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42  structures 4176  species 0  interactions 5473  sequences 52  architectures

Family: Sacchrp_dh_C (PF16653)

Summary: Saccharopine dehydrogenase C-terminal domain

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This is the Wikipedia entry entitled "Saccharopine dehydrogenase". More...

Saccharopine dehydrogenase Edit Wikipedia article

Saccharopine Dehydrogenase
PDB 1e5l EBI.jpg
Saccharopine dehydrogenase from Magnaporthe grisea
Identifiers
Symbol Saccharop_dh
Pfam PF03435
Pfam clan CL0063
InterPro IPR005097
SCOP 1ff9
SUPERFAMILY 1ff9
saccharopine dehydrogenase (putative)
Identifiers
Symbol SCCPDH
Entrez 51097
HUGO 24275
RefSeq NM_016002
UniProt Q8NBX0
Other data
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 1.5.1.7, EC 1.5.1.8, EC 1.5.1.9, and EC 1.5.1.10. 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.

Function

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:[1]

SDH

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.[2] In some organisms this enzyme is found as a bifunctional polypeptide with lysine ketoglutarate reductase (PF).

Homospermidine synthase proteins (EC). Homospermidine synthase (HSS) catalyses the synthesis of the polyamine homospermidine from 2 mol putrescine in an NAD+-dependent reaction.[3]

Structure

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).[4]

Clinical significance

Deficiencies are associated with hyperlysinemia.

References

  1. ^ 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. 
  2. ^ 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. 
  3. ^ 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. 
  4. ^ 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 page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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.

Literature references

  1. 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

  2. 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].

Domain organisation

Below is a listing of the unique domain organisations or architectures in which this domain is found. More...

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Pfam Clan

This family is a member of clan GADPH_aa-bio_dh (CL0139), which has the following description:

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

Alignments

We store a range of different sequence alignments for families. As well as the seed alignment from which the family is built, we provide the full alignment, generated by searching the sequence database (reference proteomes) using the family HMM. We also generate alignments using four representative proteomes (RP) sets, the UniProtKB sequence database, the NCBI sequence database, and our metagenomics sequence database. More...

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We make a range of alignments for each Pfam-A family. You can see a description of each above. You can view these alignments in various ways but please note that some types of alignment are never generated while others may not be available for all families, most commonly because the alignments are too large to handle.

  Seed
(375)
Full
(5473)
Representative proteomes UniProt
(13611)
NCBI
(16661)
Meta
(886)
RP15
(1421)
RP35
(3528)
RP55
(5275)
RP75
(7236)
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PP/heatmap 1                

1Cannot generate PP/Heatmap alignments for seeds; no PP data available

Key: ✓ available, x not generated, not available.

Format an alignment

  Seed
(375)
Full
(5473)
Representative proteomes UniProt
(13611)
NCBI
(16661)
Meta
(886)
RP15
(1421)
RP35
(3528)
RP55
(5275)
RP75
(7236)
Alignment:
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Order:
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We make all of our alignments available in Stockholm format. You can download them here as raw, plain text files or as gzip-compressed files.

  Seed
(375)
Full
(5473)
Representative proteomes UniProt
(13611)
NCBI
(16661)
Meta
(886)
RP15
(1421)
RP35
(3528)
RP55
(5275)
RP75
(7236)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped Download   Download   Download   Download   Download   Download   Download   Download   Download  

You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

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HMM logos is one way of visualising profile HMMs. Logos provide a quick overview of the properties of an HMM in a graphical form. You can see a more detailed description of HMM logos and find out how you can interpret them here. More...

Trees

This page displays the phylogenetic tree for this family's seed alignment. We use FastTree to calculate neighbour join trees with a local bootstrap based on 100 resamples (shown next to the tree nodes). FastTree calculates approximately-maximum-likelihood phylogenetic trees from our seed alignment.

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Curation and family details

This section shows the detailed information about the Pfam family. You can see the definitions of many of the terms in this section in the glossary and a fuller explanation of the scoring system that we use in the scores section of the help pages.

Curation View help on the curation process

Seed source: PDB:1FF9_A
Previous IDs: none
Type: Domain
Sequence Ontology: SO:0000417
Author: Punta M
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 information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 45638612 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 31.0 31.0
Trusted cut-off 31.1 31.1
Noise cut-off 30.9 30.9
Model length: 265
Family (HMM) version: 5
Download: download the raw HMM for this family

Species distribution

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Structures

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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