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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.

Pathwayi: formaldehyde 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)DescriptionActionsGraphical viewLength
Metal bindingi31Zinc 1; structural1
Metal bindingi33Zinc 1; structural1
Metal bindingi52Zinc 2; catalytic1
Metal bindingi54Zinc 2; catalytic1
Metal bindingi57Zinc 2; catalytic1
Metal bindingi99Zinc 1; structural1
Metal bindingi102Zinc 1; structural1

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)DescriptionActionsGraphical viewLength
Initiator methionineiRemoved1 Publication
ChainiPRO_00002203212 – 194Glutathione-dependent formaldehyde-activating enzymeAdd BLAST193

Interactioni

Subunit structurei

Homodimer.1 Publication

Protein-protein interaction databases

STRINGi318586.Pden_0015.

Structurei

Secondary structure

1194
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Helixi11 – 14Combined sources4
Beta strandi27 – 30Combined sources4
Beta strandi34 – 36Combined sources3
Beta strandi39 – 42Combined sources4
Beta strandi47 – 52Combined sources6
Beta strandi55 – 57Combined sources3
Beta strandi64 – 72Combined sources9
Helixi73 – 75Combined sources3
Beta strandi76 – 80Combined sources5
Helixi82 – 84Combined sources3
Beta strandi85 – 88Combined sources4
Beta strandi92 – 99Combined sources8
Turni100 – 102Combined sources3
Beta strandi105 – 110Combined sources6
Turni116 – 119Combined sources4
Beta strandi120 – 123Combined sources4
Helixi125 – 127Combined sources3
Beta strandi138 – 141Combined sources4
Helixi142 – 148Combined sources7
Helixi152 – 154Combined sources3
Helixi155 – 164Combined sources10
Beta strandi171 – 173Combined sources3
Helixi175 – 189Combined sources15
Beta strandi190 – 192Combined sources3

3D structure databases

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

Miscellaneous databases

EvolutionaryTraceiQ51669.

Family & Domainsi

Sequence similaritiesi

Belongs to the Gfa family.Curated

Phylogenomic databases

eggNOGiENOG4108QBQ. Bacteria.
COG3791. LUCA.

Family and domain databases

Gene3Di3.90.1590.10. 1 hit.
HAMAPiMF_00723. Formald_GSH. 1 hit.
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
PDB entryMethodResolution (Å)ChainPositionsPDBsum
1X6MX-ray2.35A/B/C/D2-194[»]
1XA8X-ray2.40A/B/C/D2-194[»]
ProteinModelPortaliQ51669.
SMRiQ51669.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi318586.Pden_0015.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Phylogenomic databases

eggNOGiENOG4108QBQ. Bacteria.
COG3791. LUCA.

Enzyme and pathway databases

UniPathwayiUPA00562; UER00621.

Miscellaneous databases

EvolutionaryTraceiQ51669.

Family and domain databases

Gene3Di3.90.1590.10. 1 hit.
HAMAPiMF_00723. Formald_GSH. 1 hit.
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...

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: November 2, 2016
This is version 80 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

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 one 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.