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179  structures 4663  species 8  interactions 27418  sequences 195  architectures

Family: DAO (PF01266)

Summary: FAD dependent oxidoreductase

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This is the Wikipedia entry entitled "FAD dependent oxidoreductase family". More...

FAD dependent oxidoreductase family Edit Wikipedia article

FAD dependent oxidoreductase
PDB 1c0i EBI.jpg
crystal structure of d-amino acid oxidase in complex with two anthranylate molecules
Identifiers
Symbol DAO
Pfam PF01266
Pfam clan CL0063
InterPro IPR006076
PROSITE PDOC00753
SCOP 1kif
SUPERFAMILY 1kif

In molecular biology, the FAD dependent oxidoreductase family of proteins is a family of FAD dependent oxidoreductases. Members of this family include Glycerol-3-phosphate dehydrogenase EC 1.1.99.5, Sarcosine oxidase beta subunit EC 1.5.3.1, D-amino-acid dehydrogenase EC 1.4.99.1, D-aspartate oxidase EC 1.4.3.1. D-amino acid oxidase EC 1.4.3.3 (DAMOX or DAO) is an FAD flavoenzyme that catalyses the oxidation of neutral and basic D-amino acids into their corresponding keto acids. DAOs have been characterised and sequenced in fungi and vertebrates where they are known to be located in the peroxisomes. D-aspartate oxidase EC 1.4.3.1 (DASOX) [1] is an enzyme, structurally related to DAO, which catalyses the same reaction but is active only toward dicarboxylic D-amino acids. In DAO, a conserved histidine has been shown [2] to be important for the enzyme's catalytic activity.

References[edit]

  1. ^ Negri A, Ceciliani F, Tedeschi G, Simonic T, Ronchi S (June 1992). "The primary structure of the flavoprotein D-aspartate oxidase from beef kidney". J. Biol. Chem. 267 (17): 11865–71. PMID 1601857. 
  2. ^ Miyano M, Fukui K, Watanabe F, Takahashi S, Tada M, Kanashiro M, Miyake Y (January 1991). "Studies on Phe-228 and Leu-307 recombinant mutants of porcine kidney D-amino acid oxidase: expression, purification, and characterization". J. Biochem. 109 (1): 171–7. PMID 1673125. 

This article incorporates text from the public domain Pfam and InterPro IPR006076

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.

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This family includes various FAD dependent oxidoreductases: Glycerol-3-phosphate dehydrogenase EC:1.1.99.5, Sarcosine oxidase beta subunit EC:1.5.3.1, D-alanine oxidase EC:1.4.99.1, D-aspartate oxidase EC:1.4.3.1.

Literature references

  1. Todone F, Vanoni MA, Mozzarelli A, Bolognesi M, Coda A, Curti B, Mattevi A; , Biochemistry 1997;36:5853-5860.: Active site plasticity in D-amino acid oxidase: a crystallographic analysis. PUBMED:9153426 EPMC:9153426


Internal database links

External database links

This tab holds annotation information from the InterPro database.

InterPro entry IPR006076

This entry includes various FAD dependent oxidoreductases: Glycerol-3-phosphate dehydrogenase (EC), Sarcosine oxidase beta subunit (EC), D-alanine oxidase (EC), D-aspartate oxidase (EC).

D-amino acid oxidase (EC) (DAMOX or DAO) is an FAD flavoenzyme that catalyzes the oxidation of neutral and basic D-amino acids into their corresponding keto acids. DAOs have been characterised and sequenced in fungi and vertebrates where they are known to be located in the peroxisomes. D-aspartate oxidase (EC) (DASOX) [PUBMED:1601857] is an enzyme, structurally related to DAO, which catalyzes the same reaction but is active only toward dicarboxylic D-amino acids. In DAO, a conserved histidine has been shown [PUBMED:1673125] to be important for the enzyme's catalytic activity.

Gene Ontology

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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

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 using the family HMM. We also generate alignments using four representative proteomes (RP) sets, 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
(530)
Full
(27418)
Representative proteomes NCBI
(47340)
Meta
(28561)
RP15
(2308)
RP35
(4853)
RP55
(6950)
RP75
(8594)
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  Seed
(530)
Full
(27418)
Representative proteomes NCBI
(47340)
Meta
(28561)
RP15
(2308)
RP35
(4853)
RP55
(6950)
RP75
(8594)
Alignment:
Format:
Order:
Sequence:
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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
(530)
Full
(27418)
Representative proteomes NCBI
(47340)
Meta
(28561)
RP15
(2308)
RP35
(4853)
RP55
(6950)
RP75
(8594)
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

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.

HMM logo

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.

Note: You can also download the data file for the tree.

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: none
Type: Domain
Author: Finn RD, Bateman A
Number in seed: 530
Number in full: 27418
Average length of the domain: 332.00 aa
Average identity of full alignment: 16 %
Average coverage of the sequence by the domain: 72.99 %

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 24.7 24.7
Trusted cut-off 24.7 24.7
Noise cut-off 24.6 24.6
Model length: 358
Family (HMM) version: 19
Download: download the raw HMM for this family

Species distribution

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Interactions

There are 8 interactions for this family. More...

GCV_T SoxD GLF Fer2_BFD DAO GCV_T_C Pyr_redox_2 Succ_DH_flav_C

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 DAO domain has been found. There are 179 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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