GLYA1_MYCTU
ID GLYA1_MYCTU Reviewed; 438 AA.
AC P9WGI9; L0T5T8; O53441;
DT 16-APR-2014, integrated into UniProtKB/Swiss-Prot.
DT 07-JAN-2015, sequence version 2.
DT 03-AUG-2022, entry version 41.
DE RecName: Full=Serine hydroxymethyltransferase 1 {ECO:0000255|HAMAP-Rule:MF_00051};
DE Short=SHM1 {ECO:0000303|PubMed:12913008};
DE Short=SHMT 1 {ECO:0000255|HAMAP-Rule:MF_00051};
DE Short=Serine methylase 1 {ECO:0000255|HAMAP-Rule:MF_00051};
DE EC=2.1.2.1 {ECO:0000255|HAMAP-Rule:MF_00051, ECO:0000269|PubMed:12913008};
GN Name=glyA1 {ECO:0000255|HAMAP-Rule:MF_00051}; Synonyms=glyA;
GN OrderedLocusNames=Rv1093; ORFNames=MTV017.46;
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 PROTEIN SEQUENCE OF 9-30, AND SEQUENCE REVISION TO N-TERMINUS.
RC STRAIN=H37Rv;
RX PubMed=34915127; DOI=10.1016/j.ygeno.2021.12.001;
RA Shi J., Meng S., Wan L., Zhang Z., Jiang S., Zhu H., Dai E., Chang L.,
RA Gao H., Wan K., Zhang L., Zhao X., Liu H., Lyu Z., Zhang Y., Xu P.;
RT "Deep N-terminomics of Mycobacterium tuberculosis H37Rv extensively correct
RT annotated encoding genes.";
RL Genomics 114:292-304(2022).
RN [3]
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 [4]
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).
RN [5]
RP X-RAY CRYSTALLOGRAPHY (1.50 ANGSTROMS) OF 13-438, AND SUBUNIT.
RG Seattle structural genomics center for infectious disease (SSGCID);
RT "Crystal structure of serine hydroxymethyltransferase from Mycobacterium
RT tuberculosis.";
RL Submitted (APR-2009) to the PDB data bank.
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 homodimer. This is unusual in the
CC SHMT family, that normally contains 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, ECO:0000269|Ref.5}.
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}.
CC -!- SEQUENCE CAUTION:
CC Sequence=CCP43846.1; Type=Erroneous initiation; Note=Truncated N-terminus.; Evidence={ECO:0000269|PubMed:34915127};
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DR EMBL; AL123456; CCP43846.1; ALT_INIT; Genomic_DNA.
DR PIR; C70896; C70896.
DR RefSeq; YP_177787.3; NC_000962.3.
DR PDB; 3H7F; X-ray; 1.50 A; A/B=13-438.
DR PDBsum; 3H7F; -.
DR AlphaFoldDB; P9WGI9; -.
DR SMR; P9WGI9; -.
DR STRING; 83332.Rv1093; -.
DR PaxDb; P9WGI9; -.
DR DNASU; 885338; -.
DR GeneID; 885338; -.
DR KEGG; mtu:Rv1093; -.
DR TubercuList; Rv1093; -.
DR eggNOG; COG0112; Bacteria.
DR BRENDA; 2.1.2.1; 3445.
DR UniPathway; UPA00193; -.
DR UniPathway; UPA00288; UER01023.
DR PHI-base; PHI:7584; -.
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:0009274; C:peptidoglycan-based cell wall; HDA:MTBBASE.
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:0042783; P:evasion of host immune response; IMP:MTBBASE.
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 3D-structure; Amino-acid biosynthesis; Cytoplasm;
KW Direct protein sequencing; One-carbon metabolism; Pyridoxal phosphate;
KW Reference proteome; Transferase.
FT CHAIN 1..438
FT /note="Serine hydroxymethyltransferase 1"
FT /id="PRO_0000113618"
FT BINDING 130
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT BINDING 134..136
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT SITE 238
FT /note="Plays an important role in substrate specificity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT MOD_RES 239
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT HELIX 17..20
FT /evidence="ECO:0007829|PDB:3H7F"
FT HELIX 22..37
FT /evidence="ECO:0007829|PDB:3H7F"
FT STRAND 38..40
FT /evidence="ECO:0007829|PDB:3H7F"
FT HELIX 50..56
FT /evidence="ECO:0007829|PDB:3H7F"
FT HELIX 59..62
FT /evidence="ECO:0007829|PDB:3H7F"
FT STRAND 71..75
FT /evidence="ECO:0007829|PDB:3H7F"
FT HELIX 78..95
FT /evidence="ECO:0007829|PDB:3H7F"
FT STRAND 98..101
FT /evidence="ECO:0007829|PDB:3H7F"
FT HELIX 107..118
FT /evidence="ECO:0007829|PDB:3H7F"
FT STRAND 124..128
FT /evidence="ECO:0007829|PDB:3H7F"
FT HELIX 130..132
FT /evidence="ECO:0007829|PDB:3H7F"
FT HELIX 136..138
FT /evidence="ECO:0007829|PDB:3H7F"
FT HELIX 144..147
FT /evidence="ECO:0007829|PDB:3H7F"
FT STRAND 148..154
FT /evidence="ECO:0007829|PDB:3H7F"
FT TURN 158..160
FT /evidence="ECO:0007829|PDB:3H7F"
FT HELIX 165..175
FT /evidence="ECO:0007829|PDB:3H7F"
FT STRAND 178..183
FT /evidence="ECO:0007829|PDB:3H7F"
FT HELIX 193..203
FT /evidence="ECO:0007829|PDB:3H7F"
FT STRAND 206..210
FT /evidence="ECO:0007829|PDB:3H7F"
FT TURN 212..214
FT /evidence="ECO:0007829|PDB:3H7F"
FT HELIX 215..219
FT /evidence="ECO:0007829|PDB:3H7F"
FT TURN 227..229
FT /evidence="ECO:0007829|PDB:3H7F"
FT STRAND 231..236
FT /evidence="ECO:0007829|PDB:3H7F"
FT STRAND 247..251
FT /evidence="ECO:0007829|PDB:3H7F"
FT HELIX 253..255
FT /evidence="ECO:0007829|PDB:3H7F"
FT HELIX 256..263
FT /evidence="ECO:0007829|PDB:3H7F"
FT TURN 264..267
FT /evidence="ECO:0007829|PDB:3H7F"
FT HELIX 273..285
FT /evidence="ECO:0007829|PDB:3H7F"
FT HELIX 289..309
FT /evidence="ECO:0007829|PDB:3H7F"
FT HELIX 312..316
FT /evidence="ECO:0007829|PDB:3H7F"
FT HELIX 322..324
FT /evidence="ECO:0007829|PDB:3H7F"
FT STRAND 327..334
FT /evidence="ECO:0007829|PDB:3H7F"
FT HELIX 342..351
FT /evidence="ECO:0007829|PDB:3H7F"
FT TURN 368..370
FT /evidence="ECO:0007829|PDB:3H7F"
FT STRAND 373..377
FT /evidence="ECO:0007829|PDB:3H7F"
FT HELIX 379..384
FT /evidence="ECO:0007829|PDB:3H7F"
FT HELIX 388..403
FT /evidence="ECO:0007829|PDB:3H7F"
FT HELIX 405..407
FT /evidence="ECO:0007829|PDB:3H7F"
FT HELIX 410..423
FT /evidence="ECO:0007829|PDB:3H7F"
FT HELIX 430..432
FT /evidence="ECO:0007829|PDB:3H7F"
SQ SEQUENCE 438 AA; 46216 MW; 7FAB0306F2C11374 CRC64;
MTAAPDARTT AVMSAPLAEV DPDIAELLAK ELGRQRDTLE MIASENFVPR AVLQAQGSVL
TNKYAEGLPG RRYYGGCEHV DVVENLARDR AKALFGAEFA NVQPHSGAQA NAAVLHALMS
PGERLLGLDL ANGGHLTHGM RLNFSGKLYE NGFYGVDPAT HLIDMDAVRA TALEFRPKVI
IAGWSAYPRV LDFAAFRSIA DEVGAKLLVD MAHFAGLVAA GLHPSPVPHA DVVSTTVHKT
LGGGRSGLIV GKQQYAKAIN SAVFPGQQGG PLMHVIAGKA VALKIAATPE FADRQRRTLS
GARIIADRLM APDVAKAGVS VVSGGTDVHL VLVDLRDSPL DGQAAEDLLH EVGITVNRNA
VPNDPRPPMV TSGLRIGTPA LATRGFGDTE FTEVADIIAT ALATGSSVDV SALKDRATRL
ARAFPLYDGL EEWSLVGR
