GLYA_PSYIN
ID GLYA_PSYIN Reviewed; 421 AA.
AC A1SUU0;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 06-FEB-2007, sequence version 1.
DT 03-AUG-2022, entry version 92.
DE RecName: Full=Serine hydroxymethyltransferase {ECO:0000255|HAMAP-Rule:MF_00051};
DE Short=SHMT {ECO:0000255|HAMAP-Rule:MF_00051};
DE Short=Serine methylase {ECO:0000255|HAMAP-Rule:MF_00051};
DE EC=2.1.2.1 {ECO:0000255|HAMAP-Rule:MF_00051};
GN Name=glyA {ECO:0000255|HAMAP-Rule:MF_00051}; OrderedLocusNames=Ping_1438;
OS Psychromonas ingrahamii (strain 37).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Alteromonadales;
OC Psychromonadaceae; Psychromonas.
OX NCBI_TaxID=357804;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=37;
RG US DOE Joint Genome Institute;
RA Copeland A., Lucas S., Lapidus A., Barry K., Detter J.C.,
RA Glavina del Rio T., Hammon N., Israni S., Dalin E., Tice H., Pitluck S.,
RA Thompson L.S., Brettin T., Bruce D., Han C., Tapia R., Schmutz J.,
RA Larimer F., Land M., Hauser L., Kyrpides N., Ivanova N., Staley J.,
RA Richardson P.;
RT "Complete sequence of Psychromonas ingrahamii 37.";
RL Submitted (JAN-2007) to the EMBL/GenBank/DDBJ databases.
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. {ECO:0000255|HAMAP-Rule:MF_00051}.
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 -!- COFACTOR:
CC Name=pyridoxal 5'-phosphate; Xref=ChEBI:CHEBI:597326;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00051};
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 -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00051}.
CC -!- SIMILARITY: Belongs to the SHMT family. {ECO:0000255|HAMAP-
CC Rule:MF_00051}.
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DR EMBL; CP000510; ABM03255.1; -; Genomic_DNA.
DR RefSeq; WP_011769815.1; NC_008709.1.
DR PDB; 4P3M; X-ray; 1.85 A; A/B=1-421.
DR PDBsum; 4P3M; -.
DR AlphaFoldDB; A1SUU0; -.
DR SMR; A1SUU0; -.
DR STRING; 357804.Ping_1438; -.
DR EnsemblBacteria; ABM03255; ABM03255; Ping_1438.
DR KEGG; pin:Ping_1438; -.
DR eggNOG; COG0112; Bacteria.
DR HOGENOM; CLU_022477_2_1_6; -.
DR OMA; VTNRNAI; -.
DR OrthoDB; 861782at2; -.
DR BRENDA; 2.1.2.1; 11857.
DR UniPathway; UPA00193; -.
DR UniPathway; UPA00288; UER01023.
DR Proteomes; UP000000639; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0004372; F:glycine hydroxymethyltransferase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0030170; F:pyridoxal phosphate binding; IEA:UniProtKB-UniRule.
DR GO; GO:0019264; P:glycine biosynthetic process from serine; IEA:UniProtKB-UniRule.
DR GO; GO:0035999; P:tetrahydrofolate interconversion; IEA:UniProtKB-UniPathway.
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; One-carbon metabolism;
KW Pyridoxal phosphate; Reference proteome; Transferase.
FT CHAIN 1..421
FT /note="Serine hydroxymethyltransferase"
FT /id="PRO_1000006301"
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 BINDING 355..357
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"
FT HELIX 8..11
FT /evidence="ECO:0007829|PDB:4P3M"
FT HELIX 13..28
FT /evidence="ECO:0007829|PDB:4P3M"
FT STRAND 29..31
FT /evidence="ECO:0007829|PDB:4P3M"
FT HELIX 41..47
FT /evidence="ECO:0007829|PDB:4P3M"
FT HELIX 50..53
FT /evidence="ECO:0007829|PDB:4P3M"
FT STRAND 62..66
FT /evidence="ECO:0007829|PDB:4P3M"
FT HELIX 71..86
FT /evidence="ECO:0007829|PDB:4P3M"
FT STRAND 89..92
FT /evidence="ECO:0007829|PDB:4P3M"
FT HELIX 98..109
FT /evidence="ECO:0007829|PDB:4P3M"
FT STRAND 115..118
FT /evidence="ECO:0007829|PDB:4P3M"
FT STRAND 141..144
FT /evidence="ECO:0007829|PDB:4P3M"
FT HELIX 156..166
FT /evidence="ECO:0007829|PDB:4P3M"
FT STRAND 169..173
FT /evidence="ECO:0007829|PDB:4P3M"
FT HELIX 184..194
FT /evidence="ECO:0007829|PDB:4P3M"
FT STRAND 197..201
FT /evidence="ECO:0007829|PDB:4P3M"
FT TURN 203..205
FT /evidence="ECO:0007829|PDB:4P3M"
FT HELIX 206..210
FT /evidence="ECO:0007829|PDB:4P3M"
FT TURN 218..220
FT /evidence="ECO:0007829|PDB:4P3M"
FT STRAND 221..230
FT /evidence="ECO:0007829|PDB:4P3M"
FT STRAND 238..242
FT /evidence="ECO:0007829|PDB:4P3M"
FT HELIX 246..256
FT /evidence="ECO:0007829|PDB:4P3M"
FT TURN 257..260
FT /evidence="ECO:0007829|PDB:4P3M"
FT HELIX 266..278
FT /evidence="ECO:0007829|PDB:4P3M"
FT HELIX 282..304
FT /evidence="ECO:0007829|PDB:4P3M"
FT STRAND 308..310
FT /evidence="ECO:0007829|PDB:4P3M"
FT STRAND 318..322
FT /evidence="ECO:0007829|PDB:4P3M"
FT TURN 324..327
FT /evidence="ECO:0007829|PDB:4P3M"
FT HELIX 330..339
FT /evidence="ECO:0007829|PDB:4P3M"
FT STRAND 361..365
FT /evidence="ECO:0007829|PDB:4P3M"
FT HELIX 367..371
FT /evidence="ECO:0007829|PDB:4P3M"
FT HELIX 376..395
FT /evidence="ECO:0007829|PDB:4P3M"
FT HELIX 399..416
FT /evidence="ECO:0007829|PDB:4P3M"
FT STRAND 419..421
FT /evidence="ECO:0007829|PDB:4P3M"
SQ SEQUENCE 421 AA; 45183 MW; 1E6179B8FFDC7639 CRC64;
MFNRDMNIAD YDPELWQSIT DEVQRQEDHI ELIASENYTS PRVMEAQGSQ LTNKYAEGYP
GKRYYGGCEY VDVAESLAIE RAKSLFGADY ANVQPHSGSQ ANAAVYQALC APGDTILGMS
LAHGGHLTHG SHVSFSGKMY NAVQYGITPE TGILDYAEIE RLAVEHKPTM IIAGFSAYSG
IVDWAKFREI ADKVGAYLFV DMAHVAGLVA AGLYPNPVPF ADVVTTTTHK TLGGPRGGLI
LAKANEAIEK KLNSAVFPGQ QGGPLMHVIA AKAVAFKECA EPEFAVYQQQ VLDNAKAMVK
SFLARGYKIV SGGTENHLFL VDLIAQDITG KEADAALGNA HITVNKNSVP NDPRSPFVTS
GLRIGTPALA RRGVNAQQSA ELALWMCDVL DAIKDEAKLA TTITAVKVKV AALCKACPVY
G
