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Conserved domains on  [gi|937935864|dbj|BAT10778|]
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Os10g0406600 [Oryza sativa Japonica Group]

Protein Classification

LYR motif-containing protein( domain architecture ID 1563021)

LYR motif-containing protein may play a key role in the assembly and function of complexes I, II, and III; LYR motifs are molecular signatures of specific recipient Fe-S proteins or accessory factors that assist Fe-S cluster delivery; similar to Caenorhabditis elegans protein FMC1 homolog

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Complex1_LYR_SF super family cl40429
LYR (leucine-tyrosine-arginine) motif found in Complex1_LYR-like superfamily; The ...
 9-77 2.00e-13

LYR (leucine-tyrosine-arginine) motif found in Complex1_LYR-like superfamily; The Complex1_LYR-like superfamily consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N-terminus. The human genome has at least ten LYR proteins that were predominantly identified as mitochondrial proteins. Some family members were also found in the cytosol or nucleus. LYR motif-containing protein 4 (LYRM4) represents the only LYR protein that is directly involved in the first steps of Fe-S cluster generation. Other LYR proteins have been identified as accessory subunits or assembly factors of mitochondrial OXPHOS (oxidative phosphorylation) complexes I, II, III and V, and they play specific roles in acetate metabolism.


The actual alignment was detected with superfamily member cd20264:

Pssm-ID: 477356  Cd Length: 69  Bit Score: 59.07  E-value: 2.00e-13
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 937935864  9 EALSLFRSLLRTARQFSDYNIREYARRRAADAFRENRALGDAVAAAAVFADGKKQLEVAKRQAVVYSLY 77
Cdd:cd20264   1 QVLSLYRALLREARKFPDYNFREYFLRRIRDAFRENKNLKDPEEIKKLYEEGEEQLEVLKRQAIINQMY 69
 
Name Accession Description Interval E-value
Complex1_LYR_LYRM4 cd20264
LYR (leucine-tyrosine-arginine) motif found in LYR motif-containing protein 4 (LYRM4) and ...
 9-77 2.00e-13

LYR (leucine-tyrosine-arginine) motif found in LYR motif-containing protein 4 (LYRM4) and similar proteins; LYRM4, also called ISD11, is a eukaryote-specific component of the mitochondrial biogenesis of Fe-S clusters which are essential cofactors in multiple processes, including oxidative phosphorylation. It is required for nuclear and mitochondrial iron-sulfur protein biosynthesis by forming a complex with, and stabilizing, the sulfur donor NFS1. LYRM4 belongs to the Complex1_LYR-like superfamily that consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N-terminus.


Pssm-ID: 380759  Cd Length: 69  Bit Score: 59.07  E-value: 2.00e-13
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 937935864  9 EALSLFRSLLRTARQFSDYNIREYARRRAADAFRENRALGDAVAAAAVFADGKKQLEVAKRQAVVYSLY 77
Cdd:cd20264   1 QVLSLYRALLREARKFPDYNFREYFLRRIRDAFRENKNLKDPEEIKKLYEEGEEQLEVLKRQAIINQMY 69
Complex1_LYR pfam05347
Complex 1 protein (LYR family); Proteins in this family include an accessory subunit of the ...
 8-32 1.86e-04

Complex 1 protein (LYR family); Proteins in this family include an accessory subunit of the higher eukaryotic NADH dehydrogenase complex. In Saccharomyces cerevisiae, the Isd11 protein has been shown to play a role in Fe/S cluster biogenesis in mitochondria. We have named this family LYR after a highly conserved tripeptide motif close to the N-terminus of these proteins.


Pssm-ID: 428432  Cd Length: 59  Bit Score: 36.02  E-value: 1.86e-04
                         10        20
                 ....*....|....*....|....*
gi 937935864   8 AEALSLFRSLLRTARQFSDYNIREY 32
Cdd:pfam05347  1 RQVLSLYRALLRAARKFPDYNFREY 25
 
Name Accession Description Interval E-value
Complex1_LYR_LYRM4 cd20264
LYR (leucine-tyrosine-arginine) motif found in LYR motif-containing protein 4 (LYRM4) and ...
 9-77 2.00e-13

LYR (leucine-tyrosine-arginine) motif found in LYR motif-containing protein 4 (LYRM4) and similar proteins; LYRM4, also called ISD11, is a eukaryote-specific component of the mitochondrial biogenesis of Fe-S clusters which are essential cofactors in multiple processes, including oxidative phosphorylation. It is required for nuclear and mitochondrial iron-sulfur protein biosynthesis by forming a complex with, and stabilizing, the sulfur donor NFS1. LYRM4 belongs to the Complex1_LYR-like superfamily that consists of proteins of diverse functions that are exclusively found in eukaryotes and contain the conserved tripeptide 'LYR' close to the N-terminus.


Pssm-ID: 380759  Cd Length: 69  Bit Score: 59.07  E-value: 2.00e-13
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 937935864  9 EALSLFRSLLRTARQFSDYNIREYARRRAADAFRENRALGDAVAAAAVFADGKKQLEVAKRQAVVYSLY 77
Cdd:cd20264   1 QVLSLYRALLREARKFPDYNFREYFLRRIRDAFRENKNLKDPEEIKKLYEEGEEQLEVLKRQAIINQMY 69
Complex1_LYR pfam05347
Complex 1 protein (LYR family); Proteins in this family include an accessory subunit of the ...
 8-32 1.86e-04

Complex 1 protein (LYR family); Proteins in this family include an accessory subunit of the higher eukaryotic NADH dehydrogenase complex. In Saccharomyces cerevisiae, the Isd11 protein has been shown to play a role in Fe/S cluster biogenesis in mitochondria. We have named this family LYR after a highly conserved tripeptide motif close to the N-terminus of these proteins.


Pssm-ID: 428432  Cd Length: 59  Bit Score: 36.02  E-value: 1.86e-04
                         10        20
                 ....*....|....*....|....*
gi 937935864   8 AEALSLFRSLLRTARQFSDYNIREY 32
Cdd:pfam05347  1 RQVLSLYRALLRAARKFPDYNFREY 25
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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