XYLB_HUMAN
ID XYLB_HUMAN Reviewed; 536 AA.
AC O75191; B2RAW4; B4DDT2; B9EH64;
DT 04-APR-2006, integrated into UniProtKB/Swiss-Prot.
DT 05-MAY-2009, sequence version 3.
DT 03-AUG-2022, entry version 145.
DE RecName: Full=Xylulose kinase;
DE Short=Xylulokinase;
DE EC=2.7.1.17;
GN Name=XYLB;
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), AND VARIANT
RP GLU-85.
RC TISSUE=Kidney, and Mammary gland;
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 GENOMIC DNA].
RX PubMed=16641997; DOI=10.1038/nature04728;
RA Muzny D.M., Scherer S.E., Kaul R., Wang J., Yu J., Sudbrak R., Buhay C.J.,
RA Chen R., Cree A., Ding Y., Dugan-Rocha S., Gill R., Gunaratne P.,
RA Harris R.A., Hawes A.C., Hernandez J., Hodgson A.V., Hume J., Jackson A.,
RA Khan Z.M., Kovar-Smith C., Lewis L.R., Lozado R.J., Metzker M.L.,
RA Milosavljevic A., Miner G.R., Morgan M.B., Nazareth L.V., Scott G.,
RA Sodergren E., Song X.-Z., Steffen D., Wei S., Wheeler D.A., Wright M.W.,
RA Worley K.C., Yuan Y., Zhang Z., Adams C.Q., Ansari-Lari M.A., Ayele M.,
RA Brown M.J., Chen G., Chen Z., Clendenning J., Clerc-Blankenburg K.P.,
RA Chen R., Chen Z., Davis C., Delgado O., Dinh H.H., Dong W., Draper H.,
RA Ernst S., Fu G., Gonzalez-Garay M.L., Garcia D.K., Gillett W., Gu J.,
RA Hao B., Haugen E., Havlak P., He X., Hennig S., Hu S., Huang W.,
RA Jackson L.R., Jacob L.S., Kelly S.H., Kube M., Levy R., Li Z., Liu B.,
RA Liu J., Liu W., Lu J., Maheshwari M., Nguyen B.-V., Okwuonu G.O.,
RA Palmeiri A., Pasternak S., Perez L.M., Phelps K.A., Plopper F.J., Qiang B.,
RA Raymond C., Rodriguez R., Saenphimmachak C., Santibanez J., Shen H.,
RA Shen Y., Subramanian S., Tabor P.E., Verduzco D., Waldron L., Wang J.,
RA Wang J., Wang Q., Williams G.A., Wong G.K.-S., Yao Z., Zhang J., Zhang X.,
RA Zhao G., Zhou J., Zhou Y., Nelson D., Lehrach H., Reinhardt R.,
RA Naylor S.L., Yang H., Olson M., Weinstock G., Gibbs R.A.;
RT "The DNA sequence, annotation and analysis of human chromosome 3.";
RL Nature 440:1194-1198(2006).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA], AND VARIANT GLU-85.
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 [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 1).
RC TISSUE=Lung, and Testis;
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 [5]
RP NUCLEOTIDE SEQUENCE [MRNA] OF 1-512 (ISOFORM 1), AND VARIANTS GLU-85 AND
RP ASN-262.
RC TISSUE=Liver;
RX PubMed=9763671; DOI=10.1159/000015076;
RA Tamari M., Daigo Y., Ishikawa S., Nakamura Y.;
RT "Genomic structure of a novel human gene (XYLB) on chromosome 3p22-->p21.3
RT encoding a xylulokinase-like protein.";
RL Cytogenet. Cell Genet. 82:101-104(1998).
RN [6]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RX PubMed=21269460; DOI=10.1186/1752-0509-5-17;
RA Burkard T.R., Planyavsky M., Kaupe I., Breitwieser F.P., Buerckstuemmer T.,
RA Bennett K.L., Superti-Furga G., Colinge J.;
RT "Initial characterization of the human central proteome.";
RL BMC Syst. Biol. 5:17-17(2011).
RN [7]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Liver;
RX PubMed=24275569; DOI=10.1016/j.jprot.2013.11.014;
RA Bian Y., Song C., Cheng K., Dong M., Wang F., Huang J., Sun D., Wang L.,
RA Ye M., Zou H.;
RT "An enzyme assisted RP-RPLC approach for in-depth analysis of human liver
RT phosphoproteome.";
RL J. Proteomics 96:253-262(2014).
RN [8]
RP X-RAY CRYSTALLOGRAPHY (1.68 ANGSTROMS) IN COMPLEX WITH D-XYLULOSE AND ADP,
RP CATALYTIC ACTIVITY, FUNCTION, SUBUNIT, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX PubMed=23179721; DOI=10.1074/jbc.m112.427997;
RA Bunker R.D., Bulloch E.M., Dickson J.M., Loomes K.M., Baker E.N.;
RT "Structure and function of human xylulokinase, an enzyme with important
RT roles in carbohydrate metabolism.";
RL J. Biol. Chem. 288:1643-1652(2013).
CC -!- FUNCTION: Phosphorylates D-xylulose to produce D-xylulose 5-phosphate,
CC a molecule that may play an important role in the regulation of glucose
CC metabolism and lipogenesis. {ECO:0000269|PubMed:23179721}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + D-xylulose = ADP + D-xylulose 5-phosphate + H(+);
CC Xref=Rhea:RHEA:10964, ChEBI:CHEBI:15378, ChEBI:CHEBI:17140,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:57737, ChEBI:CHEBI:456216;
CC EC=2.7.1.17; Evidence={ECO:0000269|PubMed:23179721};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=24 uM for D-xylulose {ECO:0000269|PubMed:23179721};
CC -!- SUBUNIT: Monomer. {ECO:0000269|PubMed:23179721}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=2;
CC Name=1;
CC IsoId=O75191-1; Sequence=Displayed;
CC Name=2;
CC IsoId=O75191-2; Sequence=VSP_055522;
CC -!- SIMILARITY: Belongs to the FGGY kinase family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAA31527.1; Type=Miscellaneous discrepancy; Note=Probable cloning artifact.; Evidence={ECO:0000305};
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DR EMBL; AK293325; BAG56843.1; -; mRNA.
DR EMBL; AK314386; BAG37011.1; -; mRNA.
DR EMBL; AP006191; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; AP006193; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; CH471055; EAW64532.1; -; Genomic_DNA.
DR EMBL; BC137076; AAI37077.1; -; mRNA.
DR EMBL; BC137080; AAI37081.1; -; mRNA.
DR EMBL; AB015046; BAA31527.1; ALT_SEQ; mRNA.
DR CCDS; CCDS2678.1; -. [O75191-1]
DR RefSeq; NP_005099.2; NM_005108.3. [O75191-1]
DR PDB; 4BC2; X-ray; 1.97 A; A/B/C=1-536.
DR PDB; 4BC3; X-ray; 1.68 A; A/B/C=1-536.
DR PDB; 4BC4; X-ray; 1.79 A; A/B/C=1-536.
DR PDB; 4BC5; X-ray; 1.98 A; A/B/C=1-536.
DR PDBsum; 4BC2; -.
DR PDBsum; 4BC3; -.
DR PDBsum; 4BC4; -.
DR PDBsum; 4BC5; -.
DR AlphaFoldDB; O75191; -.
DR SMR; O75191; -.
DR BioGRID; 115268; 10.
DR IntAct; O75191; 1.
DR STRING; 9606.ENSP00000207870; -.
DR iPTMnet; O75191; -.
DR MetOSite; O75191; -.
DR PhosphoSitePlus; O75191; -.
DR BioMuta; XYLB; -.
DR EPD; O75191; -.
DR jPOST; O75191; -.
DR MassIVE; O75191; -.
DR MaxQB; O75191; -.
DR PaxDb; O75191; -.
DR PeptideAtlas; O75191; -.
DR PRIDE; O75191; -.
DR ProteomicsDB; 3889; -.
DR ProteomicsDB; 49863; -. [O75191-1]
DR Antibodypedia; 28592; 83 antibodies from 19 providers.
DR DNASU; 9942; -.
DR Ensembl; ENST00000207870.8; ENSP00000207870.3; ENSG00000093217.11. [O75191-1]
DR GeneID; 9942; -.
DR KEGG; hsa:9942; -.
DR MANE-Select; ENST00000207870.8; ENSP00000207870.3; NM_005108.4; NP_005099.2.
DR UCSC; uc003cic.3; human. [O75191-1]
DR CTD; 9942; -.
DR DisGeNET; 9942; -.
DR GeneCards; XYLB; -.
DR HGNC; HGNC:12839; XYLB.
DR HPA; ENSG00000093217; Tissue enhanced (liver).
DR MIM; 604049; gene.
DR neXtProt; NX_O75191; -.
DR OpenTargets; ENSG00000093217; -.
DR PharmGKB; PA37430; -.
DR VEuPathDB; HostDB:ENSG00000093217; -.
DR eggNOG; KOG2531; Eukaryota.
DR GeneTree; ENSGT01000000214434; -.
DR HOGENOM; CLU_016149_8_0_1; -.
DR InParanoid; O75191; -.
DR OMA; QHGTVFW; -.
DR OrthoDB; 592116at2759; -.
DR PhylomeDB; O75191; -.
DR TreeFam; TF313643; -.
DR BRENDA; 2.7.1.17; 2681.
DR PathwayCommons; O75191; -.
DR Reactome; R-HSA-5661270; Formation of xylulose-5-phosphate.
DR BioGRID-ORCS; 9942; 12 hits in 1080 CRISPR screens.
DR ChiTaRS; XYLB; human.
DR GenomeRNAi; 9942; -.
DR Pharos; O75191; Tbio.
DR PRO; PR:O75191; -.
DR Proteomes; UP000005640; Chromosome 3.
DR RNAct; O75191; protein.
DR Bgee; ENSG00000093217; Expressed in right lobe of liver and 117 other tissues.
DR ExpressionAtlas; O75191; baseline and differential.
DR Genevisible; O75191; HS.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0016773; F:phosphotransferase activity, alcohol group as acceptor; IBA:GO_Central.
DR GO; GO:0004856; F:xylulokinase activity; IDA:UniProtKB.
DR GO; GO:0005975; P:carbohydrate metabolic process; TAS:ProtInc.
DR GO; GO:0042732; P:D-xylose metabolic process; IEA:UniProtKB-KW.
DR GO; GO:0006091; P:generation of precursor metabolites and energy; TAS:ProtInc.
DR GO; GO:0019640; P:glucuronate catabolic process to xylulose 5-phosphate; TAS:Reactome.
DR GO; GO:0016310; P:phosphorylation; IBA:GO_Central.
DR GO; GO:0005998; P:xylulose catabolic process; TAS:BHF-UCL.
DR GO; GO:0005997; P:xylulose metabolic process; IDA:UniProtKB.
DR CDD; cd07776; FGGY_D-XK_euk; 1.
DR InterPro; IPR043129; ATPase_NBD.
DR InterPro; IPR000577; Carb_kinase_FGGY.
DR InterPro; IPR018485; Carb_kinase_FGGY_C.
DR InterPro; IPR018484; Carb_kinase_FGGY_N.
DR InterPro; IPR042024; D-XK_euk.
DR Pfam; PF02782; FGGY_C; 1.
DR Pfam; PF00370; FGGY_N; 1.
DR PIRSF; PIRSF000538; GlpK; 1.
DR SUPFAM; SSF53067; SSF53067; 2.
PE 1: Evidence at protein level;
KW 3D-structure; Alternative splicing; ATP-binding; Carbohydrate metabolism;
KW Kinase; Nucleotide-binding; Reference proteome; Transferase;
KW Xylose metabolism.
FT CHAIN 1..536
FT /note="Xylulose kinase"
FT /id="PRO_0000230985"
FT BINDING 99
FT /ligand="substrate"
FT BINDING 170
FT /ligand="substrate"
FT BINDING 280
FT /ligand="substrate"
FT BINDING 281
FT /ligand="substrate"
FT BINDING 355
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 441..442
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT BINDING 445
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT VAR_SEQ 1..137
FT /note="Missing (in isoform 2)"
FT /evidence="ECO:0000303|PubMed:14702039"
FT /id="VSP_055522"
FT VARIANT 85
FT /note="D -> E (in dbSNP:rs17118)"
FT /evidence="ECO:0000269|PubMed:14702039,
FT ECO:0000269|PubMed:9763671, ECO:0000269|Ref.3"
FT /id="VAR_055151"
FT VARIANT 133
FT /note="D -> N (in dbSNP:rs2234610)"
FT /id="VAR_055152"
FT VARIANT 139
FT /note="D -> E (in dbSNP:rs151611)"
FT /id="VAR_055153"
FT VARIANT 262
FT /note="Y -> N (in dbSNP:rs196380)"
FT /evidence="ECO:0000269|PubMed:9763671"
FT /id="VAR_055154"
FT VARIANT 348
FT /note="N -> D (in dbSNP:rs2234622)"
FT /id="VAR_055155"
FT STRAND 9..15
FT /evidence="ECO:0007829|PDB:4BC3"
FT STRAND 17..26
FT /evidence="ECO:0007829|PDB:4BC3"
FT STRAND 31..38
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 39..42
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 44..46
FT /evidence="ECO:0007829|PDB:4BC3"
FT STRAND 52..54
FT /evidence="ECO:0007829|PDB:4BC3"
FT STRAND 61..64
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 65..81
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 86..88
FT /evidence="ECO:0007829|PDB:4BC3"
FT STRAND 89..96
FT /evidence="ECO:0007829|PDB:4BC3"
FT STRAND 101..105
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 108..113
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 121..125
FT /evidence="ECO:0007829|PDB:4BC3"
FT STRAND 132..135
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 143..153
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 156..163
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 172..182
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 184..188
FT /evidence="ECO:0007829|PDB:4BC3"
FT STRAND 190..195
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 196..205
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 213..216
FT /evidence="ECO:0007829|PDB:4BC3"
FT STRAND 218..220
FT /evidence="ECO:0007829|PDB:4BC4"
FT TURN 224..227
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 231..237
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 241..245
FT /evidence="ECO:0007829|PDB:4BC3"
FT STRAND 254..257
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 260..266
FT /evidence="ECO:0007829|PDB:4BC3"
FT STRAND 273..275
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 280..287
FT /evidence="ECO:0007829|PDB:4BC3"
FT STRAND 295..311
FT /evidence="ECO:0007829|PDB:4BC3"
FT STRAND 316..323
FT /evidence="ECO:0007829|PDB:4BC3"
FT STRAND 326..339
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 340..350
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 355..363
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 369..371
FT /evidence="ECO:0007829|PDB:4BC3"
FT STRAND 373..379
FT /evidence="ECO:0007829|PDB:4BC3"
FT STRAND 382..384
FT /evidence="ECO:0007829|PDB:4BC3"
FT STRAND 388..392
FT /evidence="ECO:0007829|PDB:4BC3"
FT STRAND 398..400
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 404..425
FT /evidence="ECO:0007829|PDB:4BC3"
FT STRAND 436..440
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 441..444
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 446..456
FT /evidence="ECO:0007829|PDB:4BC3"
FT STRAND 460..462
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 468..481
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 484..486
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 489..493
FT /evidence="ECO:0007829|PDB:4BC3"
FT STRAND 500..503
FT /evidence="ECO:0007829|PDB:4BC3"
FT HELIX 509..530
FT /evidence="ECO:0007829|PDB:4BC3"
SQ SEQUENCE 536 AA; 58382 MW; E2FC1C45308D71A8 CRC64;
MAEHAPRRCC LGWDFSTQQV KVVAVDAELN VFYEESVHFD RDLPEFGTQG GVHVHKDGLT
VTSPVLMWVQ ALDIILEKMK ASGFDFSQVL ALSGAGQQHG SIYWKAGAQQ ALTSLSPDLR
LHQQLQDCFS ISDCPVWMDS STTAQCRQLE AAVGGAQALS CLTGSRAYER FTGNQIAKIY
QQNPEAYSHT ERISLVSSFA ASLFLGSYSP IDYSDGSGMN LLQIQDKVWS QACLGACAPH
LEEKLSPPVP SCSVVGAISS YYVQRYGFPP GCKVVAFTGD NPASLAGMRL EEGDIAVSLG
TSDTLFLWLQ EPMPALEGHI FCNPVDSQHY MALLCFKNGS LMREKIRNES VSRSWSDFSK
ALQSTEMGNG GNLGFYFDVM EITPEIIGRH RFNTENHKVA AFPGDVEVRA LIEGQFMAKR
IHAEGLGYRV MSKTKILATG GASHNREILQ VLADVFDAPV YVIDTANSAC VGSAYRAFHG
LAGGTDVPFS EVVKLAPNPR LAATPSPGAS QVYEALLPQY AKLEQRILSQ TRGPPE
