ID   XDH2_ARATH              Reviewed;        1353 AA.
AC   F4JLI5; Q6R2R5; Q9SW45;
DT   16-MAY-2012, integrated into UniProtKB/Swiss-Prot.
DT   28-JUN-2011, sequence version 1.
DT   27-MAR-2024, entry version 83.
DE   RecName: Full=Xanthine dehydrogenase 2;
DE            Short=AtXDH2;
DE            EC=1.17.1.4 {ECO:0000250|UniProtKB:Q8GUQ8};
GN   Name=XDH2; OrderedLocusNames=At4g34900; ORFNames=T11I11.140;
OS   Arabidopsis thaliana (Mouse-ear cress).
OC   Eukaryota; Viridiplantae; Streptophyta; Embryophyta; Tracheophyta;
OC   Spermatophyta; Magnoliopsida; eudicotyledons; Gunneridae; Pentapetalae;
OC   rosids; malvids; Brassicales; Brassicaceae; Camelineae; Arabidopsis.
OX   NCBI_TaxID=3702;
RN   [1]
RP   NUCLEOTIDE SEQUENCE [MRNA].
RX   PubMed=14726515; DOI=10.1074/jbc.m312929200;
RA   Hesberg C., Haensch R., Mendel R.R., Bittner F.;
RT   "Tandem orientation of duplicated xanthine dehydrogenase genes from
RT   Arabidopsis thaliana: differential gene expression and enzyme activities.";
RL   J. Biol. Chem. 279:13547-13554(2004).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=cv. Columbia;
RX   PubMed=10617198; DOI=10.1038/47134;
RA   Mayer K.F.X., Schueller C., Wambutt R., Murphy G., Volckaert G., Pohl T.,
RA   Duesterhoeft A., Stiekema W., Entian K.-D., Terryn N., Harris B.,
RA   Ansorge W., Brandt P., Grivell L.A., Rieger M., Weichselgartner M.,
RA   de Simone V., Obermaier B., Mache R., Mueller M., Kreis M., Delseny M.,
RA   Puigdomenech P., Watson M., Schmidtheini T., Reichert B., Portetelle D.,
RA   Perez-Alonso M., Boutry M., Bancroft I., Vos P., Hoheisel J.,
RA   Zimmermann W., Wedler H., Ridley P., Langham S.-A., McCullagh B.,
RA   Bilham L., Robben J., van der Schueren J., Grymonprez B., Chuang Y.-J.,
RA   Vandenbussche F., Braeken M., Weltjens I., Voet M., Bastiaens I., Aert R.,
RA   Defoor E., Weitzenegger T., Bothe G., Ramsperger U., Hilbert H., Braun M.,
RA   Holzer E., Brandt A., Peters S., van Staveren M., Dirkse W., Mooijman P.,
RA   Klein Lankhorst R., Rose M., Hauf J., Koetter P., Berneiser S., Hempel S.,
RA   Feldpausch M., Lamberth S., Van den Daele H., De Keyser A., Buysshaert C.,
RA   Gielen J., Villarroel R., De Clercq R., van Montagu M., Rogers J.,
RA   Cronin A., Quail M.A., Bray-Allen S., Clark L., Doggett J., Hall S.,
RA   Kay M., Lennard N., McLay K., Mayes R., Pettett A., Rajandream M.A.,
RA   Lyne M., Benes V., Rechmann S., Borkova D., Bloecker H., Scharfe M.,
RA   Grimm M., Loehnert T.-H., Dose S., de Haan M., Maarse A.C., Schaefer M.,
RA   Mueller-Auer S., Gabel C., Fuchs M., Fartmann B., Granderath K., Dauner D.,
RA   Herzl A., Neumann S., Argiriou A., Vitale D., Liguori R., Piravandi E.,
RA   Massenet O., Quigley F., Clabauld G., Muendlein A., Felber R., Schnabl S.,
RA   Hiller R., Schmidt W., Lecharny A., Aubourg S., Chefdor F., Cooke R.,
RA   Berger C., Monfort A., Casacuberta E., Gibbons T., Weber N., Vandenbol M.,
RA   Bargues M., Terol J., Torres A., Perez-Perez A., Purnelle B., Bent E.,
RA   Johnson S., Tacon D., Jesse T., Heijnen L., Schwarz S., Scholler P.,
RA   Heber S., Francs P., Bielke C., Frishman D., Haase D., Lemcke K.,
RA   Mewes H.-W., Stocker S., Zaccaria P., Bevan M., Wilson R.K.,
RA   de la Bastide M., Habermann K., Parnell L., Dedhia N., Gnoj L., Schutz K.,
RA   Huang E., Spiegel L., Sekhon M., Murray J., Sheet P., Cordes M.,
RA   Abu-Threideh J., Stoneking T., Kalicki J., Graves T., Harmon G.,
RA   Edwards J., Latreille P., Courtney L., Cloud J., Abbott A., Scott K.,
RA   Johnson D., Minx P., Bentley D., Fulton B., Miller N., Greco T., Kemp K.,
RA   Kramer J., Fulton L., Mardis E., Dante M., Pepin K., Hillier L.W.,
RA   Nelson J., Spieth J., Ryan E., Andrews S., Geisel C., Layman D., Du H.,
RA   Ali J., Berghoff A., Jones K., Drone K., Cotton M., Joshu C., Antonoiu B.,
RA   Zidanic M., Strong C., Sun H., Lamar B., Yordan C., Ma P., Zhong J.,
RA   Preston R., Vil D., Shekher M., Matero A., Shah R., Swaby I.K.,
RA   O'Shaughnessy A., Rodriguez M., Hoffman J., Till S., Granat S., Shohdy N.,
RA   Hasegawa A., Hameed A., Lodhi M., Johnson A., Chen E., Marra M.A.,
RA   Martienssen R., McCombie W.R.;
RT   "Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana.";
RL   Nature 402:769-777(1999).
RN   [3]
RP   GENOME REANNOTATION.
RC   STRAIN=cv. Columbia;
RX   PubMed=27862469; DOI=10.1111/tpj.13415;
RA   Cheng C.Y., Krishnakumar V., Chan A.P., Thibaud-Nissen F., Schobel S.,
RA   Town C.D.;
RT   "Araport11: a complete reannotation of the Arabidopsis thaliana reference
RT   genome.";
RL   Plant J. 89:789-804(2017).
RN   [4]
RP   FUNCTION.
RX   PubMed=17872919; DOI=10.1093/pcp/pcm119;
RA   Nakagawa A., Sakamoto S., Takahashi M., Morikawa H., Sakamoto A.;
RT   "The RNAi-mediated silencing of xanthine dehydrogenase impairs growth and
RT   fertility and accelerates leaf senescence in transgenic Arabidopsis
RT   plants.";
RL   Plant Cell Physiol. 48:1484-1495(2007).
CC   -!- FUNCTION: Key enzyme involved in purine catabolism. Catalyzes the
CC       oxidation of hypoxanthine to xanthine and the oxidation of xanthine to
CC       urate. Regulates the level of ureides and plays a role during plant
CC       growth and development and senescence. {ECO:0000269|PubMed:17872919}.
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=H2O + NAD(+) + xanthine = H(+) + NADH + urate;
CC         Xref=Rhea:RHEA:16669, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC         ChEBI:CHEBI:17712, ChEBI:CHEBI:17775, ChEBI:CHEBI:57540,
CC         ChEBI:CHEBI:57945; EC=1.17.1.4;
CC         Evidence={ECO:0000250|UniProtKB:Q8GUQ8};
CC   -!- CATALYTIC ACTIVITY:
CC       Reaction=H2O + hypoxanthine + NAD(+) = H(+) + NADH + xanthine;
CC         Xref=Rhea:RHEA:24670, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378,
CC         ChEBI:CHEBI:17368, ChEBI:CHEBI:17712, ChEBI:CHEBI:57540,
CC         ChEBI:CHEBI:57945; EC=1.17.1.4;
CC         Evidence={ECO:0000250|UniProtKB:Q8GUQ8};
CC   -!- COFACTOR:
CC       Name=[2Fe-2S] cluster; Xref=ChEBI:CHEBI:190135; Evidence={ECO:0000250};
CC       Note=Binds 2 [2Fe-2S] clusters. {ECO:0000250};
CC   -!- COFACTOR:
CC       Name=FAD; Xref=ChEBI:CHEBI:57692; Evidence={ECO:0000250};
CC   -!- COFACTOR:
CC       Name=Mo-molybdopterin; Xref=ChEBI:CHEBI:71302; Evidence={ECO:0000250};
CC       Note=Binds 1 Mo-molybdopterin (Mo-MPT) cofactor per subunit.
CC       {ECO:0000250};
CC   -!- SUBUNIT: Homodimer. {ECO:0000250}.
CC   -!- TISSUE SPECIFICITY: Expressed in roots, leaves, stems, flowers and
CC       siliques.
CC   -!- MISCELLANEOUS: Plants silencing simultaneously XDH1 and XDH2 show
CC       reduced growth, impaired silique development, increased seed sterility,
CC       precocious senescence of mature leaves and overaccumulation of
CC       xanthine. {ECO:0000305|PubMed:17872919}.
CC   -!- SIMILARITY: Belongs to the xanthine dehydrogenase family.
CC       {ECO:0000305}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=CAB45451.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
CC       Sequence=CAB80207.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};
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DR   EMBL; AY518202; AAR99079.1; -; mRNA.
DR   EMBL; AL079347; CAB45451.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; AL161586; CAB80207.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; CP002687; AEE86435.1; -; Genomic_DNA.
DR   PIR; T10236; T10236.
DR   RefSeq; NP_195216.2; NM_119656.3.
DR   AlphaFoldDB; F4JLI5; -.
DR   SMR; F4JLI5; -.
DR   STRING; 3702.F4JLI5; -.
DR   PaxDb; 3702-AT4G34900-1; -.
DR   ProteomicsDB; 242524; -.
DR   EnsemblPlants; AT4G34900.1; AT4G34900.1; AT4G34900.
DR   GeneID; 829642; -.
DR   Gramene; AT4G34900.1; AT4G34900.1; AT4G34900.
DR   KEGG; ath:AT4G34900; -.
DR   Araport; AT4G34900; -.
DR   TAIR; AT4G34900; XDH2.
DR   eggNOG; KOG0430; Eukaryota.
DR   HOGENOM; CLU_001681_1_2_1; -.
DR   InParanoid; F4JLI5; -.
DR   OrthoDB; 761229at2759; -.
DR   PRO; PR:F4JLI5; -.
DR   Proteomes; UP000006548; Chromosome 4.
DR   ExpressionAtlas; F4JLI5; baseline and differential.
DR   GO; GO:0005886; C:plasma membrane; HDA:TAIR.
DR   GO; GO:0051537; F:2 iron, 2 sulfur cluster binding; IEA:UniProtKB-KW.
DR   GO; GO:0071949; F:FAD binding; IEA:InterPro.
DR   GO; GO:0005506; F:iron ion binding; IEA:InterPro.
DR   GO; GO:0004854; F:xanthine dehydrogenase activity; IEA:UniProtKB-EC.
DR   GO; GO:0046110; P:xanthine metabolic process; IMP:UniProtKB.
DR   Gene3D; 3.10.20.30; -; 1.
DR   Gene3D; 3.30.465.10; -; 1.
DR   Gene3D; 1.10.150.120; [2Fe-2S]-binding domain; 1.
DR   Gene3D; 3.90.1170.50; Aldehyde oxidase/xanthine dehydrogenase, a/b hammerhead; 1.
DR   Gene3D; 3.30.365.10; Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain; 4.
DR   Gene3D; 3.30.390.50; CO dehydrogenase flavoprotein, C-terminal domain; 1.
DR   Gene3D; 3.30.43.10; Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase, domain 2; 1.
DR   InterPro; IPR002888; 2Fe-2S-bd.
DR   InterPro; IPR036884; 2Fe-2S-bd_dom_sf.
DR   InterPro; IPR036010; 2Fe-2S_ferredoxin-like_sf.
DR   InterPro; IPR001041; 2Fe-2S_ferredoxin-type.
DR   InterPro; IPR006058; 2Fe2S_fd_BS.
DR   InterPro; IPR000674; Ald_Oxase/Xan_DH_a/b.
DR   InterPro; IPR036856; Ald_Oxase/Xan_DH_a/b_sf.
DR   InterPro; IPR016208; Ald_Oxase/xanthine_DH-like.
DR   InterPro; IPR008274; AldOxase/xan_DH_MoCoBD1.
DR   InterPro; IPR046867; AldOxase/xan_DH_MoCoBD2.
DR   InterPro; IPR037165; AldOxase/xan_DH_Mopterin-bd_sf.
DR   InterPro; IPR012675; Beta-grasp_dom_sf.
DR   InterPro; IPR005107; CO_DH_flav_C.
DR   InterPro; IPR036683; CO_DH_flav_C_dom_sf.
DR   InterPro; IPR016166; FAD-bd_PCMH.
DR   InterPro; IPR036318; FAD-bd_PCMH-like_sf.
DR   InterPro; IPR016167; FAD-bd_PCMH_sub1.
DR   InterPro; IPR016169; FAD-bd_PCMH_sub2.
DR   InterPro; IPR002346; Mopterin_DH_FAD-bd.
DR   PANTHER; PTHR11908; XANTHINE DEHYDROGENASE; 1.
DR   PANTHER; PTHR11908:SF100; XANTHINE DEHYDROGENASE; 1.
DR   Pfam; PF01315; Ald_Xan_dh_C; 1.
DR   Pfam; PF03450; CO_deh_flav_C; 1.
DR   Pfam; PF00941; FAD_binding_5; 1.
DR   Pfam; PF00111; Fer2; 1.
DR   Pfam; PF01799; Fer2_2; 1.
DR   Pfam; PF02738; MoCoBD_1; 1.
DR   Pfam; PF20256; MoCoBD_2; 1.
DR   PIRSF; PIRSF000127; Xanthine_DH; 1.
DR   SMART; SM01008; Ald_Xan_dh_C; 1.
DR   SMART; SM01092; CO_deh_flav_C; 1.
DR   SUPFAM; SSF54292; 2Fe-2S ferredoxin-like; 1.
DR   SUPFAM; SSF55447; CO dehydrogenase flavoprotein C-terminal domain-like; 1.
DR   SUPFAM; SSF47741; CO dehydrogenase ISP C-domain like; 1.
DR   SUPFAM; SSF54665; CO dehydrogenase molybdoprotein N-domain-like; 1.
DR   SUPFAM; SSF56176; FAD-binding/transporter-associated domain-like; 1.
DR   SUPFAM; SSF56003; Molybdenum cofactor-binding domain; 1.
DR   PROSITE; PS00197; 2FE2S_FER_1; 1.
DR   PROSITE; PS51085; 2FE2S_FER_2; 1.
DR   PROSITE; PS51387; FAD_PCMH; 1.
DR   Genevisible; F4JLI5; AT.
PE   2: Evidence at transcript level;
KW   2Fe-2S; FAD; Flavoprotein; Iron; Iron-sulfur; Metal-binding; Molybdenum;
KW   NAD; Oxidoreductase; Reference proteome.
FT   CHAIN           1..1353
FT                   /note="Xanthine dehydrogenase 2"
FT                   /id="PRO_0000417458"
FT   DOMAIN          7..93
FT                   /note="2Fe-2S ferredoxin-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
FT   DOMAIN          249..434
FT                   /note="FAD-binding PCMH-type"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00718"
FT   ACT_SITE        1289
FT                   /note="Proton acceptor"
FT                   /evidence="ECO:0000250"
FT   BINDING         45
FT                   /ligand="[2Fe-2S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:190135"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
FT   BINDING         50
FT                   /ligand="[2Fe-2S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:190135"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
FT   BINDING         53
FT                   /ligand="[2Fe-2S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:190135"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
FT   BINDING         75
FT                   /ligand="[2Fe-2S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:190135"
FT                   /ligand_label="1"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
FT   BINDING         115
FT                   /ligand="[2Fe-2S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:190135"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
FT   BINDING         118
FT                   /ligand="[2Fe-2S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:190135"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
FT   BINDING         151
FT                   /ligand="[2Fe-2S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:190135"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
FT   BINDING         153
FT                   /ligand="[2Fe-2S] cluster"
FT                   /ligand_id="ChEBI:CHEBI:190135"
FT                   /ligand_label="2"
FT                   /evidence="ECO:0000255|PROSITE-ProRule:PRU00465"
FT   BINDING         277..284
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000250"
FT   BINDING         357
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000250"
FT   BINDING         367..371
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000250"
FT   BINDING         380
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000250"
FT   BINDING         424
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000250"
FT   BINDING         442
FT                   /ligand="FAD"
FT                   /ligand_id="ChEBI:CHEBI:57692"
FT                   /evidence="ECO:0000250"
FT   BINDING         788
FT                   /ligand="Mo-molybdopterin"
FT                   /ligand_id="ChEBI:CHEBI:71302"
FT                   /ligand_part="Mo"
FT                   /ligand_part_id="ChEBI:CHEBI:28685"
FT                   /evidence="ECO:0000250"
FT   BINDING         819
FT                   /ligand="Mo-molybdopterin"
FT                   /ligand_id="ChEBI:CHEBI:71302"
FT                   /ligand_part="Mo"
FT                   /ligand_part_id="ChEBI:CHEBI:28685"
FT                   /evidence="ECO:0000250"
FT   BINDING         823
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         901
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         933
FT                   /ligand="Mo-molybdopterin"
FT                   /ligand_id="ChEBI:CHEBI:71302"
FT                   /ligand_part="Mo"
FT                   /ligand_part_id="ChEBI:CHEBI:28685"
FT                   /evidence="ECO:0000250"
FT   BINDING         935
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         1031
FT                   /ligand="substrate"
FT                   /evidence="ECO:0000250"
FT   BINDING         1100
FT                   /ligand="Mo-molybdopterin"
FT                   /ligand_id="ChEBI:CHEBI:71302"
FT                   /ligand_part="Mo"
FT                   /ligand_part_id="ChEBI:CHEBI:28685"
FT                   /evidence="ECO:0000250"
FT   CONFLICT        401
FT                   /note="V -> A (in Ref. 1; AAR99079)"
FT                   /evidence="ECO:0000305"
SQ   SEQUENCE   1353 AA;  148762 MW;  FC1AD990E687DD3A CRC64;
     MEQNEFMEAI MYVNGVRRVL PDGLAHMTLL EYLRDLGLTG TKLGCGEGGC GSCTVMVSSY
     DRESKTCVHY AVNACLAPLY SVEGMHVISI EGVGHRKLGL HPLQESLASS HGSQCGFCTP
     GFVMSMYALL RSSKNSPSEE EIEECLAGNL CRCTGYRPII DAFRVFAKSD DALYSGLSSL
     SLQDGSNICP STGKPCSCGS KTTSEAATCN EDRFQSISYS DIDGAKYTDK ELIFPPELLL
     RKLAPLKLGG NEGITWYRPV SLQNLLELKA NFPDAKLLVG NTEVGIEMRL KRLQYPVLIS
     AAQVPELNAL NVNDNGIEVG SALRLSELLR LFRKVVKERP AHETSACKAF IEQLKWFAGT
     QIRNVACIGG NICTASPISD LNPLWMASRA EFRIINCNGD VRSIPAKDFF LGYRKVDMGS
     NEILLSVFLP WTRPLEYVKE FKQAHRRDDD IAIVNGGMRV FLEEKGQQLF VSDASIVYGG
     VAPLSLRARN TEELLIGKNW NKCLLQDALK VIQSDVLIKE GAPGGMVEFR KSLTLSFFFK
     FFLWVTHHVN NVNPTIETFP PSHMSAVQLV PRFSRIGKQD YETVKQGTSV GLPEVHLSAR
     MQVTGEAEYT DDTPLPPCTL HAALVLSKVP HARILSVDDS AAKSSSGFVG LFLAKDVPGN
     NMIGPIVADE ELFATDVVTC VGQVIGVLVA DTHENAKTAA RKVDVRYQEL PAILSIKEAI
     NAKSFHPNTE RRLRKGDVEL CFQSGQCDRI IEGEVQMGGQ EHFYLEPNGS LVWTIDGGNE
     VHMISSTQAP QQHQKYVSHV LGLPMSKVVC KTKRLGGGFG GKETRSAFIA AAASVPSYLL
     NRPVKLILDR DVDMMITGHR HSFVGKYKVG FTNEGKILAL DLEIYNNGGN SMDLSLSNLE
     RAMFHSDNVY EIPHVRIVGN VCFTNFPSNT AFRGFGGPQG MLITENWIQR IAAELDKIPE
     EIKEMNFQVE GSITHYFQSL QHCTLHQLWK ELKVSSNFLK TRREADEFNS HNRWKKRGVA
     MVPTKFGISF TTKFMNQAGA LVHVYTDGTV LVTHGGVEMG QGLHTKVAQV AATAFNILLS
     SVFVSETSTD KVPNASPTAA SASSDMYGAA VLDACEQIIA RMEPVASKHN FNTFSELASA
     CYFQRIDLSA HGFHIVPELE FDWVSGKGNA YRYYTYGAAF AEVEIDTLTG DFHTRKADIM
     LDLGYSLNPT IDIGQIEGAF VQGLGWVALE ELKWGDAAHK WIKPGSLLTC GPGSYKIPSI
     NDMPFQLNVS LLKGNPNAKA IHSSKAVGEP PFFLAASAFF AIKEAIKAAR SEVGLTNWFP
     LETPATPERI RMACFDEFSA PFANSDFCPK LSV
//