Pyridoxal-phosphate-dependent serine hydroxymethyltransferase - Gramella forsetii (strain KT0803)

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A0M3N2 (GLYA_GRAFK) Reviewed, UniProtKB/Swiss-Prot

Last modified January 25, 2012. Version 40. 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:	GFO_2262

Organism

Gramella forsetii (strain KT0803) [Complete proteome] [HAMAP]

Taxonomic identifier

Taxonomic lineage

Bacteria › Bacteroidetes › Flavobacteriia › Flavobacteriales › Flavobacteriaceae › Gramella

Protein attributes

Sequence length	424 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

424

Pyridoxal-phosphate-dependent serine hydroxymethyltransferase

PRO_1000006257

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

A0M3N2 [UniParc].

Last modified December 12, 2006. Version 1.
Checksum: 25A334F39BBE7CBB
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424

46,404

        10         20         30         40         50         60 
MQRDTQVFDL IAKEKERQLN GLELIASENF VSEAVLEAAG SVLTNKYAEG YPGKRYYGGC 

        70         80         90        100        110        120 
EVVDQVEQLA IDRLKELFNA EYANVQPHSG SQANTAVFHT VMKPGDKFLG FDLSHGGHLT 

       130        140        150        160        170        180 
HGSPVNFSGK LYNPVFYGVD KETGLIDYDA VAEIAEKEKP KMIIAGASAY SREIDYKRFR 

       190        200        210        220        230        240 
EIADSVGAIL VADMAHPAGL IAKGLISDPL PHCHIVTSTT HKTLRGPRGG IILMGKDFEN 

       250        260        270        280        290        300 
PFGEKLKNGN LKKMSTMLNS GIFPGNQGGP LEHIIAAKAI AFGEALTDEF LHYTVQVKKN 

       310        320        330        340        350        360 
AEKLAQAFVE KDYKVISGGT DNHMMLIDLR NKNVSGKEAE EALSKADITV NKNMVPFDDK 

       370        380        390        400        410        420 
SPFVTSGIRI GTPAVTTRGL QENDMNKIVD LIDRVITNIE NDTELEAVKK EVNSMMSGRP 


LFVA

References

[1]

"Whole genome analysis of the marine Bacteroidetes'Gramella forsetii' reveals adaptations to degradation of polymeric organic matter."
Bauer M., Kube M., Teeling H., Richter M., Lombardot T., Allers E., Wuerdemann C.A., Quast C., Kuhl H., Knaust F., Woebken D., Bischof K., Mussmann M., Choudhuri J.V., Meyer F., Reinhardt R., Amann R.I., Gloeckner F.O.
Environ. Microbiol. 8:2201-2213(2006) [PubMed: 17107561] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
Strain: KT0803.

Cross-references

Sequence databases
EMBL GenBank DDBJ	CU207366 Genomic DNA. Translation: CAL67227.1.
RefSeq	YP_862294.1. NC_008571.1.
3D structure databases
ProteinModelPortal	A0M3N2.
SMR	A0M3N2. Positions 2-416.
ModBase	Search...
Protein-protein interaction databases
STRING	A0M3N2.
Protocols and materials databases
StructuralBiologyKnowledgebase	Search...
Genome annotation databases
GeneID	4650520.
GenomeReviews	Gene locus GFO_2262 in contig CU207366_GR.
KEGG	gfo:GFO_2262.
NMPDR	fig\|411154.5.peg.2146.
PATRIC	22073297. VBIGraFor5527_2186.
Organism-specific databases
CMR	Search...
Phylogenomic databases
eggNOG	COG0112.
HOGENOM	HBG301263.
OMA	GTSNHLM.
PhylomeDB	A0M3N2.
ProtClustDB	PRK00011.
Enzyme and pathway databases
BioCyc	GFOR411154:GFO_2262-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_GRAFK

Accession

Primary (citable) accession number: A0M3N2

Entry history

Integrated into UniProtKB/Swiss-Prot:	January 15, 2008
Last sequence update:	December 12, 2006
Last modified:	January 25, 2012
This is version 40 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