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17  structures 2288  species 1  interaction 3742  sequences 32  architectures

Family: Saccharop_dh (PF03435)

Summary: Saccharopine dehydrogenase

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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 organsims 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]

Pathology

Deficiencies are associated with hyperlysinemia.

External links

  1. ^ Kumar VP, West AH, Cook PF (2012). "Supporting role of lysine 13 and glutamate 16 in the acid-base mechanism of saccharopine dehydrogenase from Saccharomyces cerevisiae.". Arch Biochem Biophys 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". Eur. J. Biochem. 240 (2): 373–9. doi:10.1111/j.1432-1033.1996.0373h.x. PMID 8841401. 
  4. ^ Andi B, Xu H, Cook PF, West AH (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 Provide feedback

This family comprised of three structural domains that can not be separated in the linear sequence. 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. 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

  2. Azevedo RA, Lea PJ; , Amino Acids 2001;20:261-279.: Lysine metabolism in higher plants. PUBMED:11354603 EPMC:11354603


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR005097

This entry represents saccharopine dehydrogenase and homospermidine synthase.

Saccharopine dehydrogenase (EC) catalyses the condensation of l-alpha-aminoadipate-delta-semialdehyde (AASA) with l-glutamate to give an imine, which is reduced by NADPH to give saccharopine [PUBMED:19449898]. In some organisms this enzyme is found as a bifunctional polypeptide with lysine ketoglutarate reductase (PF). Saccharopine dehydrogenase can also function as a saccharopine reductase. Saccharopine is an intermediate in lysine metabolism.

Homospermidine synthase (HSS) (EC) catalyses the synthesis of the polyamine homospermidine from 2 putrescine molecules in an NAD+-dependent reaction [PUBMED:8841401]. HSS evolved from the alternative spermidine biosynthetic pathway enzyme carboxyspermidine dehydrogenase [PUBMED:19196710, PUBMED:20194510] and the structure of HSS is related to lysine metabolic enzymes [PUBMED:20194510].

Gene Ontology

The mapping between Pfam and Gene Ontology is provided by InterPro. If you use this data please cite InterPro.

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 NADP_Rossmann (CL0063), which has the following description:

A class of redox enzymes are two domain proteins. One domain, termed the catalytic domain, confers substrate specificity and the precise reaction of the enzyme. The other domain, which is common to this class of redox enzymes, is a Rossmann-fold domain. The Rossmann domain binds nicotinamide adenine dinucleotide (NAD+) and it is this cofactor that reversibly accepts a hydride ion, which is lost or gained by the substrate in the redox reaction. Rossmann domains have an alpha/beta fold, which has a central beta sheet, with approximately five alpha helices found surrounding the beta sheet.The strands forming the beta sheet are found in the following characteristic order 654123. The inter sheet crossover of the stands in the sheet form the NAD+ binding site [1]. In some more distantly relate Rossmann domains the NAD+ cofactor is replaced by the functionally similar cofactor FAD.

The clan contains the following 180 members:

2-Hacid_dh_C 3Beta_HSD 3HCDH_N adh_short adh_short_C2 ADH_zinc_N ADH_zinc_N_2 AdoHcyase_NAD AdoMet_MTase AlaDh_PNT_C Amino_oxidase ApbA AviRa Bac_GDH Bin3 CheR CMAS CmcI CoA_binding CoA_binding_2 CoA_binding_3 Cons_hypoth95 DAO DapB_N DFP DNA_circ_N DNA_methylase DOT1 DREV dTMP_synthase DUF1442 DUF1776 DUF2431 DUF268 DUF3321 DUF43 DUF633 DUF938 DXP_redisom_C DXP_reductoisom Eco57I ELFV_dehydrog Eno-Rase_FAD_bd Eno-Rase_NADH_b Enoyl_reductase Epimerase F420_oxidored FAD_binding_2 FAD_binding_3 FAD_oxidored Fibrillarin FMO-like FmrO FtsJ G-7-MTase G6PD_N GCD14 GDI GFO_IDH_MocA GIDA GidB GLF Glyco_hydro_4 GMC_oxred_N Gp_dh_N GRAS GRDA HI0933_like HIM1 IlvN K_oxygenase KR LCM Ldh_1_N Lycopene_cycl Malic_M Mannitol_dh Met_10 Methyltrans_Mon Methyltrans_SAM Methyltransf_10 Methyltransf_11 Methyltransf_12 Methyltransf_15 Methyltransf_16 Methyltransf_17 Methyltransf_18 Methyltransf_19 Methyltransf_2 Methyltransf_20 Methyltransf_21 Methyltransf_22 Methyltransf_23 Methyltransf_24 Methyltransf_25 Methyltransf_26 Methyltransf_27 Methyltransf_28 Methyltransf_29 Methyltransf_3 Methyltransf_30 Methyltransf_31 Methyltransf_32 Methyltransf_4 Methyltransf_5 Methyltransf_7 Methyltransf_8 Methyltransf_9 Methyltransf_PK MethyltransfD12 MetW Mg-por_mtran_C Mqo MT-A70 MTS Mur_ligase N2227 N6-adenineMlase N6_Mtase N6_N4_Mtase NAD_binding_10 NAD_binding_11 NAD_binding_2 NAD_binding_3 NAD_binding_4 NAD_binding_5 NAD_binding_7 NAD_binding_8 NAD_binding_9 NAD_Gly3P_dh_N NAS NmrA NNMT_PNMT_TEMT NodS Nol1_Nop2_Fmu Nol1_Nop2_Fmu_2 NSP13 OCD_Mu_crystall PARP_regulatory PCMT PDH Polysacc_synt_2 Pox_MCEL Prenylcys_lyase PrmA PRMT5 Pyr_redox Pyr_redox_2 Pyr_redox_3 RmlD_sub_bind Rossmann-like rRNA_methylase RrnaAD Rsm22 RsmJ Saccharop_dh SAM_MT SE Semialdhyde_dh Shikimate_DH Spermine_synth Strep_67kDa_ant TehB THF_DHG_CYH_C Thi4 ThiF TPMT TrkA_N TRM TRM13 tRNA_U5-meth_tr Trp_halogenase TylF Ubie_methyltran UDPG_MGDP_dh_N UPF0020 UPF0146 V_cholerae_RfbT XdhC_C YjeF_N

Alignments

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  Seed
(82)
Full
(3742)
Representative proteomes NCBI
(4625)
Meta
(2619)
RP15
(431)
RP35
(806)
RP55
(1113)
RP75
(1319)
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  Seed
(82)
Full
(3742)
Representative proteomes NCBI
(4625)
Meta
(2619)
RP15
(431)
RP35
(806)
RP55
(1113)
RP75
(1319)
Alignment:
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  Seed
(82)
Full
(3742)
Representative proteomes NCBI
(4625)
Meta
(2619)
RP15
(431)
RP35
(806)
RP55
(1113)
RP75
(1319)
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You can also download a FASTA format file containing the full-length sequences for all sequences in the full alignment.

External links

MyHits provides a collection of tools to handle multiple sequence alignments. For example, one can refine a seed alignment (sequence addition or removal, re-alignment or manual edition) and then search databases for remote homologs using HMMER3.

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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: Pfam-B_4166 (release 6.6) & Pfam-B_6325 (Release 7.5)
Previous IDs: none
Type: Family
Author: Finn RD
Number in seed: 82
Number in full: 3742
Average length of the domain: 321.10 aa
Average identity of full alignment: 19 %
Average coverage of the sequence by the domain: 76.28 %

HMM information View help on HMM parameters

HMM build commands:
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 23193494 -E 1000 --cpu 4 HMM pfamseq
Model details:
Parameter Sequence Domain
Gathering cut-off 25.1 25.1
Trusted cut-off 25.1 25.1
Noise cut-off 25.0 25.0
Model length: 386
Family (HMM) version: 13
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Species distribution

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Interactions

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Saccharop_dh

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 Saccharop_dh domain has been found. There are 17 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 seqence.

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