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Annotation rule MF_00051
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General rule information [?]

Accession MF_00051
Dates 1-JUN-2001 (Created)
20-NOV-2019 (Last updated, Version 55)
Name SHMT
Scope
Bacteria
Archaea
Templates P0A825 (GLYA_ECOLI); D3DKC4 (GLYA_HYDTT); P9WGI9 (GLYA1_MYCTU); P9WGI7 (GLYA2_MYCTU); P39148 (GLYA_BACSU); Q58992 (GLYA_METJA); Q46A52 (GLYA_METBF); Q9UWT5 (GLYA_SACS2); O27433 (GLYA_METTH): [Recover all]
Triggered by

Propagated annotation [?]


Identifier, protein and gene names [?]

Identifier
GLYA
case <OC:Bacteria> or <OC:Methanomicrobia> or <OC:Halobacteria>
Protein name
RecName: Full=Serine hydroxymethyltransferase;
Short=SHMT;
Short=Serine methylase;
EC 2.1.2.1;
else
Protein name
RecName: Full=Serine hydroxymethyltransferase;
Short=SHMT;
Short=Serine methylase;
EC 2.1.2.-;
end case
Gene name
glyA

Comments [?]

case <OC:Bacteria>
Function Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. This reaction serves as the major source of one-carbon groups required for the biosynthesis of purines, thymidylate, methionine, and other important biomolecules. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism.
Catalytic activity RHEA:15481: (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine
EC 2.1.2.1
else case <OC:Methanomicrobia> or <OC:Halobacteria>
Function Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate (THF) serving as the one-carbon carrier. Also exhibits THF-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism.
Catalytic activity RHEA:15481: (6R)-5,10-methylene-5,6,7,8-tetrahydrofolate + glycine + H2O = (6S)-5,6,7,8-tetrahydrofolate + L-serine
EC 2.1.2.1
else case <OC:Methanobacteria> or <OC:Methanococci> or <OC:Methanopyri> or <OC:Archaeoglobi>
Function Catalyzes the reversible interconversion of serine and glycine with tetrahydromethanopterin (H4MPT) serving as the one-carbon carrier. Also exhibits a pteridine-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism.
Catalytic activity RHEA:47104: 5,10-methylenetetrahydromethanopterin + glycine + H2O = 5,6,7,8-tetrahydromethanopterin + L-serine
else
Function Catalyzes the reversible interconversion of serine and glycine with a modified folate serving as the one-carbon carrier. Also exhibits a pteridine-independent aldolase activity toward beta-hydroxyamino acids, producing glycine and aldehydes, via a retro-aldol mechanism.
end case
Cofactor pyridoxal 5'-phosphate
case <OC:Bacteria> or <OC:Methanomicrobia> or <OC:Halobacteria>
Pathway One-carbon metabolism; tetrahydrofolate interconversion.
end case
Pathway Amino-acid biosynthesis; glycine biosynthesis; glycine from L-serine: step 1/1.
Subunit Homodimer.
Subcellular location Cytoplasm.
Similarity Belongs to the SHMT family.

Keywords [?]

case <FTTag:acetylation>
Acetylation
end case
Amino-acid biosynthesis
Cytoplasm
One-carbon metabolism
Pyridoxal phosphate
Transferase

Gene Ontology [?]

GO:0004372; Molecular function: glycine hydroxymethyltransferase activity.
GO:0030170; Molecular function: pyridoxal phosphate binding.
GO:0006730; Biological process: one-carbon metabolic process.
GO:0019264; Biological process: glycine biosynthetic process from serine.
GO:0005737; Cellular component: cytoplasm.

Cross-references [?]

Pfam PF00464; SHMT; 1;
PROSITE PS00096; SHMT; 1;
PIRSF PIRSF000412; SHMT; 1;

Features [?]

From: GLYA_ECOLI (P0A825)
Key     From     To       Description   Tag   Condition   FTGroup
REGION     125     127       Substrate binding     G-x-[IL]  
REGION (Optional)     355     357       Substrate binding     [ST]-x-F  
BINDING (Optional)     35     35       Pyridoxal phosphate     S  
BINDING     55     55       Pyridoxal phosphate     Y  
BINDING     57     57       Substrate     E  
BINDING     64     64       Substrate     [FY]  
BINDING     65     65       Pyridoxal phosphate     Y  
BINDING (Optional)     99     99       Pyridoxal phosphate     [ST]  
BINDING     121     121       Substrate; via carbonyl oxygen     L  
BINDING     175     175       Pyridoxal phosphate     [ST]  
BINDING     203     203       Pyridoxal phosphate     H  
BINDING (Optional)     228     228       Pyridoxal phosphate     H  
BINDING (Optional)     235     235       Pyridoxal phosphate     R  
BINDING (Optional)     263     263       Pyridoxal phosphate; via amide nitrogen and carbonyl oxygen     G  
BINDING     363     363       Pyridoxal phosphate     R  
MOD_RES     229     229       N6-(pyridoxal phosphate)lysine     K  
case <OC:Escherichia> or <OC:Shigella>
MOD_RES     54     54       N6-acetyllysine   acetylation   K  
MOD_RES     250     250       N6-acetyllysine   acetylation   K  
MOD_RES     285     285       N6-acetyllysine   acetylation   K  
MOD_RES     354     354       N6-acetyllysine   acetylation   K  
MOD_RES     375     375       N6-acetyllysine   acetylation   K  
end case

Additional information [?]

Size range 406-574 amino acids
Related rules None
Fusion None
Comments The pteridine substrate used in this reaction by Archaea differs depending on the species. Methanomicrobia and Halobacteria appear to use tetrahydrofolate, whereas Methanobacteria and Methanococci use tetrahydromethanopterin, Sulfolobus solfataricus use tetrahydrosulfopterin, and hyperthermophiles use a modified folate (see PMID: 9783425 and references mentioned in template entries). M.tuberculosis possesses 2 SHMTs, one (O53441, Rv1093) binds 1 pyridoxal phosphate per homodimer whereas the other (O53615, Rv0070c) binds 1 pyridoxal phosphate per subunit like other characterized members of the SHMT family. Possible wrong start in ARCFU. Possible C-terminal problem in TREPA.


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