Summary: Saccharopine dehydrogenase C-terminal domain
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Saccharopine dehydrogenase Edit Wikipedia article
Saccharopine dehydrogenase from Magnaporthe grisea
|saccharopine dehydrogenase (putative)|
|Locus||Chr. 1 q44|
In molecular biology, the protein domain Saccharopine dehydrogenase (SDH), also named Saccharopine reductase, is an enzyme involved in the metabolism of the amino acid lysine, via an intermediate substance called saccharopine. The Saccharopine dehydrogenase enzyme can be classified under EC 18.104.22.168, EC 22.214.171.124, EC 126.96.36.199, and EC 188.8.131.52. It has an important function in lysine metabolism and catalyses a reaction in the alpha-Aminoadipic acid pathway. This pathway is unique to fungal organisms therefore, this molecule could be useful in the search for new antibiotics. This protein family also includes saccharopine dehydrogenase and homospermidine synthase. It is found in prokaryotes, eukaryotes and archaea.
Simplistically, SDH uses NAD+ as an oxidant to catalyse the reversible pyridine nucleotide dependent oxidative deamination of the substrate, Saccharopine, in order to form the products, lysine and alpha-ketoglutarate. This can be described by the following equation:
Saccharopine ⇌ lysine + alpha-ketoglutarate
Saccharopine dehydrogenase EC catalyses the condensation to of l-alpha-aminoadipate-delta-semialdehyde (AASA) with l-glutamate to give an imine, which is reduced by NADPH to give saccharopine. In some organisms this enzyme is found as a bifunctional polypeptide with lysine ketoglutarate reductase (PF).
There appears to be two protein domains of similar size. One domain is a Rossmann fold that binds NAD+/NADH, and the other is relatively similar. Both domains contain a six-stranded parallel beta-sheet surrounded by alpha-helices and loops (alpha/beta fold).
Deficiencies are associated with hyperlysinemia.
- Kumar VP, West AH, Cook PF (June 2012). "Supporting role of lysine 13 and glutamate 16 in the acid-base mechanism of saccharopine dehydrogenase from Saccharomyces cerevisiae". Archives of Biochemistry and Biophysics. 522 (1): 57–61. doi:10.1016/j.abb.2012.03.027. PMID 22521736.
- Vashishtha AK, West AH, Cook PF (June 2009). "Chemical mechanism of saccharopine reductase from Saccharomyces cerevisiae". Biochemistry. 48 (25): 5899–907. doi:10.1021/bi900599s. PMID 19449898.
- Tholl D, Ober D, Martin W, Kellermann J, Hartmann T (September 1996). "Purification, molecular cloning and expression in Escherichia coli of homospermidine synthase from Rhodopseudomonas viridis". European Journal of Biochemistry. 240 (2): 373–9. doi:10.1111/j.1432-1033.1996.0373h.x. PMID 8841401.
- Andi B, Xu H, Cook PF, West AH (November 2007). "Crystal structures of ligand-bound saccharopine dehydrogenase from Saccharomyces cerevisiae". Biochemistry. 46 (44): 12512–21. doi:10.1021/bi701428m. PMID 17939687.
This tab holds the annotation information that is stored in the Pfam database. As we move to using Wikipedia as our main source of annotation, the contents of this tab will be gradually replaced by the Wikipedia tab.
Saccharopine dehydrogenase C-terminal domain Provide feedback
This family comprises the C-terminal domain of saccharopine dehydrogenase. In some organisms this enzyme is found as a bifunctional polypeptide with lysine ketoglutarate reductase. The saccharopine dehydrogenase can also function as a saccharopine reductase.
Scapin G, Reddy SG, Blanchard JS;, Biochemistry. 1996;35:13540-13551.: Three-dimensional structure of meso-diaminopimelic acid dehydrogenase from Corynebacterium glutamicum. PUBMED:8885833 EPMC:8885833
Johansson E, Steffens JJ, Lindqvist Y, Schneider G; , Structure Fold Des 2000;8:1037-1047.: Crystal structure of saccharopine reductase from Magnaporthe grisea, an enzyme of the alpha-aminoadipate pathway of lysine biosynthesis. PUBMED:11080625 EPMC:11080625
This tab holds annotation information from the InterPro database.
InterPro entry IPR032095
This entry represents the C-terminal domain of saccharopine dehydrogenase and related proteins. In some organisms this enzyme is found as a bifunctional polypeptide with lysine ketoglutarate reductase. The saccharopine dehydrogenase can also function as a saccharopine reductase [PUBMED:8885833, PUBMED:11080625].
Below is a listing of the unique domain organisations or architectures in which this domain is found. More...
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This clan contains the C terminal domains of dehydrogenase enzymes involved in the biosynthesis of arginine, aspartate and aspartate derived amino acids. It also contains the C terminal domain of GAPDH, a dehydrogenase involved in glycolysis and gluconeogenesis.
The clan contains the following 15 members:AcetDehyd-dimer Biliv-reduc_cat DapB_C DAPDH_C DUF108 DXP_redisom_C G6PD_C GFO_IDH_MocA_C Gp_dh_C Homoserine_dh Inos-1-P_synth ox_reductase_C Oxidoreduct_C Sacchrp_dh_C Semialdhyde_dhC
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1Cannot generate PP/Heatmap alignments for seeds; no PP data available
Key: available, not generated, — not available.
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|Number in seed:||375|
|Number in full:||5473|
|Average length of the domain:||267.70 aa|
|Average identity of full alignment:||22 %|
|Average coverage of the sequence by the domain:||56.06 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||5|
|Download:||download the raw HMM for this family|
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Unmapped species names
The tree is built by looking at each sequence in the full alignment for the family. We take the name of the species given by UniProt and try to map that to the full taxonomic tree from NCBI. In some cases, the name chosen by UniProt does not map to any node in the NCBI tree, perhaps because the chosen name is listed as a synonym or a misspelling in the NCBI taxonomy.
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Since we reduce the species tree to only the eight main taxonomic levels, sequences that are mapped to the sub-species level in the tree would not normally be shown. Rather than leave out these species, we map them instead to their parent species. So, for example, for sequences belonging to one of the Vibrio cholerae sub-species in the NCBI taxonomy, we show them instead as belonging to the species Vibrio cholerae.
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The tree shows the occurrence of this domain across different species. More...
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For those sequences which have a structure in the Protein DataBank, we use the mapping between UniProt, PDB and Pfam coordinate systems from the PDBe group, to allow us to map Pfam domains onto UniProt sequences and three-dimensional protein structures. The table below shows the structures on which the Sacchrp_dh_C domain has been found. There are 42 instances of this domain found in the PDB. Note that there may be multiple copies of the domain in a single PDB structure, since many structures contain multiple copies of the same protein sequence.
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