GLYA2_MYCTU
ID GLYA2_MYCTU Reviewed; 425 AA.
AC P9WGI7; L0T483; O53615;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 16-APR-2014, sequence version 1.
DT 03-AUG-2022, entry version 40.
DE RecName: Full=Serine hydroxymethyltransferase 2 {ECO:0000255|HAMAP-Rule:MF_00051};
DE Short=SHM2 {ECO:0000303|PubMed:12913008};
DE Short=SHMT 2 {ECO:0000255|HAMAP-Rule:MF_00051};
DE Short=Serine methylase 2 {ECO:0000255|HAMAP-Rule:MF_00051};
DE EC=2.1.2.1 {ECO:0000255|HAMAP-Rule:MF_00051, ECO:0000269|PubMed:12913008};
GN Name=glyA2 {ECO:0000255|HAMAP-Rule:MF_00051}; OrderedLocusNames=Rv0070c;
GN ORFNames=MTV030.13c;
OS Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
OC Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
OC Mycobacterium; Mycobacterium tuberculosis complex.
OX NCBI_TaxID=83332;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=9634230; DOI=10.1038/31159;
RA Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M., Harris D.E.,
RA Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III, Tekaia F., Badcock K.,
RA Basham D., Brown D., Chillingworth T., Connor R., Davies R.M., Devlin K.,
RA Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K.,
RA Krogh A., McLean J., Moule S., Murphy L.D., Oliver S., Osborne J.,
RA Quail M.A., Rajandream M.A., Rogers J., Rutter S., Seeger K., Skelton S.,
RA Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S.,
RA Barrell B.G.;
RT "Deciphering the biology of Mycobacterium tuberculosis from the complete
RT genome sequence.";
RL Nature 393:537-544(1998).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, SERINE HYDROXYMETHYLTRANSFERASE ACTIVITY,
RP ALDOLASE ACTIVITY, COFACTOR, STOICHIOMETRY OF PLP, PH DEPENDENCE,
RP SUBCELLULAR LOCATION, AND SUBUNIT.
RX PubMed=12913008; DOI=10.1074/jbc.m306192200;
RA Chaturvedi S., Bhakuni V.;
RT "Unusual structural, functional, and stability properties of serine
RT hydroxymethyltransferase from Mycobacterium tuberculosis.";
RL J. Biol. Chem. 278:40793-40805(2003).
RN [3]
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC STRAIN=ATCC 25618 / H37Rv;
RX PubMed=21969609; DOI=10.1074/mcp.m111.011627;
RA Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B., Yadav A.K.,
RA Shrivastava P., Marimuthu A., Anand S., Sundaram H., Kingsbury R.,
RA Harsha H.C., Nair B., Prasad T.S., Chauhan D.S., Katoch K., Katoch V.M.,
RA Kumar P., Chaerkady R., Ramachandran S., Dash D., Pandey A.;
RT "Proteogenomic analysis of Mycobacterium tuberculosis by high resolution
RT mass spectrometry.";
RL Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
CC -!- FUNCTION: Catalyzes the reversible interconversion of serine and
CC glycine with tetrahydrofolate (THF) serving as the one-carbon carrier.
CC This reaction serves as the major source of one-carbon groups required
CC for the biosynthesis of purines, thymidylate, methionine, and other
CC important biomolecules. Also exhibits THF-independent aldolase activity
CC toward beta-hydroxyamino acids, producing glycine and aldehydes, via a
CC retro-aldol mechanism. Thus, is able to catalyze the cleavage of L-
CC allo-threonine. {ECO:0000269|PubMed:12913008}.
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|HAMAP-Rule:MF_00051,
CC ECO:0000269|PubMed:12913008};
CC -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00051,
CC ECO:0000269|PubMed:12913008};
CC Note=Binds 1 pyridoxal phosphate per subunit.
CC {ECO:0000269|PubMed:12913008};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is about 7.8. Is completely inactive at pH below 4.0 and
CC above 10.0. {ECO:0000269|PubMed:12913008};
CC -!- PATHWAY: One-carbon metabolism; tetrahydrofolate interconversion.
CC {ECO:0000255|HAMAP-Rule:MF_00051}.
CC -!- PATHWAY: Amino-acid biosynthesis; glycine biosynthesis; glycine from L-
CC serine: step 1/1. {ECO:0000255|HAMAP-Rule:MF_00051}.
CC -!- SUBUNIT: Homodimer. {ECO:0000255|HAMAP-Rule:MF_00051,
CC ECO:0000269|PubMed:12913008}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00051,
CC ECO:0000305|PubMed:12913008}.
CC -!- SIMILARITY: Belongs to the SHMT family. {ECO:0000255|HAMAP-
CC Rule:MF_00051, ECO:0000305}.
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DR EMBL; AL123456; CCP42793.1; -; Genomic_DNA.
DR PIR; G70848; G70848.
DR RefSeq; NP_214584.1; NC_000962.3.
DR RefSeq; WP_003899799.1; NZ_NVQJ01000005.1.
DR AlphaFoldDB; P9WGI7; -.
DR SMR; P9WGI7; -.
DR STRING; 83332.Rv0070c; -.
DR PaxDb; P9WGI7; -.
DR PRIDE; P9WGI7; -.
DR DNASU; 886983; -.
DR GeneID; 886983; -.
DR KEGG; mtu:Rv0070c; -.
DR TubercuList; Rv0070c; -.
DR eggNOG; COG0112; Bacteria.
DR OMA; ANASVMH; -.
DR PhylomeDB; P9WGI7; -.
DR BRENDA; 2.1.2.1; 3445.
DR UniPathway; UPA00193; -.
DR UniPathway; UPA00288; UER01023.
DR Proteomes; UP000001584; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IBA:GO_Central.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005886; C:plasma membrane; HDA:MTBBASE.
DR GO; GO:0004372; F:glycine hydroxymethyltransferase activity; IDA:MTBBASE.
DR GO; GO:0042803; F:protein homodimerization activity; IPI:MTBBASE.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IDA:MTBBASE.
DR GO; GO:0070905; F:serine binding; IBA:GO_Central.
DR GO; GO:0008270; F:zinc ion binding; IBA:GO_Central.
DR GO; GO:0046655; P:folic acid metabolic process; IBA:GO_Central.
DR GO; GO:0019264; P:glycine biosynthetic process from serine; IBA:GO_Central.
DR GO; GO:0006544; P:glycine metabolic process; IDA:MTBBASE.
DR GO; GO:0006565; P:L-serine catabolic process; IBA:GO_Central.
DR GO; GO:0006563; P:L-serine metabolic process; IDA:MTBBASE.
DR GO; GO:0006730; P:one-carbon metabolic process; IBA:GO_Central.
DR GO; GO:0035999; P:tetrahydrofolate interconversion; IEA:UniProtKB-UniPathway.
DR GO; GO:0046653; P:tetrahydrofolate metabolic process; IBA:GO_Central.
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 Amino-acid biosynthesis; Cytoplasm; One-carbon metabolism;
KW Pyridoxal phosphate; Reference proteome; Transferase.
FT CHAIN 1..425
FT /note="Serine hydroxymethyltransferase 2"
FT /id="PRO_0000113619"
FT BINDING 121
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT BINDING 125..127
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT SITE 229
FT /note="Plays an important role in substrate specificity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT MOD_RES 230
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
SQ SEQUENCE 425 AA; 45526 MW; 224D195C1D8BF680 CRC64;
MNTLNDSLTA FDPDIAALID GELRRQESGL EMIASENYAP LAVMQAQGSV LTNKYAEGYP
GRRYYGGCEF VDGVEQLAID RVKALFGAEY ANVQPHSGAT ANAATMHALL NPGDTILGLS
LAHGGHLTHG MRINFSGKLY HATAYEVSKE DYLVDMDAVA EAARTHRPKM IIAGWSAYPR
QLDFARFRAI ADEVDAVLMV DMAHFAGLVA AGVHPSPVPH AHVVTSTTHK TLGGPRGGII
LCNDPAIAKK INSAVFPGQQ GGPLEHVIAA KATAFKMAAQ PEFAQRQQRC LDGARILAGR
LTQPDVAERG IAVLTGGTDV HLVLVDLRDA ELDGQQAEDR LAAVDITVNR NAVPFDPRPP
MITSGLRIGT PALAARGFSH NDFRAVADLI AAALTATNDD QLGPLRAQVQ RLAARYPLYP
ELHRT
