GLYA2_BURP1
ID GLYA2_BURP1 Reviewed; 424 AA.
AC Q3JGP5;
DT 16-MAY-2006, integrated into UniProtKB/Swiss-Prot.
DT 08-NOV-2005, sequence version 1.
DT 03-AUG-2022, entry version 101.
DE RecName: Full=Serine hydroxymethyltransferase 2 {ECO:0000255|HAMAP-Rule:MF_00051};
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};
GN Name=glyA2 {ECO:0000255|HAMAP-Rule:MF_00051};
GN OrderedLocusNames=BURPS1710b_A2106;
OS Burkholderia pseudomallei (strain 1710b).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Burkholderiaceae; Burkholderia; pseudomallei group.
OX NCBI_TaxID=320372;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=1710b;
RX PubMed=20333227; DOI=10.1093/gbe/evq003;
RA Losada L., Ronning C.M., DeShazer D., Woods D., Fedorova N., Kim H.S.,
RA Shabalina S.A., Pearson T.R., Brinkac L., Tan P., Nandi T., Crabtree J.,
RA Badger J., Beckstrom-Sternberg S., Saqib M., Schutzer S.E., Keim P.,
RA Nierman W.C.;
RT "Continuing evolution of Burkholderia mallei through genome reduction and
RT large-scale rearrangements.";
RL Genome Biol. Evol. 2:102-116(2010).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (1.60 ANGSTROMS), AND SUBUNIT.
RG Seattle structural genomics center for infectious disease (SSGCID);
RT "Crystal structure of serine hydroxymethyltransferase from burkholderia
RT pseudomallei.";
RL Submitted (AUG-2008) 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. {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 ECO:0000269|Ref.2}.
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; CP000125; ABA51299.1; -; Genomic_DNA.
DR RefSeq; WP_004523136.1; NC_007435.1.
DR PDB; 3ECD; X-ray; 1.60 A; A/B/C/D=1-424.
DR PDBsum; 3ECD; -.
DR AlphaFoldDB; Q3JGP5; -.
DR SMR; Q3JGP5; -.
DR EnsemblBacteria; ABA51299; ABA51299; BURPS1710b_A2106.
DR GeneID; 56531003; -.
DR KEGG; bpm:BURPS1710b_A2106; -.
DR HOGENOM; CLU_022477_2_1_4; -.
DR OMA; RCQHSEV; -.
DR OrthoDB; 861782at2; -.
DR UniPathway; UPA00193; -.
DR UniPathway; UPA00288; UER01023.
DR EvolutionaryTrace; Q3JGP5; -.
DR Proteomes; UP000002700; Chromosome II.
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; Transferase.
FT CHAIN 1..424
FT /note="Serine hydroxymethyltransferase 2"
FT /id="PRO_0000234956"
FT BINDING 125
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT BINDING 129..131
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT BINDING 250
FT /ligand="(6S)-5,6,7,8-tetrahydrofolate"
FT /ligand_id="ChEBI:CHEBI:57453"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT SITE 233
FT /note="Plays an important role in substrate specificity"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT MOD_RES 234
FT /note="N6-(pyridoxal phosphate)lysine"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00051"
FT HELIX 6..9
FT /evidence="ECO:0007829|PDB:3ECD"
FT HELIX 12..15
FT /evidence="ECO:0007829|PDB:3ECD"
FT HELIX 17..32
FT /evidence="ECO:0007829|PDB:3ECD"
FT STRAND 33..35
FT /evidence="ECO:0007829|PDB:3ECD"
FT HELIX 45..51
FT /evidence="ECO:0007829|PDB:3ECD"
FT HELIX 54..56
FT /evidence="ECO:0007829|PDB:3ECD"
FT HELIX 77..90
FT /evidence="ECO:0007829|PDB:3ECD"
FT STRAND 93..96
FT /evidence="ECO:0007829|PDB:3ECD"
FT HELIX 102..113
FT /evidence="ECO:0007829|PDB:3ECD"
FT STRAND 119..123
FT /evidence="ECO:0007829|PDB:3ECD"
FT STRAND 145..149
FT /evidence="ECO:0007829|PDB:3ECD"
FT TURN 153..155
FT /evidence="ECO:0007829|PDB:3ECD"
FT HELIX 160..170
FT /evidence="ECO:0007829|PDB:3ECD"
FT STRAND 173..178
FT /evidence="ECO:0007829|PDB:3ECD"
FT HELIX 188..197
FT /evidence="ECO:0007829|PDB:3ECD"
FT STRAND 201..205
FT /evidence="ECO:0007829|PDB:3ECD"
FT HELIX 207..209
FT /evidence="ECO:0007829|PDB:3ECD"
FT HELIX 210..214
FT /evidence="ECO:0007829|PDB:3ECD"
FT HELIX 221..223
FT /evidence="ECO:0007829|PDB:3ECD"
FT STRAND 226..233
FT /evidence="ECO:0007829|PDB:3ECD"
FT HELIX 234..236
FT /evidence="ECO:0007829|PDB:3ECD"
FT STRAND 242..247
FT /evidence="ECO:0007829|PDB:3ECD"
FT HELIX 249..259
FT /evidence="ECO:0007829|PDB:3ECD"
FT HELIX 269..282
FT /evidence="ECO:0007829|PDB:3ECD"
FT HELIX 285..307
FT /evidence="ECO:0007829|PDB:3ECD"
FT HELIX 313..315
FT /evidence="ECO:0007829|PDB:3ECD"
FT STRAND 318..325
FT /evidence="ECO:0007829|PDB:3ECD"
FT HELIX 327..329
FT /evidence="ECO:0007829|PDB:3ECD"
FT HELIX 333..342
FT /evidence="ECO:0007829|PDB:3ECD"
FT TURN 359..361
FT /evidence="ECO:0007829|PDB:3ECD"
FT STRAND 363..369
FT /evidence="ECO:0007829|PDB:3ECD"
FT HELIX 370..374
FT /evidence="ECO:0007829|PDB:3ECD"
FT HELIX 379..398
FT /evidence="ECO:0007829|PDB:3ECD"
FT HELIX 404..419
FT /evidence="ECO:0007829|PDB:3ECD"
SQ SEQUENCE 424 AA; 45441 MW; 56789A4FFDDFC41F CRC64;
MSNANPFFSQ SLAERDASVR GAILKELERQ QSQVELIASE NIVSRAVLDA QGSVLTNKYA
EGYPGKRYYG GCEFADEVEA LAIERVKRLF NAGHANVQPH SGAQANGAVM LALAKPGDTV
LGMSLDAGGH LTHGAKPALS GKWFNALQYG VSRDTMLIDY DQVEALAQQH KPSLIIAGFS
AYPRKLDFAR FRAIADSVGA KLMVDMAHIA GVIAAGRHAN PVEHAHVVTS TTHKTLRGPR
GGFVLTNDEE IAKKINSAVF PGLQGGPLMH VIAGKAVAFG EALTDDFKTY IDRVLANAQA
LGDVLKAGGV DLVTGGTDNH LLLVDLRPKG LKGAQVEQAL ERAGITCNKN GIPFDPEKPT
ITSGIRLGTP AGTTRGFGAA EFREVGRLIL EVFEALRTNP EGDHATEQRV RREIFALCER
FPIY
