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MNME_ECOLI
ID   MNME_ECOLI              Reviewed;         454 AA.
AC   P25522; Q2M819;
DT   01-MAY-1992, integrated into UniProtKB/Swiss-Prot.
DT   15-JUL-1998, sequence version 3.
DT   03-AUG-2022, entry version 195.
DE   RecName: Full=tRNA modification GTPase MnmE {ECO:0000255|HAMAP-Rule:MF_00379};
DE            EC=3.6.-.- {ECO:0000255|HAMAP-Rule:MF_00379};
GN   Name=mnmE {ECO:0000255|HAMAP-Rule:MF_00379};
GN   Synonyms=thdF {ECO:0000255|HAMAP-Rule:MF_00379},
GN   trmE {ECO:0000255|HAMAP-Rule:MF_00379}; OrderedLocusNames=b3706, JW3684;
OS   Escherichia coli (strain K12).
OC   Bacteria; Proteobacteria; Gammaproteobacteria; Enterobacterales;
OC   Enterobacteriaceae; Escherichia.
OX   NCBI_TaxID=83333;
RN   [1]
RP   PRELIMINARY NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC   STRAIN=K12;
RX   PubMed=1917835; DOI=10.1128/jb.173.19.6018-6024.1991;
RA   Alam K.Y., Clark D.P.;
RT   "Molecular cloning and sequence of the thdF gene, which is involved in
RT   thiophene and furan oxidation by Escherichia coli.";
RL   J. Bacteriol. 173:6018-6024(1991).
RN   [2]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=7686882; DOI=10.1006/geno.1993.1230;
RA   Burland V.D., Plunkett G. III, Daniels D.L., Blattner F.R.;
RT   "DNA sequence and analysis of 136 kilobases of the Escherichia coli genome:
RT   organizational symmetry around the origin of replication.";
RL   Genomics 16:551-561(1993).
RN   [3]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / MG1655 / ATCC 47076;
RX   PubMed=9278503; DOI=10.1126/science.277.5331.1453;
RA   Blattner F.R., Plunkett G. III, Bloch C.A., Perna N.T., Burland V.,
RA   Riley M., Collado-Vides J., Glasner J.D., Rode C.K., Mayhew G.F.,
RA   Gregor J., Davis N.W., Kirkpatrick H.A., Goeden M.A., Rose D.J., Mau B.,
RA   Shao Y.;
RT   "The complete genome sequence of Escherichia coli K-12.";
RL   Science 277:1453-1462(1997).
RN   [4]
RP   NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC   STRAIN=K12 / W3110 / ATCC 27325 / DSM 5911;
RX   PubMed=16738553; DOI=10.1038/msb4100049;
RA   Hayashi K., Morooka N., Yamamoto Y., Fujita K., Isono K., Choi S.,
RA   Ohtsubo E., Baba T., Wanner B.L., Mori H., Horiuchi T.;
RT   "Highly accurate genome sequences of Escherichia coli K-12 strains MG1655
RT   and W3110.";
RL   Mol. Syst. Biol. 2:E1-E5(2006).
RN   [5]
RP   CHARACTERIZATION, AND SUBCELLULAR LOCATION.
RX   PubMed=10601028; DOI=10.1093/emboj/18.24.7063;
RA   Cabedo H., Macian F., Villarroya M., Escudero J.C., Martinez-Vicente M.,
RA   Knecht E., Armengod M.-E.;
RT   "The Escherichia coli trmE (mnmE) gene, involved in tRNA modification,
RT   codes for an evolutionarily conserved GTPase with unusual biochemical
RT   properties.";
RL   EMBO J. 18:7063-7076(1999).
RN   [6]
RP   GTPASE ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND MUTAGENESIS OF GLY-228;
RP   ASP-270; ASP-338 AND CYS-451.
RX   PubMed=12730230; DOI=10.1074/jbc.m301381200;
RA   Yim L., Martinez-Vicente M., Villarroya M., Aguado C., Knecht E.,
RA   Armengod M.-E.;
RT   "The GTPase activity and C-terminal cysteine of the Escherichia coli MnmE
RT   protein are essential for its tRNA modifying function.";
RL   J. Biol. Chem. 278:28378-28387(2003).
RN   [7]
RP   MUTAGENESIS OF ARG-224; GLY-249; THR-250; THR-251; ARG-252; ASP-253;
RP   ARG-256; ARG-275 AND ARG-288.
RX   PubMed=15983041; DOI=10.1074/jbc.m503223200;
RA   Martinez-Vicente M., Yim L., Villarroya M., Mellado M., Perez-Paya E.,
RA   Bjoerk G.R., Armengod M.-E.;
RT   "Effects of mutagenesis in the switch I region and conserved arginines of
RT   Escherichia coli MnmE protein, a GTPase involved in tRNA modification.";
RL   J. Biol. Chem. 280:30660-30670(2005).
RN   [8]
RP   INTERACTION WITH MNMG.
RC   STRAIN=K12;
RX   PubMed=17062623; DOI=10.1093/nar/gkl752;
RA   Yim L., Moukadiri I., Bjoerk G.R., Armengod M.-E.;
RT   "Further insights into the tRNA modification process controlled by proteins
RT   MnmE and GidA of Escherichia coli.";
RL   Nucleic Acids Res. 34:5892-5905(2006).
RN   [9]
RP   X-RAY CRYSTALLOGRAPHY (1.7 ANGSTROMS) OF 216-384 IN COMPLEXES WITH GDP;
RP   TRANSITION STATE ANALOG; MAGNESIUM AND POTASSIUM IONS, SUBUNIT, AND
RP   MUTAGENESIS OF ASN-226; LEU-255 AND GLU-282.
RX   PubMed=16763562; DOI=10.1038/sj.emboj.7601171;
RA   Scrima A., Wittinghofer A.;
RT   "Dimerisation-dependent GTPase reaction of MnmE: how potassium acts as
RT   GTPase-activating element.";
RL   EMBO J. 25:2940-2951(2006).
RN   [10]
RP   STRUCTURE BY NMR OF 210-377, AND BIOPHYSICOCHEMICAL PROPERTIES.
RX   PubMed=17143896; DOI=10.1002/prot.21186;
RA   Monleon D., Martinez-Vicente M., Esteve V., Yim L., Prado S.,
RA   Armengod M.-E., Celda B.;
RT   "Structural insights into the GTPase domain of Escherichia coli MnmE
RT   protein.";
RL   Proteins 66:726-739(2007).
CC   -!- FUNCTION: Exhibits a very high intrinsic GTPase hydrolysis rate.
CC       Involved in the addition of a carboxymethylaminomethyl (cmnm) group at
CC       the wobble position (U34) of certain tRNAs, forming tRNA-
CC       cmnm(5)s(2)U34.
CC   -!- COFACTOR:
CC       Name=K(+); Xref=ChEBI:CHEBI:29103;
CC       Note=Binds 1 potassium ion per subunit.;
CC   -!- ACTIVITY REGULATION: GTPase activity is strongly activated by potassium
CC       ions.
CC   -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC       Kinetic parameters:
CC         KM=511 uM for GTP {ECO:0000269|PubMed:12730230,
CC         ECO:0000269|PubMed:17143896};
CC         KM=346 uM for XTP {ECO:0000269|PubMed:12730230,
CC         ECO:0000269|PubMed:17143896};
CC         Vmax=193 nmol/min/mg enzyme with GTP as substrate
CC         {ECO:0000269|PubMed:12730230, ECO:0000269|PubMed:17143896};
CC         Vmax=100 nmol/min/mg enzyme with XTP as substrate
CC         {ECO:0000269|PubMed:12730230, ECO:0000269|PubMed:17143896};
CC       pH dependence:
CC         Optimum pH is 7.5-9.5. {ECO:0000269|PubMed:12730230,
CC         ECO:0000269|PubMed:17143896};
CC   -!- SUBUNIT: Homodimer. Heterotetramer of two MnmE and two MnmG subunits.
CC       {ECO:0000255|HAMAP-Rule:MF_00379, ECO:0000269|PubMed:16763562}.
CC   -!- INTERACTION:
CC       P25522; P25522: mnmE; NbExp=3; IntAct=EBI-550986, EBI-550986;
CC       P25522; P0A6U3: mnmG; NbExp=6; IntAct=EBI-550986, EBI-550977;
CC       P25522; P69432: pgaD; NbExp=5; IntAct=EBI-550986, EBI-562069;
CC   -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00379,
CC       ECO:0000269|PubMed:10601028}. Note=Partially associated with the inner
CC       membrane.
CC   -!- SIMILARITY: Belongs to the TRAFAC class TrmE-Era-EngA-EngB-Septin-like
CC       GTPase superfamily. TrmE GTPase family. {ECO:0000255|HAMAP-
CC       Rule:MF_00379}.
CC   -!- SEQUENCE CAUTION:
CC       Sequence=AAB19981.1; Type=Miscellaneous discrepancy; Evidence={ECO:0000305};
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DR   EMBL; S57109; AAB19981.1; ALT_SEQ; Genomic_DNA.
DR   EMBL; L10328; AAA62057.1; -; Genomic_DNA.
DR   EMBL; U00096; AAC76729.1; -; Genomic_DNA.
DR   EMBL; AP009048; BAE77587.1; -; Genomic_DNA.
DR   PIR; A38160; A38160.
DR   PIR; C65173; C65173.
DR   RefSeq; NP_418162.1; NC_000913.3.
DR   RefSeq; WP_001282346.1; NZ_SSZK01000035.1.
DR   PDB; 1RFL; NMR; -; A=210-377.
DR   PDB; 2GJ8; X-ray; 1.70 A; A/B/C/D=216-384.
DR   PDB; 2GJ9; X-ray; 2.00 A; A/B/C/D=216-384.
DR   PDB; 2GJA; X-ray; 1.85 A; A/B=216-384.
DR   PDBsum; 1RFL; -.
DR   PDBsum; 2GJ8; -.
DR   PDBsum; 2GJ9; -.
DR   PDBsum; 2GJA; -.
DR   AlphaFoldDB; P25522; -.
DR   SMR; P25522; -.
DR   BioGRID; 4261522; 160.
DR   BioGRID; 852524; 3.
DR   ComplexPortal; CPX-5361; tRNA uridine 5-carboxymethylaminomethyl modification complex.
DR   DIP; DIP-11033N; -.
DR   IntAct; P25522; 24.
DR   STRING; 511145.b3706; -.
DR   jPOST; P25522; -.
DR   PaxDb; P25522; -.
DR   PRIDE; P25522; -.
DR   EnsemblBacteria; AAC76729; AAC76729; b3706.
DR   EnsemblBacteria; BAE77587; BAE77587; BAE77587.
DR   GeneID; 948222; -.
DR   KEGG; ecj:JW3684; -.
DR   KEGG; eco:b3706; -.
DR   PATRIC; fig|1411691.4.peg.2997; -.
DR   EchoBASE; EB0990; -.
DR   eggNOG; COG0486; Bacteria.
DR   HOGENOM; CLU_019624_4_1_6; -.
DR   InParanoid; P25522; -.
DR   OMA; CEIQCHG; -.
DR   PhylomeDB; P25522; -.
DR   BioCyc; EcoCyc:EG10997-MON; -.
DR   BioCyc; MetaCyc:EG10997-MON; -.
DR   EvolutionaryTrace; P25522; -.
DR   PRO; PR:P25522; -.
DR   Proteomes; UP000000318; Chromosome.
DR   Proteomes; UP000000625; Chromosome.
DR   GO; GO:0005737; C:cytoplasm; IDA:EcoCyc.
DR   GO; GO:0005829; C:cytosol; IDA:EcoCyc.
DR   GO; GO:0002144; C:cytosolic tRNA wobble base thiouridylase complex; IPI:ComplexPortal.
DR   GO; GO:0005886; C:plasma membrane; IDA:EcoCyc.
DR   GO; GO:0019003; F:GDP binding; IDA:EcoCyc.
DR   GO; GO:0005525; F:GTP binding; IDA:EcoCyc.
DR   GO; GO:0003924; F:GTPase activity; IDA:EcoCyc.
DR   GO; GO:0042802; F:identical protein binding; IPI:IntAct.
DR   GO; GO:0030955; F:potassium ion binding; IDA:EcoCyc.
DR   GO; GO:0061077; P:chaperone-mediated protein folding; IDA:EcoCyc.
DR   GO; GO:0140018; P:regulation of cytoplasmic translational fidelity; IC:ComplexPortal.
DR   GO; GO:0009268; P:response to pH; IMP:EcoCyc.
DR   GO; GO:0030488; P:tRNA methylation; IMP:EcoCyc.
DR   GO; GO:0002926; P:tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation; IDA:ComplexPortal.
DR   GO; GO:0002098; P:tRNA wobble uridine modification; IDA:EcoCyc.
DR   CDD; cd04164; trmE; 1.
DR   Gene3D; 1.20.120.430; -; 1.
DR   Gene3D; 3.30.1360.120; -; 1.
DR   Gene3D; 3.40.50.300; -; 1.
DR   HAMAP; MF_00379; GTPase_MnmE; 1.
DR   InterPro; IPR031168; G_TrmE.
DR   InterPro; IPR006073; GTP-bd.
DR   InterPro; IPR018948; GTP-bd_TrmE_N.
DR   InterPro; IPR004520; GTPase_MnmE.
DR   InterPro; IPR027368; MnmE_dom2.
DR   InterPro; IPR025867; MnmE_helical.
DR   InterPro; IPR027417; P-loop_NTPase.
DR   InterPro; IPR005225; Small_GTP-bd_dom.
DR   InterPro; IPR027266; TrmE/GcvT_dom1.
DR   Pfam; PF01926; MMR_HSR1; 1.
DR   Pfam; PF12631; MnmE_helical; 1.
DR   Pfam; PF10396; TrmE_N; 1.
DR   SUPFAM; SSF52540; SSF52540; 1.
DR   TIGRFAMs; TIGR00450; mnmE_trmE_thdF; 1.
DR   TIGRFAMs; TIGR00231; small_GTP; 1.
DR   PROSITE; PS51709; G_TRME; 1.
PE   1: Evidence at protein level;
KW   3D-structure; Cytoplasm; GTP-binding; Hydrolase; Magnesium; Metal-binding;
KW   Nucleotide-binding; Potassium; Reference proteome; tRNA processing.
FT   CHAIN           1..454
FT                   /note="tRNA modification GTPase MnmE"
FT                   /id="PRO_0000188874"
FT   DOMAIN          216..377
FT                   /note="TrmE-type G"
FT   BINDING         23
FT                   /ligand="(6S)-5-formyl-5,6,7,8-tetrahydrofolate"
FT                   /ligand_id="ChEBI:CHEBI:57457"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00379"
FT   BINDING         80
FT                   /ligand="(6S)-5-formyl-5,6,7,8-tetrahydrofolate"
FT                   /ligand_id="ChEBI:CHEBI:57457"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00379"
FT   BINDING         120
FT                   /ligand="(6S)-5-formyl-5,6,7,8-tetrahydrofolate"
FT                   /ligand_id="ChEBI:CHEBI:57457"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00379"
FT   BINDING         226..231
FT                   /ligand="GTP"
FT                   /ligand_id="ChEBI:CHEBI:37565"
FT   BINDING         226
FT                   /ligand="K(+)"
FT                   /ligand_id="ChEBI:CHEBI:29103"
FT   BINDING         230
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT   BINDING         245..251
FT                   /ligand="GTP"
FT                   /ligand_id="ChEBI:CHEBI:37565"
FT   BINDING         245
FT                   /ligand="K(+)"
FT                   /ligand_id="ChEBI:CHEBI:29103"
FT   BINDING         247
FT                   /ligand="K(+)"
FT                   /ligand_id="ChEBI:CHEBI:29103"
FT   BINDING         250
FT                   /ligand="K(+)"
FT                   /ligand_id="ChEBI:CHEBI:29103"
FT   BINDING         251
FT                   /ligand="Mg(2+)"
FT                   /ligand_id="ChEBI:CHEBI:18420"
FT   BINDING         270..273
FT                   /ligand="GTP"
FT                   /ligand_id="ChEBI:CHEBI:37565"
FT   BINDING         335..338
FT                   /ligand="GTP"
FT                   /ligand_id="ChEBI:CHEBI:37565"
FT   BINDING         358..360
FT                   /ligand="GTP"
FT                   /ligand_id="ChEBI:CHEBI:37565"
FT   BINDING         454
FT                   /ligand="(6S)-5-formyl-5,6,7,8-tetrahydrofolate"
FT                   /ligand_id="ChEBI:CHEBI:57457"
FT                   /evidence="ECO:0000255|HAMAP-Rule:MF_00379"
FT   MUTAGEN         224
FT                   /note="R->A: 1.5-fold decrease in GTPase activity and
FT                   almost no change in affinity."
FT                   /evidence="ECO:0000269|PubMed:15983041"
FT   MUTAGEN         226
FT                   /note="N->A: 100-fold decrease in GTPase activity. 5-fold
FT                   decrease of affinity for GTP."
FT                   /evidence="ECO:0000269|PubMed:16763562"
FT   MUTAGEN         226
FT                   /note="N->K: 70-fold decrease in GTPase activity. 2-fold
FT                   decrease of affinity for GTP."
FT                   /evidence="ECO:0000269|PubMed:16763562"
FT   MUTAGEN         228
FT                   /note="G->A: Loss of GTP binding and hydrolase activity.
FT                   Completely impairs tRNA modifying function."
FT                   /evidence="ECO:0000269|PubMed:12730230"
FT   MUTAGEN         249
FT                   /note="G->A: 22-fold decrease in GTPase activity and 7-fold
FT                   increase of affinity."
FT                   /evidence="ECO:0000269|PubMed:15983041"
FT   MUTAGEN         250
FT                   /note="T->A: 4-fold decrease in GTPase activity and 1.5-
FT                   fold increase of affinity."
FT                   /evidence="ECO:0000269|PubMed:15983041"
FT   MUTAGEN         250
FT                   /note="T->S: 1.8-fold decrease in GTPase activity and 1.5-
FT                   fold increase of affinity."
FT                   /evidence="ECO:0000269|PubMed:15983041"
FT   MUTAGEN         251
FT                   /note="T->A: 92-fold decrease in GTPase activity and 59-
FT                   fold increase of affinity."
FT                   /evidence="ECO:0000269|PubMed:15983041"
FT   MUTAGEN         251
FT                   /note="T->S: 4-fold decrease in GTPase activity and 1.2-
FT                   fold decrease of affinity."
FT                   /evidence="ECO:0000269|PubMed:15983041"
FT   MUTAGEN         252
FT                   /note="R->A: 7-fold decrease in GTPase activity and 6-fold
FT                   increase of affinity."
FT                   /evidence="ECO:0000269|PubMed:15983041"
FT   MUTAGEN         252
FT                   /note="R->K: 2-fold decrease in GTPase activity and no
FT                   change in affinity."
FT                   /evidence="ECO:0000269|PubMed:15983041"
FT   MUTAGEN         253
FT                   /note="D->A: 9-fold decrease in GTPase activity and 13-fold
FT                   increase of affinity."
FT                   /evidence="ECO:0000269|PubMed:15983041"
FT   MUTAGEN         255
FT                   /note="L->D: 1.5-fold decrease in affinity for GTP."
FT                   /evidence="ECO:0000269|PubMed:16763562"
FT   MUTAGEN         256
FT                   /note="R->A: 2-fold decrease in GTPase activity and almost
FT                   no change in affinity."
FT                   /evidence="ECO:0000269|PubMed:15983041"
FT   MUTAGEN         270
FT                   /note="D->A: Does not affect GTP binding, but impairs
FT                   hydrolase activity. Completely impairs tRNA modifying
FT                   function."
FT                   /evidence="ECO:0000269|PubMed:12730230"
FT   MUTAGEN         275
FT                   /note="R->A: 6-fold decrease in GTPase activity and 1.9-
FT                   fold increase of affinity."
FT                   /evidence="ECO:0000269|PubMed:15983041"
FT   MUTAGEN         282
FT                   /note="E->A: 1900-fold decrease in GTPase activity."
FT                   /evidence="ECO:0000269|PubMed:16763562"
FT   MUTAGEN         282
FT                   /note="E->Q: 370-fold decrease in GTPase activity."
FT                   /evidence="ECO:0000269|PubMed:16763562"
FT   MUTAGEN         288
FT                   /note="R->A: 1.7-fold decrease in GTPase activity and 1.5-
FT                   fold increase of affinity."
FT                   /evidence="ECO:0000269|PubMed:15983041"
FT   MUTAGEN         338
FT                   /note="D->N: Strong decrease in GTP binding. Does not
FT                   affect hydrolase activity, but has 10-fold higher affinity
FT                   for XTP than for GTP. Partially impairs tRNA modifying
FT                   function."
FT                   /evidence="ECO:0000269|PubMed:12730230"
FT   MUTAGEN         451
FT                   /note="C->S: No change in GTP binding and hydrolase
FT                   activity. Does not affect association to the cell inner
FT                   membrane. Completely impairs tRNA modifying function."
FT                   /evidence="ECO:0000269|PubMed:12730230"
FT   STRAND          217..224
FT                   /evidence="ECO:0007829|PDB:2GJ8"
FT   HELIX           229..237
FT                   /evidence="ECO:0007829|PDB:2GJ8"
FT   STRAND          255..261
FT                   /evidence="ECO:0007829|PDB:2GJ8"
FT   STRAND          264..270
FT                   /evidence="ECO:0007829|PDB:2GJ8"
FT   HELIX           280..294
FT                   /evidence="ECO:0007829|PDB:2GJ8"
FT   STRAND          297..304
FT                   /evidence="ECO:0007829|PDB:2GJ8"
FT   TURN            305..307
FT                   /evidence="ECO:0007829|PDB:2GJ8"
FT   HELIX           313..316
FT                   /evidence="ECO:0007829|PDB:2GJ8"
FT   HELIX           318..323
FT                   /evidence="ECO:0007829|PDB:2GJ8"
FT   STRAND          330..335
FT                   /evidence="ECO:0007829|PDB:2GJ8"
FT   HELIX           337..340
FT                   /evidence="ECO:0007829|PDB:2GJ8"
FT   STRAND          345..349
FT                   /evidence="ECO:0007829|PDB:2GJ8"
FT   STRAND          352..356
FT                   /evidence="ECO:0007829|PDB:2GJ8"
FT   TURN            359..361
FT                   /evidence="ECO:0007829|PDB:2GJ8"
FT   HELIX           365..375
FT                   /evidence="ECO:0007829|PDB:2GJ8"
SQ   SEQUENCE   454 AA;  49231 MW;  032211797805D2FE CRC64;
     MSDNDTIVAQ ATPPGRGGVG ILRISGFKAR EVAETVLGKL PKPRYADYLP FKDADGSVLD
     QGIALWFPGP NSFTGEDVLE LQGHGGPVIL DLLLKRILTI PGLRIARPGE FSERAFLNDK
     LDLAQAEAIA DLIDASSEQA ARSALNSLQG AFSARVNHLV EALTHLRIYV EAAIDFPDEE
     IDFLSDGKIE AQLNDVIADL DAVRAEARQG SLLREGMKVV IAGRPNAGKS SLLNALAGRE
     AAIVTDIAGT TRDVLREHIH IDGMPLHIID TAGLREASDE VERIGIERAW QEIEQADRVL
     FMVDGTTTDA VDPAEIWPEF IARLPAKLPI TVVRNKADIT GETLGMSEVN GHALIRLSAR
     TGEGVDVLRN HLKQSMGFDT NMEGGFLARR RHLQALEQAA EHLQQGKAQL LGAWAGELLA
     EELRLAQQNL SEITGEFTSD DLLGRIFSSF CIGK
 
 
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