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Protein

Glutathione-dependent formaldehyde-activating enzyme

Gene

gfa

Organism
Paracoccus denitrificans
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione.1 Publication

Catalytic activityi

S-(hydroxymethyl)glutathione = glutathione + formaldehyde.

Cofactori

Zn2+Note: Binds 2 Zn2+ ions per subunit.

Pathway:iformaldehyde degradation

This protein is involved in step 1 of the subpathway that synthesizes formate from formaldehyde (glutathione route).
Proteins known to be involved in the 3 steps of the subpathway in this organism are:
  1. Glutathione-dependent formaldehyde-activating enzyme (gfa)
  2. no protein annotated in this organism
  3. no protein annotated in this organism
This subpathway is part of the pathway formaldehyde degradation, which is itself part of One-carbon metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes formate from formaldehyde (glutathione route), the pathway formaldehyde degradation and in One-carbon metabolism.

Sites

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Metal bindingi31 – 311Zinc 1; structural
Metal bindingi33 – 331Zinc 1; structural
Metal bindingi52 – 521Zinc 2; catalytic
Metal bindingi54 – 541Zinc 2; catalytic
Metal bindingi57 – 571Zinc 2; catalytic
Metal bindingi99 – 991Zinc 1; structural
Metal bindingi102 – 1021Zinc 1; structural

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Lyase

Keywords - Ligandi

Metal-binding, Zinc

Enzyme and pathway databases

UniPathwayiUPA00562; UER00621.

Names & Taxonomyi

Protein namesi
Recommended name:
Glutathione-dependent formaldehyde-activating enzyme (EC:4.4.1.22)
Alternative name(s):
S-(hydroxymethyl)glutathione synthase
Gene namesi
Name:gfa
OrganismiParacoccus denitrificans
Taxonomic identifieri266 [NCBI]
Taxonomic lineageiBacteriaProteobacteriaAlphaproteobacteriaRhodobacteralesRhodobacteraceaeParacoccus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11Removed1 Publication
Chaini2 – 194193Glutathione-dependent formaldehyde-activating enzymePRO_0000220321Add
BLAST

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi318586.Pden_0015.

Structurei

Secondary structure

1
194
Legend: HelixTurnBeta strand
Show more details
Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Helixi11 – 144Combined sources
Beta strandi27 – 304Combined sources
Beta strandi34 – 363Combined sources
Beta strandi39 – 424Combined sources
Beta strandi47 – 526Combined sources
Beta strandi55 – 573Combined sources
Beta strandi64 – 729Combined sources
Helixi73 – 753Combined sources
Beta strandi76 – 805Combined sources
Helixi82 – 843Combined sources
Beta strandi85 – 884Combined sources
Beta strandi92 – 998Combined sources
Turni100 – 1023Combined sources
Beta strandi105 – 1106Combined sources
Turni116 – 1194Combined sources
Beta strandi120 – 1234Combined sources
Helixi125 – 1273Combined sources
Beta strandi138 – 1414Combined sources
Helixi142 – 1487Combined sources
Helixi152 – 1543Combined sources
Helixi155 – 16410Combined sources
Beta strandi171 – 1733Combined sources
Helixi175 – 18915Combined sources
Beta strandi190 – 1923Combined sources

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1X6MX-ray2.35A/B/C/D2-194[»]
1XA8X-ray2.40A/B/C/D2-194[»]
ProteinModelPortaliQ51669.
SMRiQ51669. Positions 1-194.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ51669.

Family & Domainsi

Sequence similaritiesi

Belongs to the Gfa family.Curated

Family and domain databases

Gene3Di3.90.1590.10. 1 hit.
HAMAPiMF_00723. Formald_GSH.
InterProiIPR014185. Formald_GSH.
IPR006913. GFA/CENP-V.
IPR011057. Mss4-like.
[Graphical view]
PfamiPF04828. GFA. 1 hit.
[Graphical view]
PIRSFiPIRSF033318. Formald_GSH. 1 hit.
SUPFAMiSSF51316. SSF51316. 1 hit.
TIGRFAMsiTIGR02820. formald_GSH. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q51669-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MVDTSGVKIH PAVDNGIKPA QPGFAGGTLH CKCSTNPVRV AVRAQTAHNH
60 70 80 90 100
VCGCTKCWKP EGAIFSQVAV VGRDALEVLE GAEKLEIVNA EAPIQRHRCR
110 120 130 140 150
DCGVHMYGRI ENRDHPFYGL DFVHTELSDE DGWSAPEFAA FVSSIIESGV
160 170 180 190
DPSRMEAIRA RLRELGLEPY DALSPPLMDA IATHIAKRSG ALAA
Length:194
Mass (Da):20,967
Last modified:January 23, 2007 - v3
Checksum:i95B6E386B1756619
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U34346 Genomic DNA. Translation: AAC44550.1.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U34346 Genomic DNA. Translation: AAC44550.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
EntryMethodResolution (Å)ChainPositionsPDBsum
1X6MX-ray2.35A/B/C/D2-194[»]
1XA8X-ray2.40A/B/C/D2-194[»]
ProteinModelPortaliQ51669.
SMRiQ51669. Positions 1-194.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi318586.Pden_0015.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Enzyme and pathway databases

UniPathwayiUPA00562; UER00621.

Miscellaneous databases

EvolutionaryTraceiQ51669.

Family and domain databases

Gene3Di3.90.1590.10. 1 hit.
HAMAPiMF_00723. Formald_GSH.
InterProiIPR014185. Formald_GSH.
IPR006913. GFA/CENP-V.
IPR011057. Mss4-like.
[Graphical view]
PfamiPF04828. GFA. 1 hit.
[Graphical view]
PIRSFiPIRSF033318. Formald_GSH. 1 hit.
SUPFAMiSSF51316. SSF51316. 1 hit.
TIGRFAMsiTIGR02820. formald_GSH. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "S-formylglutathione hydrolase of Paracoccus denitrificans is homologous to human esterase D: a universal pathway for formaldehyde detoxification?"
    Harms N., Ras J., Reijnders W.N.M., van Spanning R.J.M., Stouthamer A.H.
    J. Bacteriol. 178:6296-6299(1996) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. "A glutathione-dependent formaldehyde-activating enzyme (Gfa) from Paracoccus denitrificans detected and purified via two-dimensional proton exchange NMR spectroscopy."
    Goenrich M., Bartoschek S., Hagemeier C.H., Griesinger C., Vorholt J.A.
    J. Biol. Chem. 277:3069-3072(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: PROTEIN SEQUENCE OF 2-16, FUNCTION.
  3. Cited for: X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) IN COMPLEX WITH GLUTATHIONE.

Entry informationi

Entry nameiGFA_PARDE
AccessioniPrimary (citable) accession number: Q51669
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 7, 2003
Last sequence update: January 23, 2007
Last modified: June 24, 2015
This is version 74 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Direct protein sequencing

Documents

  1. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  2. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  3. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.