M2GD_RAT
ID M2GD_RAT Reviewed; 857 AA.
AC Q63342;
DT 01-NOV-1997, integrated into UniProtKB/Swiss-Prot.
DT 01-NOV-1996, sequence version 1.
DT 03-AUG-2022, entry version 142.
DE RecName: Full=Dimethylglycine dehydrogenase, mitochondrial;
DE EC=1.5.8.4 {ECO:0000269|PubMed:2417560, ECO:0000269|PubMed:24858690};
DE AltName: Full=ME2GLYDH;
DE Flags: Precursor;
GN Name=Dmgdh;
OS Rattus norvegicus (Rat).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Rattus.
OX NCBI_TaxID=10116;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA].
RC STRAIN=Wistar; TISSUE=Liver;
RX PubMed=1710985; DOI=10.1111/j.1432-1033.1991.tb16083.x;
RA Lang H., Polster M., Brandsch R.;
RT "Rat liver dimethylglycine dehydrogenase. Flavinylation of the enzyme in
RT hepatocytes in primary culture and characterization of a cDNA clone.";
RL Eur. J. Biochem. 198:793-799(1991).
RN [2]
RP PROTEIN SEQUENCE OF 75-99, COFACTOR, AND FAD-BINDING.
RC TISSUE=Liver;
RX PubMed=4055729; DOI=10.1016/s0021-9258(17)38827-0;
RA Cook R.J., Misono K.S., Wagner C.;
RT "The amino acid sequences of the flavin-peptides of dimethylglycine
RT dehydrogenase and sarcosine dehydrogenase from rat liver mitochondria.";
RL J. Biol. Chem. 260:12998-13002(1985).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, ENZYME KINETICS, AND SUBCELLULAR LOCATION.
RX PubMed=2417560; DOI=10.1016/0003-9861(85)90516-8;
RA Porter D.H., Cook R.J., Wagner C.;
RT "Enzymatic properties of dimethylglycine dehydrogenase and sarcosine
RT dehydrogenase from rat liver.";
RL Arch. Biochem. Biophys. 243:396-407(1985).
RN [4]
RP X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) OF 2-857 IN COMPLEXES WITH FAD AND
RP TETRAHYDROFOLATE, CATALYTIC ACTIVITY, COFACTOR, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RX PubMed=24858690; DOI=10.1016/j.bbrc.2014.05.064;
RA Luka Z., Pakhomova S., Loukachevitch L.V., Newcomer M.E., Wagner C.;
RT "Folate in demethylation: the crystal structure of the rat dimethylglycine
RT dehydrogenase complexed with tetrahydrofolate.";
RL Biochem. Biophys. Res. Commun. 449:392-398(2014).
CC -!- FUNCTION: Catalyzes the demethylation of N,N-dimethylglycine to
CC sarcosine. Also has activity with sarcosine in vitro.
CC {ECO:0000269|PubMed:2417560}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(6S)-5,6,7,8-tetrahydrofolyl-(gamma-L-Glu)(n) + H(+) + N,N-
CC dimethylglycine + oxidized [electron-transfer flavoprotein] = (6R)-
CC 5,10-methylenetetrahydrofolyl-(gamma-L-Glu)(n) + reduced [electron-
CC transfer flavoprotein] + sarcosine; Xref=Rhea:RHEA:52856, Rhea:RHEA-
CC COMP:10685, Rhea:RHEA-COMP:10686, Rhea:RHEA-COMP:13257, Rhea:RHEA-
CC COMP:14738, ChEBI:CHEBI:15378, ChEBI:CHEBI:57433, ChEBI:CHEBI:57692,
CC ChEBI:CHEBI:58251, ChEBI:CHEBI:58307, ChEBI:CHEBI:136572,
CC ChEBI:CHEBI:141005; EC=1.5.8.4; Evidence={ECO:0000269|PubMed:2417560,
CC ECO:0000269|PubMed:24858690};
CC -!- COFACTOR:
CC Name=FAD; Xref=ChEBI:CHEBI:57692;
CC Evidence={ECO:0000269|PubMed:24858690, ECO:0000269|PubMed:4055729};
CC Note=Binds 1 FAD covalently per monomer. {ECO:0000269|PubMed:24858690,
CC ECO:0000269|PubMed:4055729};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=760 uM for N,N-dimethylglycine for precursor enzyme
CC {ECO:0000269|PubMed:24858690};
CC KM=580 uM for N,N-dimethylglycine for mature enzyme
CC {ECO:0000269|PubMed:24858690};
CC Note=kcat is 1.43-1.48 sec(1-). {ECO:0000269|PubMed:24858690};
CC -!- PATHWAY: Amine and polyamine degradation; betaine degradation;
CC sarcosine from betaine: step 2/2.
CC -!- SUBCELLULAR LOCATION: Mitochondrion {ECO:0000269|PubMed:2417560}.
CC -!- SIMILARITY: Belongs to the GcvT family. {ECO:0000305}.
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DR EMBL; X55995; CAA39468.1; -; mRNA.
DR PIR; S16133; S16133.
DR PDB; 4P9S; X-ray; 2.32 A; A/B=22-857.
DR PDB; 4PAA; X-ray; 2.26 A; A/B=22-857.
DR PDB; 4PAB; X-ray; 1.85 A; A/B=2-857.
DR PDBsum; 4P9S; -.
DR PDBsum; 4PAA; -.
DR PDBsum; 4PAB; -.
DR AlphaFoldDB; Q63342; -.
DR SMR; Q63342; -.
DR IntAct; Q63342; 1.
DR MINT; Q63342; -.
DR STRING; 10116.ENSRNOP00000030481; -.
DR iPTMnet; Q63342; -.
DR PhosphoSitePlus; Q63342; -.
DR PaxDb; Q63342; -.
DR PRIDE; Q63342; -.
DR UCSC; RGD:620453; rat.
DR RGD; 620453; Dmgdh.
DR eggNOG; KOG2844; Eukaryota.
DR InParanoid; Q63342; -.
DR PhylomeDB; Q63342; -.
DR BioCyc; MetaCyc:MON-16117; -.
DR BRENDA; 1.5.8.4; 5301.
DR Reactome; R-RNO-6798163; Choline catabolism.
DR UniPathway; UPA00291; UER00433.
DR PRO; PR:Q63342; -.
DR Proteomes; UP000002494; Unplaced.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005759; C:mitochondrial matrix; IBA:GO_Central.
DR GO; GO:0005739; C:mitochondrion; IDA:RGD.
DR GO; GO:0047865; F:dimethylglycine dehydrogenase activity; IDA:RGD.
DR GO; GO:0050660; F:flavin adenine dinucleotide binding; IDA:RGD.
DR GO; GO:0005542; F:folic acid binding; IDA:RGD.
DR GO; GO:0016491; F:oxidoreductase activity; IBA:GO_Central.
DR GO; GO:0006579; P:amino-acid betaine catabolic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0042426; P:choline catabolic process; ISO:RGD.
DR GO; GO:0019695; P:choline metabolic process; TAS:RGD.
DR GO; GO:0035999; P:tetrahydrofolate interconversion; IDA:RGD.
DR Gene3D; 3.30.1360.120; -; 1.
DR Gene3D; 3.50.50.60; -; 1.
DR InterPro; IPR006076; FAD-dep_OxRdtase.
DR InterPro; IPR036188; FAD/NAD-bd_sf.
DR InterPro; IPR032503; FAO_M.
DR InterPro; IPR013977; GCV_T_C.
DR InterPro; IPR006222; GCV_T_N.
DR InterPro; IPR029043; GcvT/YgfZ_C.
DR InterPro; IPR027266; TrmE/GcvT_dom1.
DR Pfam; PF01266; DAO; 1.
DR Pfam; PF16350; FAO_M; 1.
DR Pfam; PF01571; GCV_T; 1.
DR Pfam; PF08669; GCV_T_C; 1.
DR SUPFAM; SSF101790; SSF101790; 1.
DR SUPFAM; SSF51905; SSF51905; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Acetylation; Direct protein sequencing; FAD; Flavoprotein;
KW Mitochondrion; Oxidoreductase; Reference proteome; Transit peptide.
FT TRANSIT 1..43
FT /note="Mitochondrion"
FT /evidence="ECO:0000255"
FT CHAIN 44..857
FT /note="Dimethylglycine dehydrogenase, mitochondrial"
FT /id="PRO_0000010769"
FT REGION 15..39
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT BINDING 52..53
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:24858690,
FT ECO:0007744|PDB:4P9S, ECO:0007744|PDB:4PAA,
FT ECO:0007744|PDB:4PAB"
FT BINDING 73..74
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:24858690,
FT ECO:0007744|PDB:4P9S, ECO:0007744|PDB:4PAA,
FT ECO:0007744|PDB:4PAB"
FT BINDING 80..88
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:24858690,
FT ECO:0007744|PDB:4P9S, ECO:0007744|PDB:4PAA,
FT ECO:0007744|PDB:4PAB"
FT BINDING 212
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:24858690,
FT ECO:0007744|PDB:4P9S, ECO:0007744|PDB:4PAA,
FT ECO:0007744|PDB:4PAB"
FT BINDING 244
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:24858690,
FT ECO:0007744|PDB:4P9S, ECO:0007744|PDB:4PAB"
FT BINDING 390..395
FT /ligand="FAD"
FT /ligand_id="ChEBI:CHEBI:57692"
FT /evidence="ECO:0000269|PubMed:24858690,
FT ECO:0007744|PDB:4P9S, ECO:0007744|PDB:4PAA,
FT ECO:0007744|PDB:4PAB"
FT BINDING 573..575
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000269|PubMed:24858690,
FT ECO:0007744|PDB:4PAA, ECO:0007744|PDB:4PAB"
FT BINDING 669
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000269|PubMed:24858690,
FT ECO:0007744|PDB:4PAA"
FT BINDING 676..678
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000269|PubMed:24858690,
FT ECO:0007744|PDB:4PAA, ECO:0007744|PDB:4PAB"
FT BINDING 737
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000269|PubMed:24858690,
FT ECO:0007744|PDB:4PAA, ECO:0007744|PDB:4PAB"
FT MOD_RES 84
FT /note="Tele-8alpha-FAD histidine"
FT /evidence="ECO:0000269|PubMed:24858690,
FT ECO:0000269|PubMed:4055729, ECO:0007744|PDB:4P9S,
FT ECO:0007744|PDB:4PAA, ECO:0007744|PDB:4PAB"
FT MOD_RES 107
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q9DBT9"
FT MOD_RES 141
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q9DBT9"
FT MOD_RES 141
FT /note="N6-succinyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q9DBT9"
FT MOD_RES 161
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q9DBT9"
FT MOD_RES 216
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q9DBT9"
FT MOD_RES 310
FT /note="N6-succinyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q9DBT9"
FT MOD_RES 312
FT /note="N6-succinyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q9DBT9"
FT MOD_RES 328
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q9DBT9"
FT MOD_RES 353
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q9DBT9"
FT MOD_RES 427
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q9DBT9"
FT MOD_RES 427
FT /note="N6-succinyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q9DBT9"
FT MOD_RES 469
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q9DBT9"
FT MOD_RES 469
FT /note="N6-succinyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q9DBT9"
FT MOD_RES 516
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q9DBT9"
FT MOD_RES 516
FT /note="N6-succinyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q9DBT9"
FT MOD_RES 648
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q9DBT9"
FT MOD_RES 648
FT /note="N6-succinyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q9DBT9"
FT MOD_RES 757
FT /note="N6-acetyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q9DBT9"
FT MOD_RES 786
FT /note="N6-acetyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q9DBT9"
FT MOD_RES 786
FT /note="N6-succinyllysine; alternate"
FT /evidence="ECO:0000250|UniProtKB:Q9DBT9"
FT MOD_RES 788
FT /note="N6-succinyllysine"
FT /evidence="ECO:0000250|UniProtKB:Q9DBT9"
FT STRAND 41..48
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 52..63
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 68..72
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 74..76
FT /evidence="ECO:0007829|PDB:4PAB"
FT TURN 77..81
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 82..84
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 94..96
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 98..116
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 127..131
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 134..147
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 150..152
FT /evidence="ECO:0007829|PDB:4PAA"
FT STRAND 155..157
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 159..165
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 176..180
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 188..201
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 205..209
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 214..217
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 223..227
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 230..239
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 242..244
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 245..250
FT /evidence="ECO:0007829|PDB:4PAB"
FT TURN 251..253
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 259..268
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 272..275
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 283..286
FT /evidence="ECO:0007829|PDB:4PAB"
FT TURN 287..290
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 291..296
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 299..304
FT /evidence="ECO:0007829|PDB:4PAB"
FT TURN 308..310
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 315..320
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 336..338
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 339..348
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 350..353
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 357..367
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 374..377
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 384..388
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 393..410
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 418..420
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 422..424
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 431..443
FT /evidence="ECO:0007829|PDB:4PAB"
FT TURN 444..446
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 467..471
FT /evidence="ECO:0007829|PDB:4PAB"
FT TURN 472..474
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 475..480
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 483..489
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 508..520
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 523..526
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 530..537
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 540..547
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 548..550
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 557..564
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 570..580
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 583..588
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 590..592
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 593..606
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 612..615
FT /evidence="ECO:0007829|PDB:4PAB"
FT TURN 617..619
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 620..627
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 630..635
FT /evidence="ECO:0007829|PDB:4PAB"
FT TURN 644..646
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 651..657
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 660..665
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 671..680
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 681..683
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 684..694
FT /evidence="ECO:0007829|PDB:4PAB"
FT TURN 695..699
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 705..714
FT /evidence="ECO:0007829|PDB:4PAB"
FT TURN 720..722
FT /evidence="ECO:0007829|PDB:4PAB"
FT TURN 730..734
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 736..738
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 743..745
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 750..759
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 762..770
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 782..785
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 788..799
FT /evidence="ECO:0007829|PDB:4PAB"
FT TURN 800..803
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 804..812
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 813..815
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 821..826
FT /evidence="ECO:0007829|PDB:4PAB"
FT STRAND 829..835
FT /evidence="ECO:0007829|PDB:4PAB"
FT HELIX 844..857
FT /evidence="ECO:0007829|PDB:4PAB"
SQ SEQUENCE 857 AA; 96048 MW; A6FED946B8AB9878 CRC64;
MLRLGALRLR GLALRSSQGR PSSAGLREGQ ESPPSPPEWK DRAETVIIGG GCVGVSLAYH
LAKAGMRDVV LLEKSELTAG STWHAAGLTT YFHPGINLKK IHYDSIKLYE RLEEETGQVV
GFHQPGSIRL ATTPERVDEF KYQMTRTNWH ATEQYIIEPE KIHELFPLLN MDKILAGLYN
PGDGHIDPYS LTMALATGAR KYGVLLKYPA PVTSLKPRPD GTWDVETPQG SVRANRIVNA
AGFWAREVGK MIGLDHPLIP VQHQYVVTST IPEVKALKRE LPVLRDLEGS YYLRQERDGL
LFGPYESQEK MKLQASWVAH GVPPGFGKEL FESDLDRITE HVEAAMEMVP VLKKADIINI
VNGPITYSPD ILPMVGPHQG VRNYWVAIGF GYGIIHAGGV GKYLSDWILH GEPPFDLIEL
DPNRYGKWTT TQYTEAKARE SYGFNNIVGY PKEERFAGRP TQRVSGLYKI LESKCSMGFH
AGWEQPHWFY KPGQDTQYRP SFRRTNWFRP VGSEYKQVMQ RVGVIDLSPF GKFNIKGQDS
TQLLDHLCAN VIPKVGFTNI SHMLTPRGRV YAELTVSHQS PGEFLLITGS GSELHDLRWI
EEAAVRGGYD VEIRNITDEL GVLGVAGPYA RRVLQKLTSE DLSDDVFKFL QTKSLKISDI
PVTAIRISYT GELGWELYHR REDSAALYER IMNAGQEEGI DNFGTYALNA LRLEKAFRAW
GSEMNCDTNP LEAGLDYFIK LNKPADFTGK QALKQIKAKG LKRRLVCLTL ATDDVDPEGN
ESVWYKGKVI GNTTSGSYSY SIQKSLAFAY VPVELSEVGQ QVEVELLGKN YPATIIQEPL
VLTEPTRTRL QKDGRKS
