Pyridoxal-phosphate-dependent serine hydroxymethyltransferase - Helicobacter pylori (strain J99)

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Q9ZMP7 (GLYA_HELPJ) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 79. History...

Clusters with 100%, 90%, 50% identity |

Documents (2) |

Third-party data

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents Customize order

Names and origin

Protein names

Recommended name:
Pyridoxal-phosphate-dependent serine hydroxymethyltransferase
Short name=SHMT
Short name=Serine methylase
EC=2.1.2.1

Gene names

Name:	glyA
Ordered Locus Names:	jhp_0171

Organism

Helicobacter pylori (strain J99) (Campylobacter pylori J99) [Complete proteome] [HAMAP]

Taxonomic identifier

Taxonomic lineage

Bacteria › Proteobacteria › Epsilonproteobacteria › Campylobacterales › Helicobacteraceae › Helicobacter

Protein attributes

Sequence length	416 AA.
Sequence status	Complete.
Protein existence	Inferred from homology

General annotation (Comments)

Function	Catalyzes the reversible interconversion of serine and glycine with tetrahydrofolate serving as the one-carbon carrier By similarity.
Catalytic activity	5,10-methylenetetrahydrofolate + glycine + H₂O = tetrahydrofolate + L-serine. HAMAP MF_00051
Cofactor	Pyridoxal phosphate By similarity. HAMAP MF_00051
Pathway	One-carbon metabolism; tetrahydrofolate interconversion. HAMAP MF_00051 Amino-acid biosynthesis; glycine biosynthesis; glycine from L-serine: step 1/1.
Subunit structure	Homodimer By similarity.
Subcellular location	Cytoplasm By similarity HAMAP MF_00051.
Sequence similarities	Belongs to the SHMT family.

Ontologies

Keywords
Biological process	Amino-acid biosynthesis One-carbon metabolism
Cellular component	Cytoplasm
Ligand	Pyridoxal phosphate
Molecular function	Transferase
Technical term	Complete proteome
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

Chain

416

Pyridoxal-phosphate-dependent serine hydroxymethyltransferase

PRO_0000113587

Regions

Region

3

Substrate binding By similarity

Sites

Binding site

1

Pyridoxal phosphate By similarity

Binding site

1

Pyridoxal phosphate By similarity

Binding site

1

Substrate By similarity

Binding site

1

Substrate binding By similarity

Binding site

1

Pyridoxal phosphate By similarity

Binding site

1

Pyridoxal phosphate By similarity

Binding site

1

Substrate By similarity

Binding site

1

Pyridoxal phosphate By similarity

Binding site

1

Pyridoxal phosphate By similarity

Binding site

1

Pyridoxal phosphate By similarity

Binding site

1

Pyridoxal phosphate By similarity

Binding site

1

Pyridoxal phosphate; via amide nitrogen and carbonyl oxygen By similarity

Binding site

1

Pyridoxal phosphate By similarity

Amino acid modifications

Modified residue

1

N6-(pyridoxal phosphate)lysine By similarity

Sequences

Sequence

Length

Mass (Da)

Tools

Q9ZMP7 [UniParc].

Last modified May 1, 1999. Version 1.
Checksum: 58D9DC2E9E8A7D9C
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416

45,706

        10         20         30         40         50         60 
MAYFLEQTDS EIFEFIVEEF KRQNEHLEMI ASENYTFPSV MEAMGSILTN KYAEGYPNKR 

        70         80         90        100        110        120 
YYGGCEVVDK IESLAIERAK KLFNCQFANV QAHSGSQANN AVYHALLKLY DKILGMDLSC 

       130        140        150        160        170        180 
GGHLTHGAKV SLTGKHYQSF SYGVGLDGYI DYEEALKIAQ SVKPQIIVCG FSAYPREIDF 

       190        200        210        220        230        240 
KKFREIADAV GALLLGDIAH VAGLVVANEH AHPFPHCHVV SSTTHKTLRG PRGGLILTND 

       250        260        270        280        290        300 
EEIAAKIDKA IFPGTQGGPL MHVIAAKAVG FKENLKPEFK AYAKLVKSNM QVLAKTLKEK 

       310        320        330        340        350        360 
NHKLVSGGTS NHLLLMDFLD KPYSGKDADI ALGNAGITVN KNTIPGETRN PFVTSGIRIG 

       370        380        390        400        410 
SAALSARGMG AKEFEIIGNK ISDILNDINN VSLQLHVKEE LKTMANQFPV YHQPIF

References

[1]

"Genomic sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori."
Alm R.A., Ling L.-S.L., Moir D.T., King B.L., Brown E.D., Doig P.C., Smith D.R., Noonan B., Guild B.C., deJonge B.L., Carmel G., Tummino P.J., Caruso A., Uria-Nickelsen M., Mills D.M., Ives C., Gibson R., Merberg D.

expand/collapse author list

Trust T.J.
Nature 397:176-180(1999) [PubMed: 9923682] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: J99.

+

Additional computationally mapped references.

Cross-references

Sequence databases
EMBL GenBank DDBJ	AE001439 Genomic DNA. Translation: AAD05752.1.
PIR	G71965.
RefSeq	NP_222892.1. NC_000921.1.
3D structure databases
ProteinModelPortal	Q9ZMP7.
SMR	Q9ZMP7. Positions 7-410.
ModBase	Search...
Protein-protein interaction databases
IntAct	Q9ZMP7. 1 interaction.
STRING	Q9ZMP7.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	889253.
GenomeReviews	Gene locus jhp_0171 in contig AE001439_GR.
KEGG	hpj:jhp0171.
NMPDR	fig\|85963.1.peg.170.
PATRIC	20604964. VBIHelPyl98156_0194.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0112.
HOGENOM	HBG301263.
OMA	RGMGAKE.
ProtClustDB	PRK13034.
Enzyme and pathway databases
BioCyc	HPYL85963:JHP0171-MONOMER.
Family and domain databases
HAMAP	MF_00051. SHMT. [Tree]
InterPro	IPR015424. PyrdxlP-dep_Trfase_major_dom. IPR015421. PyrdxlP-dep_Trfase_major_sub1. IPR015422. PyrdxlP-dep_Trfase_major_sub2. 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. G3DSA:3.90.1150.10. PyrdxlP-dep_Trfase_major_sub2. 1 hit.
KO	K00600.
PANTHER	PTHR11680. Gly_HO-Metrfase. 1 hit.
Pfam	PF00464. SHMT. 1 hit. [Graphical view]
PIRSF	PIRSF000412. SHMT. 1 hit.
SUPFAM	SSF53383. PyrdxlP-dep_Trfase_major. 1 hit.
PROSITE	PS00096. SHMT. 1 hit. [Graphical view]
ProtoNet	Search...

Entry information

Entry name

GLYA_HELPJ

Accession

Primary (citable) accession number: Q9ZMP7

Entry history

Integrated into UniProtKB/Swiss-Prot:	May 30, 2000
Last sequence update:	May 1, 1999
Last modified:	January 25, 2012
This is version 79 of the entry and version 1 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program

Relevant documents

PATHWAY comments

Index of metabolic and biosynthesis pathways

SIMILARITY comments

Index of protein domains and families

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Names·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents