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221  structures 3999  species 2  interactions 6466  sequences 23  architectures

Family: ELFV_dehydrog (PF00208)

Summary: Glutamate/Leucine/Phenylalanine/Valine dehydrogenase

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

ELFV dehydrogenase Edit Wikipedia article

Glutamate/Leucine/Phenylalanine/Valine dehydrogenase
PDB 1b3b EBI.jpg
thermotoga maritima glutamate dehydrogenase mutant n97d, g376k
Identifiers
Symbol ELFV_dehydrog
Pfam PF00208
Pfam clan CL0063
InterPro IPR006096
PROSITE PDOC00071
SCOP 1leh
SUPERFAMILY 1leh
Glu/Leu/Phe/Val dehydrogenase, dimerisation domain
Identifiers
Symbol ELFV_dehydrog_N
Pfam PF02812
SCOP 1leh
SUPERFAMILY 1leh

In molecular biology, the ELFV dehydrogenase family of enzymes include glutamate, leucine, phenylalanine and valine dehydrogenases. These enzymes are structurally and functionally related. They contain a Gly-rich region containing a conserved Lys residue, which has been implicated in the catalytic activity, in each case a reversible oxidative deamination reaction.

Glutamate dehydrogenases EC 1.4.1.2, EC 1.4.1.3 and EC 1.4.1.4 (GluDH) are enzymes that catalyse the NAD- and/or NADP-dependent reversible deamination of L-glutamate into alpha-ketoglutarate.[1][2] GluDH isozymes are generally involved with either ammonia assimilation or glutamate catabolism. Two separate enzymes are present in yeasts: the NADP-dependent enzyme, which catalyses the amination of alpha-ketoglutarate to L-glutamate; and the NAD-dependent enzyme, which catalyses the reverse reaction [3] - this form links the L-amino acids with the Krebs cycle, which provides a major pathway for metabolic interconversion of alpha-amino acids and alpha-keto acids.[4]

Leucine dehydrogenase EC 1.4.1.9 (LeuDH) is a NAD-dependent enzyme that catalyses the reversible deamination of leucine and several other aliphatic amino acids to their keto analogues.[5] Each subunit of this octameric enzyme from Bacillus sphaericus contains 364 amino acids and folds into two domains, separated by a deep cleft. The nicotinamide ring of the NAD+ cofactor binds deep in this cleft, which is thought to close during the hydride transfer step of the catalytic cycle.

Phenylalanine dehydrogenase EC 1.4.1.20 (PheDH) is an NAD-dependent enzyme that catalyses the reversible deamidation of L-phenylalanine into phenyl-pyruvate.[6]

Valine dehydrogenase EC 1.4.1.8 (ValDH) is an NADP-dependent enzyme that catalyses the reversible deamidation of L-valine into 3-methyl-2-oxobutanoate.[7]

These enzymes contain two domains, an N-terminal dimerisation domain, and a C-terminal domain.[8]

References[edit]

  1. ^ Britton KL, Baker PJ, Rice DW, Stillman TJ (November 1992). "Structural relationship between the hexameric and tetrameric family of glutamate dehydrogenases". Eur. J. Biochem. 209 (3): 851–9. doi:10.1111/j.1432-1033.1992.tb17357.x. PMID 1358610. 
  2. ^ Benachenhou-Lahfa N, Forterre P, Labedan B (April 1993). "Evolution of glutamate dehydrogenase genes: evidence for two paralogous protein families and unusual branching patterns of the archaebacteria in the universal tree of life". J. Mol. Evol. 36 (4): 335–46. PMID 8315654. 
  3. ^ Moye WS, Amuro N, Rao JK, Zalkin H (July 1985). "Nucleotide sequence of yeast GDH1 encoding nicotinamide adenine dinucleotide phosphate-dependent glutamate dehydrogenase". J. Biol. Chem. 260 (14): 8502–8. PMID 2989290. 
  4. ^ Mavrothalassitis G, Tzimagiorgis G, Mitsialis A, Zannis V, Plaitakis A, Papamatheakis J, Moschonas N (May 1988). "Isolation and characterization of cDNA clones encoding human liver glutamate dehydrogenase: evidence for a small gene family". Proc. Natl. Acad. Sci. U.S.A. 85 (10): 3494–8. doi:10.1073/pnas.85.10.3494. PMC 280238. PMID 3368458. 
  5. ^ Nagata S, Tanizawa K, Esaki N, Sakamoto Y, Ohshima T, Tanaka H, Soda K (December 1988). "Gene cloning and sequence determination of leucine dehydrogenase from Bacillus stearothermophilus and structural comparison with other NAD(P)+-dependent dehydrogenases". Biochemistry 27 (25): 9056–62. doi:10.1021/bi00425a026. PMID 3069133. 
  6. ^ Takada H, Yoshimura T, Ohshima T, Esaki N, Soda K (March 1991). "Thermostable phenylalanine dehydrogenase of Thermoactinomyces intermedius: cloning, expression, and sequencing of its gene". J. Biochem. 109 (3): 371–6. PMID 1880121. 
  7. ^ Tang L, Hutchinson CR (July 1993). "Sequence, transcriptional, and functional analyses of the valine (branched-chain amino acid) dehydrogenase gene of Streptomyces coelicolor". J. Bacteriol. 175 (13): 4176–85. PMC 204847. PMID 8320231. 
  8. ^ Baker, P. J.; Turnbull, A. P.; Sedelnikova, S. E.; Stillman, T. J.; Rice, D. W. (1995). "A role for quaternary structure in the substrate specificity of leucine dehydrogenase". Structure (London, England : 1993) 3 (7): 693–705. doi:10.1016/S0969-2126(01)00204-0. PMID 8591046.  edit

This article incorporates text from the public domain Pfam and InterPro IPR006096

This page is based on a Wikipedia article. The text is available under the Creative Commons Attribution/Share-Alike License.

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Glutamate/Leucine/Phenylalanine/Valine dehydrogenase Provide feedback

No Pfam abstract.

Literature references

  1. Baker PJ, Turnbull AP, Sedelnikova SE, Stillman TJ, Rice DW; , Structure 1995;3:693-705.: A role for quaternary structure in the substrate specificity of leucine dehydrogenase. PUBMED:8591046 EPMC:8591046


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006096

Glutamate, leucine, phenylalanine and valine dehydrogenases are structurally and functionally related. They contain a Gly-rich region containing a conserved Lys residue, which has been implicated in the catalytic activity, in each case a reversible oxidative deamination reaction.

Glutamate dehydrogenases (EC, EC, and EC) (GluDH) are enzymes that catalyse the NAD- and/or NADP-dependent reversible deamination of L-glutamate into alpha-ketoglutarate [PUBMED:1358610, PUBMED:8315654]. GluDH isozymes are generally involved with either ammonia assimilation or glutamate catabolism. Two separate enzymes are present in yeasts: the NADP-dependent enzyme, which catalyses the amination of alpha-ketoglutarate to L-glutamate; and the NAD-dependent enzyme, which catalyses the reverse reaction [PUBMED:2989290] - this form links the L-amino acids with the Krebs cycle, which provides a major pathway for metabolic interconversion of alpha-amino acids and alpha- keto acids [PUBMED:3368458].

Leucine dehydrogenase (EC) (LeuDH) is a NAD-dependent enzyme that catalyses the reversible deamination of leucine and several other aliphatic amino acids to their keto analogues [PUBMED:3069133]. Each subunit of this octameric enzyme from Bacillus sphaericus contains 364 amino acids and folds into two domains, separated by a deep cleft. The nicotinamide ring of the NAD+ cofactor binds deep in this cleft, which is thought to close during the hydride transfer step of the catalytic cycle.

Phenylalanine dehydrogenase (EC) (PheDH) is na NAD-dependent enzyme that catalyses the reversible deamidation of L-phenylalanine into phenyl-pyruvate [PUBMED:1880121].

Valine dehydrogenase (EC) (ValDH) is an NADP-dependent enzyme that catalyses the reversible deamidation of L-valine into 3-methyl-2-oxobutanoate [PUBMED:8320231].

This entry represents the C-terminal domain of these proteins.

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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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
(124)
Full
(6466)
Representative proteomes NCBI
(5816)
Meta
(1828)
RP15
(635)
RP35
(1175)
RP55
(1539)
RP75
(1773)
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  Seed
(124)
Full
(6466)
Representative proteomes NCBI
(5816)
Meta
(1828)
RP15
(635)
RP35
(1175)
RP55
(1539)
RP75
(1773)
Alignment:
Format:
Order:
Sequence:
Gaps:
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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
(124)
Full
(6466)
Representative proteomes NCBI
(5816)
Meta
(1828)
RP15
(635)
RP35
(1175)
RP55
(1539)
RP75
(1773)
Raw Stockholm Download   Download   Download   Download   Download   Download   Download   Download  
Gzipped 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.

External links

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HMM logo

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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: Prosite
Previous IDs: E_L_F_V_dh; GLFV_dehydrog;
Type: Domain
Author: Finn RD
Number in seed: 124
Number in full: 6466
Average length of the domain: 223.60 aa
Average identity of full alignment: 33 %
Average coverage of the sequence by the domain: 52.44 %

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 21.3 21.3
Trusted cut-off 21.3 21.3
Noise cut-off 21.2 21.2
Model length: 244
Family (HMM) version: 16
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 2 interactions for this family. More...

ELFV_dehydrog_N ELFV_dehydrog

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 ELFV_dehydrog domain has been found. There are 221 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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