Skip Header

You are using a version of browser that may not display all the features of this website. Please consider upgrading your browser.
Protein

LYR motif-containing protein 4

Gene

LYRM4

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Required for nuclear and mitochondrial iron-sulfur protein biosynthesis.2 Publications

Pathwayi: iron-sulfur cluster biosynthesis

This protein is involved in the pathway iron-sulfur cluster biosynthesis, which is part of Cofactor biosynthesis.
View all proteins of this organism that are known to be involved in the pathway iron-sulfur cluster biosynthesis and in Cofactor biosynthesis.

GO - Biological processi

Complete GO annotation...

Enzyme and pathway databases

ReactomeiR-HSA-1362409. Mitochondrial iron-sulfur cluster biogenesis.
UniPathwayiUPA00266.

Names & Taxonomyi

Protein namesi
Recommended name:
LYR motif-containing protein 4
Gene namesi
Name:LYRM4
Synonyms:C6orf149, ISD11
ORF Names:CGI-203
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 6

Organism-specific databases

HGNCiHGNC:21365. LYRM4.

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Mitochondrion, Nucleus

Pathology & Biotechi

Involvement in diseasei

Combined oxidative phosphorylation deficiency 19 (COXPD19)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA mitochondrial disorder characterized by respiratory distress, hypotonia, and severe lactic acidosis in the newborn period. Other features include gastroesophageal reflux and elevated liver enzymes with normal synthetic function.
See also OMIM:615595
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti68 – 681R → L in COXPD19; can form a normal complex with NFS1 but the desulfurase enzymatic activity of this complex is severely decreased compared to control. 1 Publication
Corresponds to variant rs587777218 [ dbSNP | Ensembl ].
VAR_070943

Keywords - Diseasei

Disease mutation

Organism-specific databases

MalaCardsiLYRM4.
MIMi615595. phenotype.
Orphaneti397593. Severe neonatal lactic acidosis due to NFS1-ISD11 complex deficiency.
PharmGKBiPA162394762.

Polymorphism and mutation databases

BioMutaiLYRM4.
DMDMi46576652.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 9191LYR motif-containing protein 4PRO_0000174308Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei47 – 471N6-succinyllysineBy similarity

Proteomic databases

EPDiQ9HD34.
MaxQBiQ9HD34.
PaxDbiQ9HD34.
PeptideAtlasiQ9HD34.
PRIDEiQ9HD34.
TopDownProteomicsiQ9HD34.

PTM databases

iPTMnetiQ9HD34.
PhosphoSiteiQ9HD34.

Expressioni

Tissue specificityi

Reduced mRNA levels in Friedreich ataxia patients.1 Publication

Gene expression databases

BgeeiQ9HD34.
CleanExiHS_LYRM4.
ExpressionAtlasiQ9HD34. baseline and differential.
GenevisibleiQ9HD34. HS.

Organism-specific databases

HPAiHPA030362.

Interactioni

Subunit structurei

Interacts with FXN. Interaction is increased by nickel. Interaction is inhibited by calcium, magnesium, manganese, copper, cobalt, zinc, and iron. Forms a complex with the cytosolic/nuclear form of NFS1. The complex increased the stability of NFS1.3 Publications

Protein-protein interaction databases

BioGridi121391. 9 interactions.
IntActiQ9HD34. 2 interactions.
STRINGi9606.ENSP00000443900.

Structurei

3D structure databases

ProteinModelPortaliQ9HD34.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the complex I LYR family.Curated

Phylogenomic databases

eggNOGiKOG3801. Eukaryota.
ENOG41124X5. LUCA.
GeneTreeiENSGT00390000001425.
HOGENOMiHOG000038164.
HOVERGENiHBG050915.
InParanoidiQ9HD34.
OMAiNIREYTC.
PhylomeDBiQ9HD34.

Family and domain databases

InterProiIPR008011. Complex1_LYR.
[Graphical view]
PfamiPF05347. Complex1_LYR. 1 hit.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9HD34-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAASSRAQVL SLYRAMLRES KRFSAYNYRT YAVRRIRDAF RENKNVKDPV
60 70 80 90
EIQTLVNKAK RDLGVIRRQV HIGQLYSTDK LIIENRDMPR T
Length:91
Mass (Da):10,758
Last modified:March 1, 2001 - v1
Checksum:iF0C5919CA701F3F3
GO

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti11 – 111S → A.1 Publication
Corresponds to variant rs2224391 [ dbSNP | Ensembl ].
VAR_024551
Natural varianti68 – 681R → L in COXPD19; can form a normal complex with NFS1 but the desulfurase enzymatic activity of this complex is severely decreased compared to control. 1 Publication
Corresponds to variant rs587777218 [ dbSNP | Ensembl ].
VAR_070943

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF285118 mRNA. Translation: AAG01155.1.
AF170070 mRNA. Translation: AAF25797.1.
AK291158 mRNA. Translation: BAF83847.1.
AL035653 Genomic DNA. No translation available.
AL121978 Genomic DNA. No translation available.
AL162381 Genomic DNA. No translation available.
BC009552 mRNA. Translation: AAH09552.1.
CCDSiCCDS4493.1.
RefSeqiNP_001158313.1. NM_001164841.2.
NP_065141.3. NM_020408.5.
UniGeneiHs.387755.

Genome annotation databases

EnsembliENST00000330636; ENSP00000418787; ENSG00000214113.
GeneIDi57128.
KEGGihsa:57128.
UCSCiuc003mwp.5. human.

Keywords - Coding sequence diversityi

Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF285118 mRNA. Translation: AAG01155.1.
AF170070 mRNA. Translation: AAF25797.1.
AK291158 mRNA. Translation: BAF83847.1.
AL035653 Genomic DNA. No translation available.
AL121978 Genomic DNA. No translation available.
AL162381 Genomic DNA. No translation available.
BC009552 mRNA. Translation: AAH09552.1.
CCDSiCCDS4493.1.
RefSeqiNP_001158313.1. NM_001164841.2.
NP_065141.3. NM_020408.5.
UniGeneiHs.387755.

3D structure databases

ProteinModelPortaliQ9HD34.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi121391. 9 interactions.
IntActiQ9HD34. 2 interactions.
STRINGi9606.ENSP00000443900.

PTM databases

iPTMnetiQ9HD34.
PhosphoSiteiQ9HD34.

Polymorphism and mutation databases

BioMutaiLYRM4.
DMDMi46576652.

Proteomic databases

EPDiQ9HD34.
MaxQBiQ9HD34.
PaxDbiQ9HD34.
PeptideAtlasiQ9HD34.
PRIDEiQ9HD34.
TopDownProteomicsiQ9HD34.

Protocols and materials databases

DNASUi57128.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000330636; ENSP00000418787; ENSG00000214113.
GeneIDi57128.
KEGGihsa:57128.
UCSCiuc003mwp.5. human.

Organism-specific databases

CTDi57128.
GeneCardsiLYRM4.
HGNCiHGNC:21365. LYRM4.
HPAiHPA030362.
MalaCardsiLYRM4.
MIMi613311. gene.
615595. phenotype.
neXtProtiNX_Q9HD34.
Orphaneti397593. Severe neonatal lactic acidosis due to NFS1-ISD11 complex deficiency.
PharmGKBiPA162394762.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiKOG3801. Eukaryota.
ENOG41124X5. LUCA.
GeneTreeiENSGT00390000001425.
HOGENOMiHOG000038164.
HOVERGENiHBG050915.
InParanoidiQ9HD34.
OMAiNIREYTC.
PhylomeDBiQ9HD34.

Enzyme and pathway databases

UniPathwayiUPA00266.
ReactomeiR-HSA-1362409. Mitochondrial iron-sulfur cluster biogenesis.

Miscellaneous databases

GenomeRNAii57128.
PROiQ9HD34.
SOURCEiSearch...

Gene expression databases

BgeeiQ9HD34.
CleanExiHS_LYRM4.
ExpressionAtlasiQ9HD34. baseline and differential.
GenevisibleiQ9HD34. HS.

Family and domain databases

InterProiIPR008011. Complex1_LYR.
[Graphical view]
PfamiPF05347. Complex1_LYR. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "Identification of the human crooked neck gene by comparative gene identification."
    Lai C.-H., Chiu J.-Y., Lin W.-C.
    Biochim. Biophys. Acta 1517:449-454(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  2. "A gene cloned by one-hybrid system."
    Niu H.R., Ma K.T., Zhang N.H.
    Submitted (JUL-1999) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA].
  3. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
  4. "The DNA sequence and analysis of human chromosome 6."
    Mungall A.J., Palmer S.A., Sims S.K., Edwards C.A., Ashurst J.L., Wilming L., Jones M.C., Horton R., Hunt S.E., Scott C.E., Gilbert J.G.R., Clamp M.E., Bethel G., Milne S., Ainscough R., Almeida J.P., Ambrose K.D., Andrews T.D.
    , Ashwell R.I.S., Babbage A.K., Bagguley C.L., Bailey J., Banerjee R., Barker D.J., Barlow K.F., Bates K., Beare D.M., Beasley H., Beasley O., Bird C.P., Blakey S.E., Bray-Allen S., Brook J., Brown A.J., Brown J.Y., Burford D.C., Burrill W., Burton J., Carder C., Carter N.P., Chapman J.C., Clark S.Y., Clark G., Clee C.M., Clegg S., Cobley V., Collier R.E., Collins J.E., Colman L.K., Corby N.R., Coville G.J., Culley K.M., Dhami P., Davies J., Dunn M., Earthrowl M.E., Ellington A.E., Evans K.A., Faulkner L., Francis M.D., Frankish A., Frankland J., French L., Garner P., Garnett J., Ghori M.J., Gilby L.M., Gillson C.J., Glithero R.J., Grafham D.V., Grant M., Gribble S., Griffiths C., Griffiths M.N.D., Hall R., Halls K.S., Hammond S., Harley J.L., Hart E.A., Heath P.D., Heathcott R., Holmes S.J., Howden P.J., Howe K.L., Howell G.R., Huckle E., Humphray S.J., Humphries M.D., Hunt A.R., Johnson C.M., Joy A.A., Kay M., Keenan S.J., Kimberley A.M., King A., Laird G.K., Langford C., Lawlor S., Leongamornlert D.A., Leversha M., Lloyd C.R., Lloyd D.M., Loveland J.E., Lovell J., Martin S., Mashreghi-Mohammadi M., Maslen G.L., Matthews L., McCann O.T., McLaren S.J., McLay K., McMurray A., Moore M.J.F., Mullikin J.C., Niblett D., Nickerson T., Novik K.L., Oliver K., Overton-Larty E.K., Parker A., Patel R., Pearce A.V., Peck A.I., Phillimore B.J.C.T., Phillips S., Plumb R.W., Porter K.M., Ramsey Y., Ranby S.A., Rice C.M., Ross M.T., Searle S.M., Sehra H.K., Sheridan E., Skuce C.D., Smith S., Smith M., Spraggon L., Squares S.L., Steward C.A., Sycamore N., Tamlyn-Hall G., Tester J., Theaker A.J., Thomas D.W., Thorpe A., Tracey A., Tromans A., Tubby B., Wall M., Wallis J.M., West A.P., White S.S., Whitehead S.L., Whittaker H., Wild A., Willey D.J., Wilmer T.E., Wood J.M., Wray P.W., Wyatt J.C., Young L., Younger R.M., Bentley D.R., Coulson A., Durbin R.M., Hubbard T., Sulston J.E., Dunham I., Rogers J., Beck S.
    Nature 425:805-811(2003) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA], VARIANT ALA-11.
    Tissue: Pancreas.
  6. "Mitochondrial frataxin interacts with ISD11 of the NFS1/ISCU complex and multiple mitochondrial chaperones."
    Shan Y., Napoli E., Cortopassi G.
    Hum. Mol. Genet. 16:929-941(2007) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 45-58, FUNCTION, INTERACTION WITH FXN, SUBCELLULAR LOCATION, TISSUE SPECIFICITY.
  7. "A novel role for human Nfs1 in the cytoplasm: Nfs1 acts as a sulfur donor for MOCS3, a protein involved in molybdenum cofactor biosynthesis."
    Marelja Z., Stoecklein W., Nimtz M., Leimkuehler S.
    J. Biol. Chem. 283:25178-25185(2008) [PubMed] [Europe PMC] [Abstract]
    Cited for: INTERACTION WITH NFS1.
  8. "Human ISD11 is essential for both iron-sulfur cluster assembly and maintenance of normal cellular iron homeostasis."
    Shi Y., Ghosh M.C., Tong W.H., Rouault T.A.
    Hum. Mol. Genet. 18:3014-3025(2009) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION, SUBCELLULAR LOCATION, INTERACTION WITH NFS1.
  9. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  10. Cited for: IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
  11. "Mutations in LYRM4, encoding iron-sulfur cluster biogenesis factor ISD11, cause deficiency of multiple respiratory chain complexes."
    Lim S.C., Friemel M., Marum J.E., Tucker E.J., Bruno D.L., Riley L.G., Christodoulou J., Kirk E.P., Boneh A., DeGennaro C.M., Springer M., Mootha V.K., Rouault T.A., Leimkuhler S., Thorburn D.R., Compton A.G.
    Hum. Mol. Genet. 22:4460-4473(2013) [PubMed] [Europe PMC] [Abstract]
    Cited for: VARIANT COXPD19 LEU-68, CHARACTERIZATION OF VARIANT COXPD19 LEU-68.

Entry informationi

Entry nameiLYRM4_HUMAN
AccessioniPrimary (citable) accession number: Q9HD34
Secondary accession number(s): A8K543, Q5XKP1
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 26, 2004
Last sequence update: March 1, 2001
Last modified: July 6, 2016
This is version 115 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Miscellaneous

Reduction of LYRM4 levels by siRNA increases the total iron content, and reduces cytosolic and mitochondrial aconitase activities and NFS1 protein levels.

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. Human chromosome 6
    Human chromosome 6: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.