Human supragingival plaque; Human mucosa; Human subgingival plaque	Metabolic reconstruction
Bacteria	Verrucomicrobia	1	Human ; Human feces	Metabolic reconstruction
Bacteria	Bacteroidetes	129	Human feces; Human appendix biopsy; Human ; Human stool; Human urine; Human gastric fluid; Human saliva; Human subgingival plaque; Human supragingival plaque	Metabolic reconstruction
Archaea	Thaumarchaeota	1		Metabolic reconstruction
Bacteria	Fusobacteria	14	Human feces; Human	Metabolic reconstruction
Bacteria	Synergistetes	4	Human feces	Metabolic reconstruction
Archaea	Euryarchaeota	5		Metabolic reconstruction
Bacteria	Planctomycetes	1	Human feces	Metabolic reconstruction
Archaea	Crenarchaeota	1		Metabolic reconstruction
Bacteria	Tenericutes	2	Human feces	Metabolic reconstruction
Eukaryota/Fungi	Ascomycota	1		Metabolic reconstruction
Bacteria	Spirochaetes	1	Human feces	Metabolic reconstruction

Exposure Sources

Source Type	Activity	Data Source	Reference

Host Biospecimen and Location

Host and Biospecimen	Status	Mean	Std	Min	Max	Units	Age	Sex	Health Condition	Data Source	Reference
Human Feces	Detected but not Quantified									HMDB

External Links

Not Available

References

Synthesis Reference

Not Available

General References

Noronha A, Modamio J, Jarosz Y, Guerard E, Sompairac N, Preciat G, Danielsdottir AD, Krecke M, Merten D, Haraldsdottir HS, Heinken A, Heirendt L, Magnusdottir S, Ravcheev DA, Sahoo S, Gawron P, Friscioni L, Garcia B, Prendergast M, Puente A, Rodrigues M, Roy A, Rouquaya M, Wiltgen L, Zagare A, John E, Krueger M, Kuperstein I, Zinovyev A, Schneider R, Fleming RMT, Thiele I: The Virtual Metabolic Human database: integrating human and gut microbiome metabolism with nutrition and disease. Nucleic Acids Res. 2019 Jan 8;47(D1):D614-D624. doi: 10.1093/nar/gky992. [PubMed:30371894 ]

Showing metabocard for 2,3,4,5-Tetrahydrodipicolinate (MMDBc0049956)

MOL for #<Metabolite:0x00007f537e319d58>

3D MOL for #<Metabolite:0x00007f537e319d58>

3D SDF for #<Metabolite:0x00007f537e319d58>

3D-SDF for #<Metabolite:0x00007f537e319d58>

PDB for #<Metabolite:0x00007f537e319d58>

3D PDB for #<Metabolite:0x00007f537e319d58>

SMILES for #<Metabolite:0x00007f537e319d58>

INCHI for #<Metabolite:0x00007f537e319d58>

Structure for #<Metabolite:0x00007f537e319d58>

3D Structure for #<Metabolite:0x00007f537e319d58>