Q3SZ20

PR
Gene name
SHMT2
Protein name
Serine hydroxymethyltransferase, mitochondrial
Names
SHMT, Glycine hydroxymethyltransferase, Serine methylase
Species
Bos taurus (Bovine)
KEGG Pathway
bta:507197
EC number
2.1.2.1: Hydroxymethyl-, formyl- and related transferases
Protein Class

Descriptions

The autoinhibited protein was predicted that may have potential autoinhibitory elements via cis-regPred.

Autoinhibitory domains (AIDs)

1-81 (Predicted disordered autoinhibitory region) PR

Target domain

Relief mechanism

Assay

cis-regPred

Accessory elements

No accessory elements

References

Autoinhibited structure

Activated structure

1 structures for Q3SZ20

Entry ID Method Resolution Chain Position Source
AF-Q3SZ20-F1 Predicted AlphaFoldDB

164 variants for Q3SZ20

Variant ID(s) Position Change Description Diseaes Association Provenance
rs437687895 3 S>P No EVA
rs467604578 5 S>F No EVA
rs441896098 21 G>V No EVA
rs474732356 43 W>C No EVA
rs453097288 51 D>A No EVA
rs433982247 53 D>G No EVA
rs466884175 55 E>V No EVA
rs433249179 70 G>V No EVA
rs467581335 79 F>S No EVA
rs449132247 81 S>R No EVA
rs478932396 83 A>G No EVA
rs477178278 85 L>R No EVA
rs450088777 89 G>R No EVA
rs461535078 91 C>W No EVA
rs483077693 91 C>Y No EVA
rs472953701 92 L>R No EVA
rs443133123 92 L>V No EVA
rs460771217 93 N>I No EVA
rs438420221 94 N>T No EVA
rs471353229 96 Y>D No EVA
rs456269954 96 Y>S No EVA
rs437693760 97 S>W No EVA
rs474035275 99 G>C No EVA
rs433735974 100 Y>D No EVA
rs445049049 104 R>G No EVA
rs480286110 112 V>E No EVA
rs451050497 112 V>M No EVA
rs440124408 116 E>G No EVA
rs457651919 117 L>M No EVA
rs439367121 117 L>P No EVA
rs441890836 119 C>F No EVA
rs457275258 119 C>G No EVA
rs474252074 121 R>P No EVA
rs455637639 122 R>Q No EVA
rs467087762 125 E>* No EVA
rs433364731 132 A>S No EVA
rs433364731 132 A>T No EVA
rs469563514 136 V>F No EVA
rs451228115 137 N>H No EVA
rs435872928 138 V>A No EVA
rs468869500 139 Q>H No EVA
rs446429336 141 Y>S No EVA
rs457688765 142 S>C No EVA
rs479167362 142 S>P No EVA
rs445696878 143 G>R No EVA
rs463499674 144 S>P No EVA
rs474925082 145 P>Q No EVA
rs441940956 145 P>T No EVA
rs459617493 147 N>I No EVA
rs473352405 150 A>D No EVA
rs451861767 151 Y>F No EVA
rs433251160 153 A>D No EVA
rs476086772 154 L>R No EVA
rs457485459 155 L>Q No EVA
rs435759537 158 H>P No EVA
rs447097644 159 D>E No EVA
rs468856268 159 D>H No EVA
rs463987619 164 L>V No EVA
rs481708021 166 L>F No EVA
rs445735398 166 L>V No EVA
rs463430774 167 P>A No EVA
rs448205993 168 D>A No EVA
rs481213491 168 D>E No EVA
rs448205993 168 D>G No EVA
rs459595089 169 G>V No EVA
rs473438211 171 H>P No EVA
rs449932523 207 D>A No EVA
rs437876438 214 R>Q No EVA
rs467610246 215 L>I No EVA
rs481171511 216 F>C No EVA
rs448489796 216 F>L No EVA
rs437028211 234 Y>N No EVA
rs432027733 245 K>T No EVA
rs471627744 263 V>A No EVA
rs454848203 267 P>H No EVA
rs437758385 278 T>P No EVA
rs457928089 286 R>S No EVA
rs479967161 287 S>L No EVA
rs471848202 291 F>S No EVA
rs456485082 292 Y>C No EVA
rs456485082 292 Y>F No EVA
rs437964241 294 K>R No EVA
rs437964241 294 K>T No EVA
rs455789560 296 V>G No EVA
rs474313584 296 V>L No EVA
rs434206837 298 A>D No EVA
rs445589926 300 D>A No EVA
rs467163078 300 D>H No EVA
rs433456136 301 P>H No EVA
rs433456136 301 P>R No EVA
rs469662662 302 K>Q No EVA
rs450419756 306 E>D No EVA
rs461722426 307 I>M No EVA
rs480198427 307 I>T No EVA
rs479445226 311 F>L No EVA
rs457766382 311 F>L No EVA
rs439351609 313 D>N No EVA
rs463620897 320 F>S No EVA
rs474183257 323 L>V No EVA
rs434045482 324 Q>H No EVA
rs876152529 325 G>A No EVA
rs473626567 326 G>A No EVA
rs451935697 327 P>L No EVA
rs433337855 328 H>P No EVA
rs469665656 329 N>D No EVA
rs876169348 329 N>S No EVA
rs451136398 330 H>Q No EVA
rs435227261 331 A>D No EVA
rs134372589 337 V>G No EVA
rs479332715 340 K>Q No EVA
rs445797249 341 Q>H No EVA
rs464063160 341 Q>L No EVA
rs453443237 342 A>G No EVA
rs876039958 344 T>A No EVA
rs434389403 344 T>N No EVA
rs452139302 350 Y>D No EVA
rs436872180 354 I>F No EVA
rs208182982 358 A>S No EVA
rs448289555 359 Q>* No EVA
rs448289555 359 Q>E No EVA
rs466071365 359 Q>H No EVA
rs436126184 359 Q>P No EVA
rs447571643 362 A>G No EVA
rs479839056 364 A>V No EVA
rs458129954 367 E>V No EVA
rs463771668 375 G>C No EVA
rs476193245 386 L>F No EVA
rs454667989 391 L>R No EVA
rs472254573 394 A>D No EVA
rs465283594 417 S>R No EVA
rs456363047 420 T>P No EVA
rs467466426 427 G>E No EVA
rs466109033 435 G>V No EVA
rs436302438 435 G>W No EVA
rs715413624 439 D>E No EVA
rs447679326 439 D>G No EVA
rs477686636 443 K>* No EVA
rs465500809 444 V>A No EVA
rs461596728 449 D>Y No EVA
rs526550119 450 E>G No EVA
rs442453481 451 G>C No EVA
rs478598263 453 N>H No EVA
rs460283871 456 L>F No EVA
rs438463991 458 V>A No EVA
rs438463991 458 V>E No EVA
rs438463991 458 V>G No EVA
rs456281716 459 K>E No EVA
rs444189581 459 K>R No EVA
rs455430699 460 S>G No EVA
rs436394303 461 K>Q No EVA
rs472400096 462 T>P No EVA
rs444531808 465 L>I No EVA
rs474263069 465 L>P No EVA
rs467246757 475 D>V No EVA
rs451969174 477 E>K No EVA
rs432822118 478 T>I No EVA
rs468981678 481 Q>R No EVA
rs468076890 483 A>V No EVA
rs458012710 489 V>G No EVA
rs479650085 489 V>M No EVA
rs478290575 497 P>R No EVA
rs439465974 497 P>S No EVA
rs462970866 500 G>S No EVA
rs444419360 502 D>H No EVA

No associated diseases with Q3SZ20

2 regional properties for Q3SZ20

Type Name Position InterPro Accession
binding_site Serine hydroxymethyltransferase, pyridoxal phosphate binding site 272 - 288 IPR019798
domain Serine hydroxymethyltransferase-like domain 49 - 448 IPR039429

Functions

Description
EC Number 2.1.2.1 Hydroxymethyl-, formyl- and related transferases
Subcellular Localization
  • Mitochondrion
  • Mitochondrion matrix, mitochondrion nucleoid
  • Mitochondrion inner membrane
  • Cytoplasm
  • Nucleus
  • Mainly localizes in the mitochondrion
  • Also found in the cytoplasm and nucleus as part of the BRISC complex
PANTHER Family
PANTHER Subfamily
PANTHER Protein Class
PANTHER Pathway Category No pathway information available

9 GO annotations of cellular component

Name Definition
BRISC complex A protein complex that contains the FAM175B/ABRO1, BRCC3/BRCC36, BRE/BRCC45 and MERIT40/NBA1 proteins, and specifically cleaves K63-linked polyubiquitin chains.
cytoplasm The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
cytosol The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
microtubule cytoskeleton The part of the cytoskeleton (the internal framework of a cell) composed of microtubules and associated proteins.
mitochondrial inner membrane The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
mitochondrial matrix The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
mitochondrial nucleoid The region of a mitochondrion to which the DNA is confined.
mitochondrion A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
nucleus A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

8 GO annotations of molecular function

Name Definition
chromatin binding Binding to chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
glycine hydroxymethyltransferase activity Catalysis of the reaction: 5,10-methylenetetrahydrofolate + glycine + H2O = tetrahydrofolate + L-serine.
mRNA 5'-UTR binding Binding to an mRNA molecule at its 5' untranslated region.
mRNA regulatory element binding translation repressor activity Antagonizes the ribosome-mediated translation of mRNA into a polypeptide via direct binding (through a selective and non-covalent interaction) to nucleic acid.
protein homodimerization activity Binding to an identical protein to form a homodimer.
pyridoxal phosphate binding Binding to pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
serine binding Binding to 2-amino-3-hydroxypropanoic acid.
zinc ion binding Binding to a zinc ion (Zn).

16 GO annotations of biological process

Name Definition
folic acid metabolic process The chemical reactions and pathways involving folic acid, pteroylglutamic acid. Folic acid is widely distributed as a member of the vitamin B complex and is essential for the synthesis of purine and pyrimidines.
glycine biosynthetic process from serine The chemical reactions and pathways resulting in the formation of glycine from other compounds, including serine.
glycine metabolic process The chemical reactions and pathways involving glycine, aminoethanoic acid.
L-serine catabolic process The chemical reactions and pathways resulting in the breakdown of L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
L-serine metabolic process The chemical reactions and pathways involving L-serine, the L-enantiomer of serine, i.e. (2S)-2-amino-3-hydroxypropanoic acid.
one-carbon metabolic process The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
protein homotetramerization The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
protein K63-linked deubiquitination A protein deubiquitination process in which a K63-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 63 of the ubiquitin monomers, is removed from a protein.
protein tetramerization The formation of a protein tetramer, a macromolecular structure consisting of four noncovalently associated identical or nonidentical subunits.
purine nucleobase biosynthetic process The chemical reactions and pathways resulting in the formation of purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
regulation of aerobic respiration Any process that modulates the frequency, rate or extent of aerobic respiration.
regulation of mitochondrial translation Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA in a mitochondrion.
regulation of oxidative phosphorylation Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the phosphorylation of ADP to ATP that accompanies the oxidation of a metabolite through the operation of the respiratory chain. Oxidation of compounds establishes a proton gradient across the membrane, providing the energy for ATP synthesis.
response to type I interferon Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a type I interferon stimulus. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
tetrahydrofolate interconversion The chemical reactions and pathways by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesise other tetrahydrofolate molecules.
tetrahydrofolate metabolic process The chemical reactions and pathways involving tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.

2 homologous proteins in AiPD

UniProt AC Gene Name Protein Name Species Evidence Code
P37292 SHM1 Serine hydroxymethyltransferase, mitochondrial Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Baker's yeast) PR
P34897 SHMT2 Serine hydroxymethyltransferase, mitochondrial Homo sapiens (Human) PR
10 20 30 40 50 60
MLSFSFIWAT RPLRRCGQLV GMAVRCQHSE AAQTQTGEAS KGWSGQESLS DSDPEMWELL
70 80 90 100 110 120
RREKDRQCRG LELIASENFC SRAALEALGS CLNNKYSEGY PGKRYYGGAE VVDEIELLCQ
130 140 150 160 170 180
RRALEAFDLD PAQWGVNVQP YSGSPANLAA YTALLQPHDR IMGLDLPDGG HLTHGYMSDV
190 200 210 220 230 240
KRISATSIFF ESMPYKLNPQ TGLIDYDQLA LTARLFKPRL IIAGTSAYAR LIDYARMREV
250 260 270 280 290 300
CDEVKAHLLA DMAHISGLVA AKVIPSPFKH ADIVTTTTHK TLRGARSGLI FYRKGVQAVD
310 320 330 340 350 360
PKTGREIPYT FEDRINFAVF PSLQGGPHNH AIAAVAVALK QACTPMFREY SLQILKNAQA
370 380 390 400 410 420
MANALLERGY SLVSGGTDNH LVLVDLRPKG LDGARAERVL ELVSITANKN TCPGDRSAIT
430 440 450 460 470 480
PGGLRLGAPA LTSRGFLEDD FRKVVGFIDE GVNIGLEVKS KTTKLQDFKS FLLKDPETSH
490 500
QLADLRQRVE QFARAFPMPG FDDH