PYRD1_HUMAN
ID PYRD1_HUMAN Reviewed; 500 AA.
AC Q8WU10; A6NKI6; B3KWN8; Q9H6P1;
DT 08-APR-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2002, sequence version 1.
DT 03-AUG-2022, entry version 166.
DE RecName: Full=Pyridine nucleotide-disulfide oxidoreductase domain-containing protein 1;
DE EC=1.8.1.-;
GN Name=PYROXD1;
OS Homo sapiens (Human).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae;
OC Homo.
OX NCBI_TaxID=9606;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS 1 AND 2).
RC TISSUE=Brain, and Hepatoma;
RX PubMed=14702039; DOI=10.1038/ng1285;
RA Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R.,
RA Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H.,
RA Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.,
RA Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K.,
RA Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H.,
RA Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M.,
RA Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K.,
RA Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T.,
RA Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M.,
RA Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S.,
RA Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H.,
RA Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K.,
RA Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N.,
RA Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S.,
RA Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O.,
RA Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H.,
RA Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B.,
RA Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y.,
RA Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K.,
RA Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T.,
RA Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T.,
RA Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y.,
RA Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H.,
RA Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y.,
RA Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H.,
RA Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O.,
RA Isogai T., Sugano S.;
RT "Complete sequencing and characterization of 21,243 full-length human
RT cDNAs.";
RL Nat. Genet. 36:40-45(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Melanoma;
RX PubMed=17974005; DOI=10.1186/1471-2164-8-399;
RA Bechtel S., Rosenfelder H., Duda A., Schmidt C.P., Ernst U.,
RA Wellenreuther R., Mehrle A., Schuster C., Bahr A., Bloecker H., Heubner D.,
RA Hoerlein A., Michel G., Wedler H., Koehrer K., Ottenwaelder B., Poustka A.,
RA Wiemann S., Schupp I.;
RT "The full-ORF clone resource of the German cDNA consortium.";
RL BMC Genomics 8:399-399(2007).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RX PubMed=16541075; DOI=10.1038/nature04569;
RA Scherer S.E., Muzny D.M., Buhay C.J., Chen R., Cree A., Ding Y.,
RA Dugan-Rocha S., Gill R., Gunaratne P., Harris R.A., Hawes A.C.,
RA Hernandez J., Hodgson A.V., Hume J., Jackson A., Khan Z.M., Kovar-Smith C.,
RA Lewis L.R., Lozado R.J., Metzker M.L., Milosavljevic A., Miner G.R.,
RA Montgomery K.T., Morgan M.B., Nazareth L.V., Scott G., Sodergren E.,
RA Song X.-Z., Steffen D., Lovering R.C., Wheeler D.A., Worley K.C., Yuan Y.,
RA Zhang Z., Adams C.Q., Ansari-Lari M.A., Ayele M., Brown M.J., Chen G.,
RA Chen Z., Clerc-Blankenburg K.P., Davis C., Delgado O., Dinh H.H.,
RA Draper H., Gonzalez-Garay M.L., Havlak P., Jackson L.R., Jacob L.S.,
RA Kelly S.H., Li L., Li Z., Liu J., Liu W., Lu J., Maheshwari M.,
RA Nguyen B.-V., Okwuonu G.O., Pasternak S., Perez L.M., Plopper F.J.H.,
RA Santibanez J., Shen H., Tabor P.E., Verduzco D., Waldron L., Wang Q.,
RA Williams G.A., Zhang J., Zhou J., Allen C.C., Amin A.G., Anyalebechi V.,
RA Bailey M., Barbaria J.A., Bimage K.E., Bryant N.P., Burch P.E.,
RA Burkett C.E., Burrell K.L., Calderon E., Cardenas V., Carter K., Casias K.,
RA Cavazos I., Cavazos S.R., Ceasar H., Chacko J., Chan S.N., Chavez D.,
RA Christopoulos C., Chu J., Cockrell R., Cox C.D., Dang M., Dathorne S.R.,
RA David R., Davis C.M., Davy-Carroll L., Deshazo D.R., Donlin J.E.,
RA D'Souza L., Eaves K.A., Egan A., Emery-Cohen A.J., Escotto M., Flagg N.,
RA Forbes L.D., Gabisi A.M., Garza M., Hamilton C., Henderson N.,
RA Hernandez O., Hines S., Hogues M.E., Huang M., Idlebird D.G., Johnson R.,
RA Jolivet A., Jones S., Kagan R., King L.M., Leal B., Lebow H., Lee S.,
RA LeVan J.M., Lewis L.C., London P., Lorensuhewa L.M., Loulseged H.,
RA Lovett D.A., Lucier A., Lucier R.L., Ma J., Madu R.C., Mapua P.,
RA Martindale A.D., Martinez E., Massey E., Mawhiney S., Meador M.G.,
RA Mendez S., Mercado C., Mercado I.C., Merritt C.E., Miner Z.L., Minja E.,
RA Mitchell T., Mohabbat F., Mohabbat K., Montgomery B., Moore N., Morris S.,
RA Munidasa M., Ngo R.N., Nguyen N.B., Nickerson E., Nwaokelemeh O.O.,
RA Nwokenkwo S., Obregon M., Oguh M., Oragunye N., Oviedo R.J., Parish B.J.,
RA Parker D.N., Parrish J., Parks K.L., Paul H.A., Payton B.A., Perez A.,
RA Perrin W., Pickens A., Primus E.L., Pu L.-L., Puazo M., Quiles M.M.,
RA Quiroz J.B., Rabata D., Reeves K., Ruiz S.J., Shao H., Sisson I.,
RA Sonaike T., Sorelle R.P., Sutton A.E., Svatek A.F., Svetz L.A.,
RA Tamerisa K.S., Taylor T.R., Teague B., Thomas N., Thorn R.D., Trejos Z.Y.,
RA Trevino B.K., Ukegbu O.N., Urban J.B., Vasquez L.I., Vera V.A.,
RA Villasana D.M., Wang L., Ward-Moore S., Warren J.T., Wei X., White F.,
RA Williamson A.L., Wleczyk R., Wooden H.S., Wooden S.H., Yen J., Yoon L.,
RA Yoon V., Zorrilla S.E., Nelson D., Kucherlapati R., Weinstock G.,
RA Gibbs R.A.;
RT "The finished DNA sequence of human chromosome 12.";
RL Nature 440:346-351(2006).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RA Mural R.J., Istrail S., Sutton G.G., Florea L., Halpern A.L., Mobarry C.M.,
RA Lippert R., Walenz B., Shatkay H., Dew I., Miller J.R., Flanigan M.J.,
RA Edwards N.J., Bolanos R., Fasulo D., Halldorsson B.V., Hannenhalli S.,
RA Turner R., Yooseph S., Lu F., Nusskern D.R., Shue B.C., Zheng X.H.,
RA Zhong F., Delcher A.L., Huson D.H., Kravitz S.A., Mouchard L., Reinert K.,
RA Remington K.A., Clark A.G., Waterman M.S., Eichler E.E., Adams M.D.,
RA Hunkapiller M.W., Myers E.W., Venter J.C.;
RL Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases.
RN [5]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Kidney;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [6]
RP ACETYLATION [LARGE SCALE ANALYSIS] AT MET-1, AND IDENTIFICATION BY MASS
RP SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=19413330; DOI=10.1021/ac9004309;
RA Gauci S., Helbig A.O., Slijper M., Krijgsveld J., Heck A.J., Mohammed S.;
RT "Lys-N and trypsin cover complementary parts of the phosphoproteome in a
RT refined SCX-based approach.";
RL Anal. Chem. 81:4493-4501(2009).
RN [7]
RP FUNCTION, SUBCELLULAR LOCATION, INVOLVEMENT IN MFM8, VARIANTS MFM8 SER-155
RP AND HIS-372, AND CHARACTERIZATION OF VARIANTS MFM8 SER-155 AND HIS-372.
RX PubMed=27745833; DOI=10.1016/j.ajhg.2016.09.005;
RA O'Grady G.L., Best H.A., Sztal T.E., Schartner V., Sanjuan-Vazquez M.,
RA Donkervoort S., Abath Neto O., Sutton R.B., Ilkovski B., Romero N.B.,
RA Stojkovic T., Dastgir J., Waddell L.B., Boland A., Hu Y., Williams C.,
RA Ruparelia A.A., Maisonobe T., Peduto A.J., Reddel S.W., Lek M.,
RA Tukiainen T., Cummings B.B., Joshi H., Nectoux J., Brammah S.,
RA Deleuze J.F., Ing V.O., Ramm G., Ardicli D., Nowak K.J., Talim B.,
RA Topaloglu H., Laing N.G., North K.N., MacArthur D.G., Friant S.,
RA Clarke N.F., Bryson-Richardson R.J., Boennemann C.G., Laporte J.,
RA Cooper S.T.;
RT "Variants in the oxidoreductase PYROXD1 cause early-onset myopathy with
RT internalized nuclei and myofibrillar disorganization.";
RL Am. J. Hum. Genet. 99:1086-1105(2016).
RN [8]
RP INVOLVEMENT IN LIMB-GIRDLE MUSCULAR DYSTROPHY, VARIANT SER-155, AND
RP CHARACTERIZATION OF VARIANT SER-155.
RX PubMed=30345904; DOI=10.1152/physiolgenomics.00036.2018;
RA Saha M., Reddy H.M., Salih M., Estrella E., Jones M.D., Mitsuhashi S.,
RA Cho K.A., Suzuki-Hatano S., Rizzo S.A., Hamad M.H., Mukhtar M.M.,
RA Hamed A.A., Elseed M.A., Lek M., Valkanas E., MacArthur D.G., Kunkel L.M.,
RA Pacak C.A., Draper I., Kang P.B.;
RT "The impact of PYROXD1 deficiency on cellular respiration and correlations
RT with genetic analyses of limb-girdle muscular dystrophy in Saudi Arabia and
RT Sudan.";
RL Physiol. Genomics 50:929-939(2018).
CC -!- FUNCTION: Probable FAD-dependent oxidoreductase; involved in the
CC cellular oxidative stress response (PubMed:27745833). Required for
CC normal sarcomere structure and muscle fiber integrity (By similarity).
CC {ECO:0000250|UniProtKB:Q6PBT5, ECO:0000269|PubMed:27745833}.
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000250|UniProtKB:O52582};
CC Note=Binds 1 FAD per subunit. {ECO:0000250|UniProtKB:O52582};
CC -!- INTERACTION:
CC Q8WU10; Q96BW1: UPRT; NbExp=10; IntAct=EBI-742933, EBI-742943;
CC -!- SUBCELLULAR LOCATION: Nucleus {ECO:0000269|PubMed:27745833}. Cytoplasm
CC {ECO:0000269|PubMed:27745833}. Cytoplasm, myofibril, sarcomere
CC {ECO:0000269|PubMed:27745833}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=Q8WU10-1; Sequence=Displayed;
CC Name=2;
CC IsoId=Q8WU10-2; Sequence=VSP_055828;
CC -!- DISEASE: Myopathy, myofibrillar, 8 (MFM8) [MIM:617258]: A form of
CC myofibrillar myopathy, a group of chronic neuromuscular disorders
CC characterized at ultrastructural level by disintegration of the
CC sarcomeric Z disk and myofibrils, and replacement of the normal
CC myofibrillar markings by small dense granules, or larger hyaline
CC masses, or amorphous material. MFM8 is an autosomal recessive form,
CC clinically characterized by slowly progressive symmetrical weakness
CC affecting both proximal and distal muscles, with normal to moderately
CC elevated creatine kinase. Mild facial weakness, a high palate, nasal
CC speech, and swallowing difficulties are typical features, mild
CC restrictive lung disease is common, and late-onset cardiac involvement
CC may be present. {ECO:0000269|PubMed:27745833}. Note=The disease is
CC caused by variants affecting the gene represented in this entry.
CC -!- DISEASE: Note=A mutation in PYROXD1 is the cause of autosomal recessive
CC limb-girdle muscular dystrophy. The affected individual with a
CC homozygous recessive PYROXD1 mutation showed progressive muscle
CC weakness with an onset at the age of 9 years. Initial symptoms included
CC excessive falling while running, with slowly progressive weakness.
CC Difficulty navigating stairs by the age if 18, and loss of ambulation
CC at the age of 37 years. Neurological examination showed proximal
CC symmetrical muscle weakness and wasting, along with calf muscle
CC pseudohypertrophy. {ECO:0000269|PubMed:30345904}.
CC -!- SIMILARITY: Belongs to the class-I pyridine nucleotide-disulfide
CC oxidoreductase family. PYROXD1 subfamily. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAB15214.1; Type=Frameshift; Evidence={ECO:0000305};
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DR EMBL; AK025681; BAB15214.1; ALT_FRAME; mRNA.
DR EMBL; AK125461; BAG54200.1; -; mRNA.
DR EMBL; AL832441; CAH10632.1; -; mRNA.
DR EMBL; AC006559; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CH471094; EAW96428.1; -; Genomic_DNA.
DR EMBL; BC021662; AAH21662.1; -; mRNA.
DR CCDS; CCDS31755.1; -. [Q8WU10-1]
DR CCDS; CCDS86287.1; -. [Q8WU10-2]
DR RefSeq; NP_079130.2; NM_024854.3. [Q8WU10-1]
DR PDB; 6ZK7; X-ray; 3.20 A; AAAA=1-500.
DR PDBsum; 6ZK7; -.
DR AlphaFoldDB; Q8WU10; -.
DR SMR; Q8WU10; -.
DR BioGRID; 122992; 10.
DR IntAct; Q8WU10; 2.
DR STRING; 9606.ENSP00000240651; -.
DR iPTMnet; Q8WU10; -.
DR PhosphoSitePlus; Q8WU10; -.
DR BioMuta; PYROXD1; -.
DR DMDM; 74760541; -.
DR EPD; Q8WU10; -.
DR jPOST; Q8WU10; -.
DR MassIVE; Q8WU10; -.
DR MaxQB; Q8WU10; -.
DR PaxDb; Q8WU10; -.
DR PeptideAtlas; Q8WU10; -.
DR PRIDE; Q8WU10; -.
DR ProteomicsDB; 3796; -.
DR ProteomicsDB; 74622; -. [Q8WU10-1]
DR Antibodypedia; 49414; 69 antibodies from 21 providers.
DR DNASU; 79912; -.
DR Ensembl; ENST00000240651.14; ENSP00000240651.9; ENSG00000121350.16. [Q8WU10-1]
DR Ensembl; ENST00000538582.5; ENSP00000438505.1; ENSG00000121350.16. [Q8WU10-2]
DR GeneID; 79912; -.
DR KEGG; hsa:79912; -.
DR MANE-Select; ENST00000240651.14; ENSP00000240651.9; NM_024854.5; NP_079130.2.
DR UCSC; uc001rew.4; human. [Q8WU10-1]
DR CTD; 79912; -.
DR DisGeNET; 79912; -.
DR GeneCards; PYROXD1; -.
DR HGNC; HGNC:26162; PYROXD1.
DR HPA; ENSG00000121350; Low tissue specificity.
DR MalaCards; PYROXD1; -.
DR MIM; 617220; gene.
DR MIM; 617258; phenotype.
DR neXtProt; NX_Q8WU10; -.
DR OpenTargets; ENSG00000121350; -.
DR PharmGKB; PA162400525; -.
DR VEuPathDB; HostDB:ENSG00000121350; -.
DR eggNOG; KOG2755; Eukaryota.
DR GeneTree; ENSGT00390000014894; -.
DR HOGENOM; CLU_026335_0_0_1; -.
DR InParanoid; Q8WU10; -.
DR OMA; MCENLIL; -.
DR OrthoDB; 1463391at2759; -.
DR PhylomeDB; Q8WU10; -.
DR TreeFam; TF105963; -.
DR PathwayCommons; Q8WU10; -.
DR SignaLink; Q8WU10; -.
DR BioGRID-ORCS; 79912; 615 hits in 1018 CRISPR screens.
DR ChiTaRS; PYROXD1; human.
DR GenomeRNAi; 79912; -.
DR Pharos; Q8WU10; Tbio.
DR PRO; PR:Q8WU10; -.
DR Proteomes; UP000005640; Chromosome 12.
DR RNAct; Q8WU10; protein.
DR Bgee; ENSG00000121350; Expressed in buccal mucosa cell and 206 other tissues.
DR ExpressionAtlas; Q8WU10; baseline and differential.
DR Genevisible; Q8WU10; HS.
DR GO; GO:0005634; C:nucleus; IDA:UniProtKB.
DR GO; GO:0030017; C:sarcomere; IDA:UniProtKB.
DR GO; GO:0050660; F:flavin adenine dinucleotide binding; IEA:InterPro.
DR GO; GO:0016491; F:oxidoreductase activity; IEA:UniProtKB-KW.
DR GO; GO:0034599; P:cellular response to oxidative stress; IMP:UniProtKB.
DR Gene3D; 3.30.390.30; -; 1.
DR Gene3D; 3.50.50.60; -; 3.
DR InterPro; IPR036188; FAD/NAD-bd_sf.
DR InterPro; IPR023753; FAD/NAD-binding_dom.
DR InterPro; IPR016156; FAD/NAD-linked_Rdtase_dimer_sf.
DR InterPro; IPR041575; Rubredoxin_C.
DR Pfam; PF07992; Pyr_redox_2; 1.
DR Pfam; PF18267; Rubredoxin_C; 1.
DR SUPFAM; SSF51905; SSF51905; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Alternative splicing; Cytoplasm;
KW Disease variant; FAD; Flavoprotein; Limb-girdle muscular dystrophy;
KW Myofibrillar myopathy; NADP; Nucleus; Oxidoreductase; Reference proteome.
FT CHAIN 1..500
FT /note="Pyridine nucleotide-disulfide oxidoreductase domain-
FT containing protein 1"
FT /id="PRO_0000327419"
FT REGION 211..235
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 211..227
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 1
FT /note="N-acetylmethionine"
FT /evidence="ECO:0007744|PubMed:19413330"
FT VAR_SEQ 1..71
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_055828"
FT VARIANT 155
FT /note="N -> S (in MFM8; also found in a patient with limb-
FT girdle muscular dystrophy; decreased function in cellular
FT response to oxidative stress; no effect on subcellular
FT location in the nucleus and sarcomere. Overexpression in
FT C2C12 cells leads to reduced cell proliferation, migration
FT and differentiation.; dbSNP:rs781565158)"
FT /evidence="ECO:0000269|PubMed:27745833,
FT ECO:0000269|PubMed:30345904"
FT /id="VAR_077902"
FT VARIANT 372
FT /note="Q -> H (in MFM8; decreased function in cellular
FT response to oxidative stress; no effect on subcellular
FT location at nucleus and sarcomere; dbSNP:rs755208949)"
FT /evidence="ECO:0000269|PubMed:27745833"
FT /id="VAR_077903"
SQ SEQUENCE 500 AA; 55793 MW; 26F1AA7E09BA885B CRC64;
MEAARPPPTA GKFVVVGGGI AGVTCAEQLA THFPSEDILL VTASPVIKAV TNFKQISKIL
EEFDVEEQSS TMLGKRFPNI KVIESGVKQL KSEEHCIVTE DGNQHVYKKL CLCAGAKPKL
ICEGNPYVLG IRDTDSAQEF QKQLTKAKRI MIIGNGGIAL ELVYEIEGCE VIWAIKDKAI
GNTFFDAGAA EFLTSKLIAE KSEAKIAHKR TRYTTEGRKK EARSKSKADN VGSALGPDWH
EGLNLKGTKE FSHKIHLETM CEVKKIYLQD EFRILKKKSF TFPRDHKSVT ADTEMWPVYV
ELTNEKIYGC DFIVSATGVT PNVEPFLHGN SFDLGEDGGL KVDDHMHTSL PDIYAAGDIC
TTSWQLSPVW QQMRLWTQAR QMGWYAAKCM AAASSGDSID MDFSFELFAH VTKFFNYKVV
LLGKYNAQGL GSDHELMLRC TKGREYIKVV MQNGRMMGAV LIGETDLEET FENLILNQMN
LSSYGEDLLD PNIDIEDYFD
