Q51669 (GFA_PARDE) Reviewed, UniProtKB/Swiss-Prot

Names and origin

Protein names

Recommended name:
Glutathione-dependent formaldehyde-activating enzyme
EC=4.4.1.22

Alternative name(s):
S-(hydroxymethyl)glutathione synthase

Gene names

Name:

gfa

Organism

Paracoccus denitrificans

Taxonomic identifier

266 [NCBI]

Taxonomic lineage

cellular organisms › Bacteria › Proteobacteria › Alphaproteobacteria › Rhodobacterales › Rhodobacteraceae › Paracoccus

Protein attributes

Sequence length	194 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	Catalyzes the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. Ref.2
Catalytic activity	S-(hydroxymethyl)glutathione = glutathione + formaldehyde. HAMAP-Rule MF_00723
Cofactor	Binds 2 zinc ions per subunit.
Pathway	One-carbon metabolism; formaldehyde degradation; formate from formaldehyde (glutathione route): step 1/3. HAMAP-Rule MF_00723
Subunit structure	Homodimer.
Sequence similarities	Belongs to the gfa family.

Ontologies

Keywords
Ligand	Metal-binding Zinc
Molecular function	Lyase
Technical term	3D-structure Direct protein sequencing
Gene Ontology (GO)
Biological_process	formaldehyde catabolic process Inferred from electronic annotation. Source: HAMAP
Molecular_function	S-(hydroxymethyl)glutathione synthase activity Inferred from electronic annotation. Source: HAMAP zinc ion binding Inferred from electronic annotation. Source: HAMAP
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

Chain

2 – 194

193

Glutathione-dependent formaldehyde-activating enzyme HAMAP-Rule MF_00723

PRO_0000220321

Sites

Metal binding

31

1

Zinc 1; structural

Metal binding

33

1

Zinc 1; structural

Metal binding

52

1

Zinc 2; catalytic

Metal binding

54

1

Zinc 2; catalytic

Metal binding

57

1

Zinc 2; catalytic

Metal binding

99

1

Zinc 1; structural

Metal binding

102

1

Zinc 1; structural

Secondary structure

1

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194

Helix Strand Turn

Details...

Helix

11 – 14

4

Beta strand

27 – 30

4

Beta strand

34 – 36

3

Beta strand

39 – 42

4

Beta strand

47 – 52

6

Beta strand

55 – 57

3

Beta strand

64 – 72

9

Helix

73 – 75

3

Beta strand

76 – 80

5

Helix

82 – 84

3

Beta strand

85 – 88

4

Beta strand

92 – 99

8

Turn

100 – 102

3

Beta strand

105 – 110

6

Turn

116 – 119

4

Beta strand

120 – 123

4

Helix

125 – 127

3

Beta strand

138 – 141

4

Helix

142 – 148

7

Helix

152 – 154

3

Helix

155 – 164

10

Beta strand

171 – 173

3

Helix

175 – 189

15

Beta strand

190 – 192

3

Sequences

	Sequence		Length	Mass (Da)
	Q51669 [UniParc]. Last modified January 23, 2007. Version 3. Checksum: 95B6E386B1756619	FASTA	194	20,967
	10 20 30 40 50 60 MVDTSGVKIH PAVDNGIKPA QPGFAGGTLH CKCSTNPVRV AVRAQTAHNH VCGCTKCWKP 70 80 90 100 110 120 EGAIFSQVAV VGRDALEVLE GAEKLEIVNA EAPIQRHRCR DCGVHMYGRI ENRDHPFYGL 130 140 150 160 170 180 DFVHTELSDE DGWSAPEFAA FVSSIIESGV DPSRMEAIRA RLRELGLEPY DALSPPLMDA 190 IATHIAKRSG ALAA

References

[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]	"A dynamic zinc redox switch." Neculai A.M., Neculai D., Griesinger C., Vorholt J.A., Becker S. J. Biol. Chem. 280:2826-2830(2005) [PubMed] [Europe PMC] [Abstract] Cited for: X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) IN COMPLEX WITH GLUTATHIONE.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ

U34346 Genomic DNA. Translation: AAC44550.1.

3D structure databases

PDBe
RCSB PDB
PDBj

Entry	Method	Resolution (Å)	Chain	Positions	PDBsum
1X6M	X-ray	2.35	A/B/C/D	1-194	[»]
1XA8	X-ray	2.40	A/B/C/D	1-194	[»]

ProteinModelPortal

Q51669.

SMR

Q51669. Positions 1-194.

ModBase

Search...

Protocols and materials databases

StructuralBiologyKnowledgebase

Search...

Enzyme and pathway databases

UniPathway

UPA00562; UER00621.

Family and domain databases

Gene3D

3.90.1590.10. 1 hit.

HAMAP

MF_00723. Formald_GSH.

InterPro

IPR014185. Formald_GSH.
IPR006913. GFA/CENP-V.
IPR011057. Mss4-like.
[Graphical view]

Pfam

PF04828. GFA. 1 hit.
[Graphical view]

PIRSF

PIRSF033318. Formald_GSH. 1 hit.

SUPFAM

SSF51316. Mss4_like. 1 hit.

TIGRFAMs

TIGR02820. formald_GSH. 1 hit.

ProtoNet

Search...

Other

EvolutionaryTrace

Q51669.

Entry information

Entry name

GFA_PARDE

Accession

Primary (citable) accession number: Q51669

Entry history

Integrated into UniProtKB/Swiss-Prot:	November 7, 2003
Last sequence update:	January 23, 2007
Last modified:	April 3, 2013
This is version 65 of the entry and version 3 of the sequence. [Complete history]

Entry status

Reviewed (UniProtKB/Swiss-Prot)

Annotation program

Prokaryotic Protein Annotation Program