GFA_PARDE
ID GFA_PARDE Reviewed; 194 AA.
AC Q51669;
DT 07-NOV-2003, integrated into UniProtKB/Swiss-Prot.
DT 23-JAN-2007, sequence version 3.
DT 03-AUG-2022, entry version 99.
DE RecName: Full=Glutathione-dependent formaldehyde-activating enzyme;
DE EC=4.4.1.22;
DE AltName: Full=S-(hydroxymethyl)glutathione synthase;
GN Name=gfa;
OS Paracoccus denitrificans.
OC Bacteria; Proteobacteria; Alphaproteobacteria; Rhodobacterales;
OC Rhodobacteraceae; Paracoccus.
OX NCBI_TaxID=266;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RX PubMed=8892832; DOI=10.1128/jb.178.21.6296-6299.1996;
RA Harms N., Ras J., Reijnders W.N.M., van Spanning R.J.M., Stouthamer A.H.;
RT "S-formylglutathione hydrolase of Paracoccus denitrificans is homologous to
RT human esterase D: a universal pathway for formaldehyde detoxification?";
RL J. Bacteriol. 178:6296-6299(1996).
RN [2]
RP PROTEIN SEQUENCE OF 2-16, AND FUNCTION.
RX PubMed=11741920; DOI=10.1074/jbc.c100579200;
RA Goenrich M., Bartoschek S., Hagemeier C.H., Griesinger C., Vorholt J.A.;
RT "A glutathione-dependent formaldehyde-activating enzyme (Gfa) from
RT Paracoccus denitrificans detected and purified via two-dimensional proton
RT exchange NMR spectroscopy.";
RL J. Biol. Chem. 277:3069-3072(2002).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.35 ANGSTROMS) IN COMPLEX WITH GLUTATHIONE.
RX PubMed=15548539; DOI=10.1074/jbc.c400517200;
RA Neculai A.M., Neculai D., Griesinger C., Vorholt J.A., Becker S.;
RT "A dynamic zinc redox switch.";
RL J. Biol. Chem. 280:2826-2830(2005).
CC -!- FUNCTION: Catalyzes the condensation of formaldehyde and glutathione to
CC S-hydroxymethylglutathione. {ECO:0000269|PubMed:11741920}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=S-(hydroxymethyl)glutathione = formaldehyde + glutathione;
CC Xref=Rhea:RHEA:22488, ChEBI:CHEBI:16842, ChEBI:CHEBI:57925,
CC ChEBI:CHEBI:58758; EC=4.4.1.22;
CC -!- COFACTOR:
CC Name=Zn(2+); Xref=ChEBI:CHEBI:29105;
CC Evidence={ECO:0000255|PROSITE-ProRule:PRU01239};
CC Note=Binds 2 Zn(2+) ions per subunit. {ECO:0000255|PROSITE-
CC ProRule:PRU01239};
CC -!- PATHWAY: One-carbon metabolism; formaldehyde degradation; formate from
CC formaldehyde (glutathione route): step 1/3.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|PubMed:15548539}.
CC -!- SIMILARITY: Belongs to the Gfa family. {ECO:0000305}.
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DR EMBL; U34346; AAC44550.1; -; Genomic_DNA.
DR RefSeq; WP_011746365.1; NZ_PPGA01000008.1.
DR PDB; 1X6M; X-ray; 2.35 A; A/B/C/D=2-194.
DR PDB; 1XA8; X-ray; 2.40 A; A/B/C/D=2-194.
DR PDBsum; 1X6M; -.
DR PDBsum; 1XA8; -.
DR AlphaFoldDB; Q51669; -.
DR SMR; Q51669; -.
DR OMA; ECGTHMY; -.
DR BRENDA; 4.4.1.22; 3341.
DR UniPathway; UPA00562; UER00621.
DR EvolutionaryTrace; Q51669; -.
DR GO; GO:0051907; F:S-(hydroxymethyl)glutathione synthase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0008270; F:zinc ion binding; IEA:UniProtKB-UniRule.
DR GO; GO:0046294; P:formaldehyde catabolic process; IEA:UniProtKB-UniRule.
DR HAMAP; MF_00723; Formald_GSH; 1.
DR InterPro; IPR006913; CENP-V/GFA.
DR InterPro; IPR014185; Formald_GSH.
DR InterPro; IPR011057; Mss4-like_sf.
DR Pfam; PF04828; GFA; 1.
DR PIRSF; PIRSF033318; Formald_GSH; 1.
DR SUPFAM; SSF51316; SSF51316; 1.
DR TIGRFAMs; TIGR02820; formald_GSH; 1.
DR PROSITE; PS51891; CENP_V_GFA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Direct protein sequencing; Lyase; Metal-binding; Zinc.
FT INIT_MET 1
FT /note="Removed"
FT /evidence="ECO:0000269|PubMed:11741920"
FT CHAIN 2..194
FT /note="Glutathione-dependent formaldehyde-activating
FT enzyme"
FT /id="PRO_0000220321"
FT DOMAIN 24..171
FT /note="CENP-V/GFA"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01239"
FT BINDING 31
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="structural"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01239"
FT BINDING 33
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="structural"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01239"
FT BINDING 52
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01239"
FT BINDING 54
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01239"
FT BINDING 57
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="2"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01239"
FT BINDING 99
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="structural"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01239"
FT BINDING 102
FT /ligand="Zn(2+)"
FT /ligand_id="ChEBI:CHEBI:29105"
FT /ligand_label="1"
FT /ligand_note="structural"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU01239"
FT HELIX 11..14
FT /evidence="ECO:0007829|PDB:1X6M"
FT STRAND 27..30
FT /evidence="ECO:0007829|PDB:1X6M"
FT STRAND 34..36
FT /evidence="ECO:0007829|PDB:1X6M"
FT STRAND 39..42
FT /evidence="ECO:0007829|PDB:1X6M"
FT STRAND 47..52
FT /evidence="ECO:0007829|PDB:1X6M"
FT STRAND 55..57
FT /evidence="ECO:0007829|PDB:1X6M"
FT STRAND 64..72
FT /evidence="ECO:0007829|PDB:1X6M"
FT HELIX 73..75
FT /evidence="ECO:0007829|PDB:1X6M"
FT STRAND 76..80
FT /evidence="ECO:0007829|PDB:1X6M"
FT HELIX 82..84
FT /evidence="ECO:0007829|PDB:1X6M"
FT STRAND 85..88
FT /evidence="ECO:0007829|PDB:1X6M"
FT STRAND 92..99
FT /evidence="ECO:0007829|PDB:1X6M"
FT TURN 100..102
FT /evidence="ECO:0007829|PDB:1X6M"
FT STRAND 105..110
FT /evidence="ECO:0007829|PDB:1X6M"
FT TURN 116..119
FT /evidence="ECO:0007829|PDB:1X6M"
FT STRAND 120..123
FT /evidence="ECO:0007829|PDB:1X6M"
FT HELIX 125..127
FT /evidence="ECO:0007829|PDB:1X6M"
FT STRAND 138..141
FT /evidence="ECO:0007829|PDB:1X6M"
FT HELIX 142..148
FT /evidence="ECO:0007829|PDB:1X6M"
FT HELIX 152..154
FT /evidence="ECO:0007829|PDB:1X6M"
FT HELIX 155..164
FT /evidence="ECO:0007829|PDB:1X6M"
FT STRAND 171..173
FT /evidence="ECO:0007829|PDB:1X6M"
FT HELIX 175..189
FT /evidence="ECO:0007829|PDB:1X6M"
FT STRAND 190..192
FT /evidence="ECO:0007829|PDB:1X6M"
SQ SEQUENCE 194 AA; 20967 MW; 95B6E386B1756619 CRC64;
MVDTSGVKIH PAVDNGIKPA QPGFAGGTLH CKCSTNPVRV AVRAQTAHNH VCGCTKCWKP
EGAIFSQVAV VGRDALEVLE GAEKLEIVNA EAPIQRHRCR DCGVHMYGRI ENRDHPFYGL
DFVHTELSDE DGWSAPEFAA FVSSIIESGV DPSRMEAIRA RLRELGLEPY DALSPPLMDA
IATHIAKRSG ALAA
