Summary: Phytanoyl-CoA dioxygenase (PhyH)
Phytanoyl-CoA dioxygenase (PhyH) Provide feedback
This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins, ectoine hydroxylases and a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalysing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterised by the accumulation of phytanic acid in plasma and tissues .
Jansen GA, Hogenhout EM, Ferdinandusse S, Waterham HR, Ofman R, Jakobs C, Skjeldal OH, Wanders RJ; , Hum Mol Genet 2000;9:1195-1200.: Human phytanoyl-CoA hydroxylase: resolution of the gene structure and the molecular basis of Refsum's disease. PUBMED:10767344 EPMC:10767344
Prabhu J, Schauwecker F, Grammel N, Keller U, Bernhard M; , Appl Environ Microbiol. 2004;70:3130-3132.: Functional expression of the ectoine hydroxylase gene (thpD) from Streptomyces chrysomallus in Halomonas elongata. PUBMED:15128576 EPMC:15128576
Internal database links
|SCOOP:||2OG-FeII_Oxy_3 2OG-FeII_Oxy_5 DUF1479|
This tab holds annotation information from the InterPro database.
InterPro entry IPR008775This family is made up of several eukaryotic phytanoyl-CoA dioxygenase (PhyH) proteins as well as a number of bacterial deoxygenases. PhyH is a peroxisomal enzyme catalysing the first step of phytanic acid alpha-oxidation. PhyH deficiency causes Refsum's disease (RD) which is an inherited neurological syndrome biochemically characterised by the accumulation of phytanic acid in plasma and tissues [PUBMED:10767344].
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This clan represents the conserved barrel domain of the 'cupin' superfamily  ('cupa' is the Latin term for a small barrel). The cupin fold is found in a wide variety of enzymes, but notably contains the non-enzymatic seed storage proteins also.
The clan contains the following 61 members:2OG-Fe_Oxy_2 2OG-FeII_Oxy 2OG-FeII_Oxy_2 2OG-FeII_Oxy_3 2OG-FeII_Oxy_4 2OG-FeII_Oxy_5 3-HAO AIM24 AraC_binding AraC_binding_2 AraC_N ARD Asp_Arg_Hydrox Auxin_BP CDO_I CENP-C_C cNMP_binding CsiD Cupin_1 Cupin_2 Cupin_3 Cupin_4 Cupin_5 Cupin_6 Cupin_7 Cupin_8 DIOX_N DMSP_lyase dTDP_sugar_isom DUF1255 DUF1479 DUF1971 DUF386 DUF4437 DUF4867 Ectoine_synth EutQ FdtA FTO_NTD GPI HgmA HutD JmjC JmjN KduI Lyx_isomer MannoseP_isomer Ofd1_CTDD Oxygenase-NA PCO_ADO PhyH Pirin Pirin_C PMI_typeI Popeye Pox_C4_C10 TauD Tet_JBP Ureidogly_lyase VIT VIT_2
We make a range of alignments for each Pfam-A family:
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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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Curation and family details
|Seed source:||Pfam-B_5670 (release 8.0)|
|Number in seed:||39|
|Number in full:||7031|
|Average length of the domain:||206.40 aa|
|Average identity of full alignment:||15 %|
|Average coverage of the sequence by the domain:||65.51 %|
|HMM build commands:||
build method: hmmbuild -o /dev/null HMM SEED
search method: hmmsearch -Z 26740544 -E 1000 --cpu 4 HMM pfamseq
|Family (HMM) version:||12|
|Download:||download the raw HMM for this family|
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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 PhyH domain has been found. There are 102 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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