GLYC_BOMMO
ID GLYC_BOMMO Reviewed; 465 AA.
AC Q2F5L3; A0A3S5XFE5;
DT 10-FEB-2021, integrated into UniProtKB/Swiss-Prot.
DT 21-MAR-2006, sequence version 1.
DT 25-MAY-2022, entry version 102.
DE RecName: Full=Serine hydroxymethyltransferase {ECO:0000255|RuleBase:RU000585, ECO:0000303|PubMed:31298425};
DE Short=SHMT {ECO:0000303|PubMed:31298425};
DE EC=2.1.2.1 {ECO:0000255|RuleBase:RU000585, ECO:0000269|PubMed:31298425};
DE AltName: Full=Glycine hydroxymethyltransferase {ECO:0000305};
DE AltName: Full=Serine methylase {ECO:0000305};
DE AltName: Full=bmSHMT {ECO:0000303|PubMed:31298425};
GN Name=692975 {ECO:0000312|EnsemblMetazoa:BGIBMGA007079-TA};
OS Bombyx mori (Silk moth).
OC Eukaryota; Metazoa; Ecdysozoa; Arthropoda; Hexapoda; Insecta; Pterygota;
OC Neoptera; Endopterygota; Lepidoptera; Glossata; Ditrysia; Bombycoidea;
OC Bombycidae; Bombycinae; Bombyx.
OX NCBI_TaxID=7091 {ECO:0000312|EMBL:ABD36354.1};
RN [1] {ECO:0000312|EMBL:BBG28363.1}
RP NUCLEOTIDE SEQUENCE [MRNA], FUNCTION, CATALYTIC ACTIVITY,
RP BIOPHYSICOCHEMICAL PROPERTIES, TISSUE SPECIFICITY, AND MUTAGENESIS OF
RP HIS-119; HIS-132 AND HIS-135.
RC STRAIN=p50T {ECO:0000303|PubMed:31298425};
RC TISSUE=Larva {ECO:0000303|PubMed:31298425};
RX PubMed=31298425; DOI=10.1002/arch.21594;
RA Haque M.R., Hirowatari A., Nai N., Furuya S., Yamamoto K.;
RT "Serine hydroxymethyltransferase from the silkworm Bombyx mori:
RT Identification, distribution, and biochemical characterization.";
RL Arch. Insect Biochem. Physiol. 102:e21594-e21594(2019).
RN [2] {ECO:0000312|EMBL:ABD36354.1}
RP NUCLEOTIDE SEQUENCE [MRNA].
RA Niu B.L., Meng Z.Q., Weng H.B., Shen W.F., He L.H., Zheng K.F., Ye S.T.,
RA Lin T.B., Chen J.E.;
RT "Blast silkworm EST database for functional genes.";
RL Submitted (NOV-2005) to the EMBL/GenBank/DDBJ databases.
RN [3] {ECO:0000312|EnsemblMetazoa:BGIBMGA007079-TA}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=p50T {ECO:0000312|EnsemblMetazoa:BGIBMGA007079-TA};
RX PubMed=19121390; DOI=10.1016/j.ibmb.2008.11.004;
RG International Silkworm Genome Consortium;
RT "The genome of a lepidopteran model insect, the silkworm Bombyx mori.";
RL Insect Biochem. Mol. Biol. 38:1036-1045(2008).
CC -!- FUNCTION: Interconversion of serine and glycine.
CC {ECO:0000255|RuleBase:RU000585, ECO:0000269|PubMed:31298425}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=(6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O =
CC (6S)-5,6,7,8-tetrahydrofolate + L-serine; Xref=Rhea:RHEA:15481,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15636, ChEBI:CHEBI:33384,
CC ChEBI:CHEBI:57305, ChEBI:CHEBI:57453; EC=2.1.2.1;
CC Evidence={ECO:0000255|RuleBase:RU000585,
CC ECO:0000269|PubMed:31298425};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:15483;
CC Evidence={ECO:0000269|PubMed:31298425};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000255|PIRSR:PIRSR000412-50,
CC ECO:0000255|RuleBase:RU000585, ECO:0000305|PubMed:31298425};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.8 mM for L-serine (at pH 3.0 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:31298425};
CC KM=0.055 mM for tetrahydrofolate (at pH 3.0 and 30 degrees Celsius)
CC {ECO:0000269|PubMed:31298425};
CC Note=The kcat/Km for tetrahydrofolate is 0.081 mM(-1)sec(-1). The
CC kcat/Km for L-serine is 0.0022 mM(-1)sec(-1).
CC {ECO:0000269|PubMed:31298425};
CC pH dependence:
CC Optimum pH is 3.0. Stable under acidic conditions. Retains over 70%
CC of its original activity at pH range of 3-6.
CC {ECO:0000269|PubMed:31298425};
CC Temperature dependence:
CC Optimum temperature is 30 degrees Celsius.
CC {ECO:0000269|PubMed:31298425};
CC -!- PATHWAY: One-carbon metabolism; tetrahydrofolate interconversion.
CC {ECO:0000255|RuleBase:RU000585, ECO:0000305|PubMed:31298425}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000250|UniProtKB:P34896}.
CC -!- TISSUE SPECIFICITY: Highest expression in the ovary and testis. 6- to
CC 7-fold lower expression in hemocyte, silk gland, midgut and fat body.
CC {ECO:0000269|PubMed:31298425}.
CC -!- SIMILARITY: Belongs to the SHMT family.
CC {ECO:0000255|RuleBase:RU000585}.
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DR EMBL; LC422686; BBG28363.1; -; mRNA.
DR EMBL; DQ311410; ABD36354.1; -; mRNA.
DR EMBL; BABH01014817; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR RefSeq; NP_001040279.1; NM_001046814.1.
DR RefSeq; XP_012551202.1; XM_012695748.1.
DR AlphaFoldDB; Q2F5L3; -.
DR SMR; Q2F5L3; -.
DR STRING; 7091.BGIBMGA007079-TA; -.
DR EnsemblMetazoa; BGIBMGA007079-RA; BGIBMGA007079-TA; BGIBMGA007079.
DR GeneID; 692975; -.
DR KEGG; bmor:692975; -.
DR eggNOG; KOG2467; Eukaryota.
DR HOGENOM; CLU_022477_0_1_1; -.
DR InParanoid; Q2F5L3; -.
DR OMA; SHPAGLI; -.
DR OrthoDB; 372408at2759; -.
DR UniPathway; UPA00193; -.
DR Proteomes; UP000005204; Unassembled WGS sequence.
DR GO; GO:0004372; F:glycine hydroxymethyltransferase activity; IDA:UniProtKB.
DR GO; GO:0008168; F:methyltransferase activity; IEA:UniProtKB-KW.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IC:UniProtKB.
DR GO; GO:0019264; P:glycine biosynthetic process from serine; IDA:UniProtKB.
DR GO; GO:0006565; P:L-serine catabolic process; IDA:UniProtKB.
DR GO; GO:0032259; P:methylation; IEA:UniProtKB-KW.
DR GO; GO:0051289; P:protein homotetramerization; ISS:UniProtKB.
DR GO; GO:0035999; P:tetrahydrofolate interconversion; IDA:UniProtKB.
DR CDD; cd00378; SHMT; 1.
DR Gene3D; 3.40.640.10; -; 1.
DR Gene3D; 3.90.1150.10; -; 1.
DR HAMAP; MF_00051; SHMT; 1.
DR InterPro; IPR015424; PyrdxlP-dep_Trfase.
DR InterPro; IPR015421; PyrdxlP-dep_Trfase_major.
DR InterPro; IPR015422; PyrdxlP-dep_Trfase_small.
DR InterPro; IPR001085; Ser_HO-MeTrfase.
DR InterPro; IPR019798; Ser_HO-MeTrfase_PLP_BS.
DR InterPro; IPR039429; SHMT-like_dom.
DR PANTHER; PTHR11680; PTHR11680; 1.
DR Pfam; PF00464; SHMT; 1.
DR PIRSF; PIRSF000412; SHMT; 1.
DR SUPFAM; SSF53383; SSF53383; 1.
DR PROSITE; PS00096; SHMT; 1.
PE 1: Evidence at protein level;
KW Methyltransferase; One-carbon metabolism; Pyridoxal phosphate;
KW Reference proteome; Transferase.
FT CHAIN 1..465
FT /note="Serine hydroxymethyltransferase"
FT /id="PRO_0000451752"
FT MOD_RES 241
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000255|PIRSR:PIRSR000412-50"
FT MUTAGEN 119
FT /note="H->A: The kcat/Km for tetrahydrofolate is 1.1-fold
FT lower than that of the wild-type. The kcat/Km for L-serine
FT decreases to 30% compared to the wild-type."
FT /evidence="ECO:0000269|PubMed:31298425"
FT MUTAGEN 132
FT /note="H->A: The kcat/Km for tetrahydrofolate is 7.4-fold
FT lower than that of the wild-type."
FT /evidence="ECO:0000269|PubMed:31298425"
FT MUTAGEN 135
FT /note="H->A: The kcat/Km for tetrahydrofolate is 1.7-fold
FT lower than that of the wild-type. The kcat/Km for L-serine
FT decreases to 32% compared to the wild-type."
FT /evidence="ECO:0000269|PubMed:31298425"
FT CONFLICT 136
FT /note="G -> D (in Ref. 1; BBG28363)"
FT /evidence="ECO:0000305"
FT CONFLICT 417
FT /note="E -> D (in Ref. 1; BBG28363)"
FT /evidence="ECO:0000305"
SQ SEQUENCE 465 AA; 51221 MW; AF1C124C12E83FB1 CRC64;
MSAKLLNSNL WEADPELFDI IVKEKDRQRA GLEMIASENF TSVPVLQCLS SCLHNKYSEG
MPNQRYYGGN EYIDEIEILA QNRSLEAYRL KSEEWGVNVQ PYSGSPANFA VYTGIVEPHG
RIMGLDLPDG GHLTHGFFTA TKKISATSIF FESMPYKVDP KSGLIDYDKL AETAKLFKPR
LIIAGMSCYS RCLDYKRFRE IADANGAYLM ADMAHVSGLV AAGVIPSPFE YCDIVTTTTH
KTLRGPRAGV IFFRKGVRSV KANGQKVMYD LESKINQAVF PGLQGGPHNH AIAAIATAMK
QATTTEFVEY QKQVIKNAQR LCEGLISRGY SIATGGTDVH LALVDLRGVG LRGAPAERVL
ELCSVACNKN TVPGDISALN PSGIRLGTPA LTTRGLKEAD IDKVVDFIDR ALKIGLEIIK
VSGLKLVDFN KAIEENAEFK KKIENLKEEV ENYSKSFPLP GFDKY
