Reviewed, UniProtKB/Swiss-Prot P07511 (GLYC_RABIT)

Names and origin

Protein names

Recommended name:
    Serine hydroxymethyltransferase, cytosolic
      Short name=SHMT
      Short name=Serine methylase
    EC=2.1.2.1
Alternative name(s):
    Glycine hydroxymethyltransferase

Gene names

Name:

SHMT1

Organism

Oryctolagus cuniculus (Rabbit)

Taxonomic identifier

9986 [NCBI]

Taxonomic lineage

Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Lagomorpha › Leporidae › Oryctolagus

Protein attributes

Sequence length	484 AA.
Sequence status	Complete.
Sequence processing	The displayed sequence is further processed into a mature form.
Protein existence	Evidence at protein level.

General annotation (Comments)

Function	Interconversion of serine and glycine.
Catalytic activity	5,10-methylenetetrahydrofolate + glycine + H2O = tetrahydrofolate + L-serine.
Cofactor	Pyridoxal phosphate.
Pathway	One-carbon metabolism; tetrahydrofolate interconversion.
Subunit structure	Homotetramer.
Subcellular location	Cytoplasm.
Post-translational modification	Deamidation of asparagine produces alternatively aspartate or isoaspartate, which in turn can be converted to aspartate through carboxylmethylation/demethylation.
Miscellaneous	In eukaryotes there are two forms of the enzymes: a cytosolic one and a mitochondrial one.
Sequence similarities	Belongs to the SHMT family.

Ontologies

Keywords
Biological process	One-carbon metabolism
Cellular component	Cytoplasm
Ligand	Pyridoxal phosphate
Molecular function	Transferase
PTM	Acetylation Phosphoprotein
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological process	L-serine metabolic process Inferred from electronic annotation. Source: InterPro glycine metabolic process Inferred from electronic annotation. Source: InterPro one-carbon metabolic process Inferred from electronic annotation. Source: UniProtKB-KW
Cellular component	cytoplasm Inferred from electronic annotation. Source: UniProtKB-SubCell
Molecular function	glycine hydroxymethyltransferase activity Inferred from electronic annotation. Source: EC pyridoxal phosphate binding Inferred from electronic annotation. Source: InterPro
Complete GO annotation...

Sequence annotation (Features)

Feature key

Position(s)

Length

Description

Graphical view

Feature identifier

Molecule processing

Initiator methionine

1

1

Removed Ref.2 Ref.3

Chain

2 – 484

483

Serine hydroxymethyltransferase, cytosolic

PRO_0000113506

Sites

Active site

204

1

Nucleophile Probable

Active site

256

1

Proton donor By similarity

Amino acid modifications

Modified residue

2

1

N-acetylalanine Ref.2

Modified residue

6

1

Aspartyl isopeptide (Asn); alternate

Modified residue

6

1

Deamidated asparagine; alternate

Modified residue

34

1

Phosphotyrosine By similarity

Modified residue

257

1

N6-(pyridoxal phosphate)lysine

Secondary structure

1

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

.

484

Helix Strand Turn

Details...

Beta strand

22 – 24

3

Helix

26 – 29

4

Helix

31 – 46

16

Beta strand

47 – 49

3

Helix

59 – 64

6

Helix

68 – 71

4

Beta strand

78 – 80

3

Beta strand

82 – 84

3

Helix

89 – 103

15

Turn

108 – 110

3

Beta strand

111 – 114

4

Helix

120 – 131

12

Beta strand

137 – 141

5

Turn

143 – 146

4

Helix

149 – 151

3

Helix

162 – 166

5

Beta strand

167 – 172

6

Turn

176 – 178

3

Helix

183 – 193

11

Beta strand

196 – 200

5

Helix

211 – 220

10

Beta strand

224 – 228

5

Turn

230 – 232

3

Helix

233 – 238

6

Helix

244 – 246

3

Beta strand

249 – 259

11

Beta strand

265 – 270

6

Helix

288 – 296

9

Turn

297 – 300

4

Helix

306 – 320

15

Helix

322 – 343

22

Turn

344 – 346

3

Beta strand

355 – 362

8

Helix

363 – 366

4

Helix

370 – 379

10

Beta strand

385 – 387

3

Beta strand

400 – 404

5

Helix

406 – 409

4

Turn

410 – 412

3

Helix

415 – 437

23

Helix

445 – 454

10

Helix

456 – 475

20

Beta strand

480 – 482

3

Sequences

	Sequence		Length	Mass (Da)
	P07511-1 [UniParc]. Last modified January 23, 2007. Version 2. Checksum: C2742A5A8052C5BF	FASTA	484	52,975
	10 20 30 40 50 60 MATAVNGAPR DAALWSSHEQ MLAQPLKDSD AEVYDIIKKE SNRQRVGLEL IASENFASRA 70 80 90 100 110 120 VLEALGSCLN NKYSEGYPGQ RYYGGTEHID ELETLCQKRA LQAYGLDPQC WGVNVQPYSG 130 140 150 160 170 180 SPANFAVYTA LVEPHGRIMG LDLPDGGHLT HGFMTDKKKI SATSIFFESM AYKVNPDTGY 190 200 210 220 230 240 IDYDRLEENA RLFHPKLIIA GTSCYSRNLD YGRLRKIADE NGAYLMADMA HISGLVVAGV 250 260 270 280 290 300 VPSPFEHCHV VTTTTHKTLR GCRAGMIFYR RGVRSVDPKT GKEILYNLES LINSAVFPGL 310 320 330 340 350 360 QGGPHNHAIA GVAVALKQAM TPEFKEYQRQ VVANCRALSA ALVELGYKIV TGGSDNHLIL 370 380 390 400 410 420 VDLRSKGTDG GRAEKVLEAC SIACNKNTCP GDKSALRPSG LRLGTPALTS RGLLEKDFQK 430 440 450 460 470 480 VAHFIHRGIE LTVQIQDDTG PRATLKEFKE KLAGDEKHQR AVRALRQEVE SFAALFPLPG LPGF

References

[1]	"Nucleotide sequence and expression of a cDNA encoding rabbit liver cytosolic serine hydroxymethyltransferase." Byrne P.C., Sanders P.G., Snell K. Biochem. J. 286:117-123(1992) [PubMed: 1381582] [Abstract] Cited for: NUCLEOTIDE SEQUENCE [MRNA]. Strain: New Zealand white. Tissue: Liver.
[2]	"The primary structure of rabbit liver cytosolic serine hydroxymethyltransferase." Martini F., Angelaccio S., Pascarella S., Barra D., Bossa F., Schirch V. J. Biol. Chem. 262:5499-5509(1987) [PubMed: 3553178] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-484. Tissue: Liver.
[3]	"Evidence for the in vivo deamidation and isomerization of an asparaginyl residue in cytosolic serine hydroxymethyltransferase." Artigues A., Birkett A., Schirch V. J. Biol. Chem. 265:4853-4858(1990) [PubMed: 2318867] [Abstract] Cited for: PROTEIN SEQUENCE OF 2-15, DEAMIDATION AT ASN-6.
[4]	"Evidence for a sulfhydryl group at the active site of serine transhydroxymethylase." Schirch L., Slagel S., Barra D., Martini F., Bossa F. J. Biol. Chem. 255:2986-2989(1980) [PubMed: 7358720] [Abstract] Cited for: PROTEIN SEQUENCE OF 194-205, ACTIVE SITE CYS-204.
[5]	"Crystal structure of rabbit cytosolic serine hydroxymethyltransferase at 2.8-A resolution: mechanistic implications." Scarsdale J.N., Kazanina G., Radaev S., Schirch V., Wright H.T. Biochemistry 38:8347-8358(1999) [PubMed: 10387080] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.8 ANGSTROMS). Strain: New Zealand white. Tissue: Liver.
+	Additional computationally mapped references.

Cross-references

Sequence databases

EMBLGenBankDDBJ

Z11846 mRNA. Translation: CAA77870.1.

PIR

XYRBSC. S24342.

RefSeq

NP_001095187.1.

UniGene

Ocu.2076

3D structure databases

PDBPDBe

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1CJ0	X-ray	2.80	A/B	15-484	[»]
1LS3	X-ray	2.70	A/B/C/D	2-484	[»]
1RV3	X-ray	2.40	A/B	2-483	[»]
1RV4	X-ray	2.95	A/B	2-483	[»]
1RVU	X-ray	2.50	A/B	2-483	[»]
1RVY	X-ray	2.90	A/B	2-483	[»]

ModBase

Search...

Genome annotation databases

GeneID

100009405.

Organism-specific databases

CTD

100009405.

Phylogenomic databases

HOVERGEN

P07511.

Enzyme and pathway databases

BRENDA

2.1.2.1. 255.

Family and domain databases

InterPro

IPR015424. PyrdxlP-dep_Trfase_major.
IPR015421. PyrdxlP-dep_Trfase_major_sub1.
IPR001085. Ser_HO-MeTrfase.
IPR019798. Ser_HO-MeTrfase_PLP_BS.
[Graphical view]

Gene3D

G3DSA:3.40.640.10. PyrdxlP-dep_Trfase_major_sub1. 1 hit.

PANTHER

PTHR11680. Gly_HO-Metrfase. 1 hit.

Pfam

PF00464. SHMT. 1 hit.
[Graphical view]

PIRSF

PIRSF000412. SHMT. 1 hit.

PROSITE

PS00096. SHMT. 1 hit.
[Graphical view]

ProtoNet

Search...

Entry information

Entry name

GLYC_RABIT

Accession

Primary (citable) accession number: P07511

Entry history

Integrated into UniProtKB/Swiss-Prot:	April 1, 1988
Last sequence update:	January 23, 2007
Last modified:	November 24, 2009
This is version 90 of the entry and version 2 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation project

HPI (Human Proteome Initiative)