NAGA_VIBCH
ID NAGA_VIBCH Reviewed; 378 AA.
AC O32445; Q9KTA9;
DT 15-JUL-1998, integrated into UniProtKB/Swiss-Prot.
DT 01-DEC-2000, sequence version 2.
DT 03-AUG-2022, entry version 124.
DE RecName: Full=N-acetylglucosamine-6-phosphate deacetylase {ECO:0000250|UniProtKB:P0AF18};
DE Short=GlcNAc 6-P deacetylase {ECO:0000250|UniProtKB:P0AF18};
DE EC=3.5.1.25 {ECO:0000250|UniProtKB:P0AF18};
GN Name=nagA; OrderedLocusNames=VC_0994;
OS Vibrio cholerae serotype O1 (strain ATCC 39315 / El Tor Inaba N16961).
OC Bacteria; Proteobacteria; Gammaproteobacteria; Vibrionales; Vibrionaceae;
OC Vibrio.
OX NCBI_TaxID=243277;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA].
RC STRAIN=NON-O1 / 1148A;
RX PubMed=9301118; DOI=10.1271/bbb.61.1349;
RA Yamano N., Oura N., Wang J., Fujishima S.;
RT "Cloning and sequencing of the genes for N-acetylglucosamine use that
RT construct divergent operons (nagE-nagAC) from Vibrio cholerae non-O1.";
RL Biosci. Biotechnol. Biochem. 61:1349-1353(1997).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 39315 / El Tor Inaba N16961;
RX PubMed=10952301; DOI=10.1038/35020000;
RA Heidelberg J.F., Eisen J.A., Nelson W.C., Clayton R.A., Gwinn M.L.,
RA Dodson R.J., Haft D.H., Hickey E.K., Peterson J.D., Umayam L.A., Gill S.R.,
RA Nelson K.E., Read T.D., Tettelin H., Richardson D.L., Ermolaeva M.D.,
RA Vamathevan J.J., Bass S., Qin H., Dragoi I., Sellers P., McDonald L.A.,
RA Utterback T.R., Fleischmann R.D., Nierman W.C., White O., Salzberg S.L.,
RA Smith H.O., Colwell R.R., Mekalanos J.J., Venter J.C., Fraser C.M.;
RT "DNA sequence of both chromosomes of the cholera pathogen Vibrio
RT cholerae.";
RL Nature 406:477-483(2000).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.53 ANGSTROMS) IN COMPLEXES WITH NICKEL AND
RP FRUCTOSE-6-PHOSPHATE, COFACTOR, AND SUBUNIT.
RG Center for structural genomics of infectious diseases (CSGID);
RT "X-ray crystal structure of N-acetylglucosamine-6-phosphate deacetylase
RT from Vibrio cholerae complexed with fructose 6-phosphate.";
RL Submitted (AUG-2009) to the PDB data bank.
CC -!- FUNCTION: Involved in the first committed step in the biosynthesis of
CC amino-sugar-nucleotides. Catalyzes the hydrolysis of the N-acetyl group
CC of N-acetylglucosamine-6-phosphate (GlcNAc-6-P) to yield glucosamine 6-
CC phosphate and acetate. {ECO:0000250|UniProtKB:P0AF18}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + N-acetyl-D-glucosamine 6-phosphate = acetate + D-
CC glucosamine 6-phosphate; Xref=Rhea:RHEA:22936, ChEBI:CHEBI:15377,
CC ChEBI:CHEBI:30089, ChEBI:CHEBI:57513, ChEBI:CHEBI:58725; EC=3.5.1.25;
CC Evidence={ECO:0000250|UniProtKB:P0AF18};
CC -!- COFACTOR:
CC Name=a divalent metal cation; Xref=ChEBI:CHEBI:60240;
CC Evidence={ECO:0000269|Ref.3};
CC Note=Binds 1 divalent metal cation per subunit. Ni(2+) ion is seen in
CC the structure. {ECO:0000269|Ref.3};
CC -!- PATHWAY: Amino-sugar metabolism; N-acetylneuraminate degradation; D-
CC fructose 6-phosphate from N-acetylneuraminate: step 4/5. {ECO:0000305}.
CC -!- SUBUNIT: Homodimer. {ECO:0000269|Ref.3}.
CC -!- SIMILARITY: Belongs to the metallo-dependent hydrolases superfamily.
CC NagA family. {ECO:0000305}.
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DR EMBL; D87820; BAA22834.1; -; Genomic_DNA.
DR EMBL; AE003852; AAF94155.1; -; Genomic_DNA.
DR PIR; E82254; E82254.
DR PIR; JC5649; JC5649.
DR RefSeq; NP_230640.1; NC_002505.1.
DR RefSeq; WP_000271133.1; NZ_LT906614.1.
DR PDB; 3EGJ; X-ray; 2.90 A; A/B=1-378.
DR PDB; 3IV8; X-ray; 2.53 A; A/B/C/D=1-378.
DR PDBsum; 3EGJ; -.
DR PDBsum; 3IV8; -.
DR AlphaFoldDB; O32445; -.
DR SMR; O32445; -.
DR STRING; 243277.VC_0994; -.
DR DNASU; 2614247; -.
DR EnsemblBacteria; AAF94155; AAF94155; VC_0994.
DR GeneID; 57739680; -.
DR KEGG; vch:VC_0994; -.
DR PATRIC; fig|243277.26.peg.947; -.
DR eggNOG; COG1820; Bacteria.
DR HOGENOM; CLU_032482_2_2_6; -.
DR OMA; HAFNAMP; -.
DR BioCyc; MetaCyc:MON-16875; -.
DR BioCyc; VCHO:VC0994-MON; -.
DR UniPathway; UPA00629; UER00683.
DR EvolutionaryTrace; O32445; -.
DR Proteomes; UP000000584; Chromosome 1.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0047419; F:N-acetylgalactosamine-6-phosphate deacetylase activity; IEA:UniProtKB-EC.
DR GO; GO:0008448; F:N-acetylglucosamine-6-phosphate deacetylase activity; ISS:UniProtKB.
DR GO; GO:0005975; P:carbohydrate metabolic process; IEA:UniProtKB-KW.
DR GO; GO:0006046; P:N-acetylglucosamine catabolic process; ISS:UniProtKB.
DR GO; GO:0019262; P:N-acetylneuraminate catabolic process; IEA:UniProtKB-UniPathway.
DR GO; GO:0051289; P:protein homotetramerization; ISS:UniProtKB.
DR CDD; cd00854; NagA; 1.
DR Gene3D; 2.30.40.10; -; 1.
DR InterPro; IPR006680; Amidohydro-rel.
DR InterPro; IPR003764; GlcNAc_6-P_deAcase.
DR InterPro; IPR011059; Metal-dep_hydrolase_composite.
DR InterPro; IPR032466; Metal_Hydrolase.
DR PANTHER; PTHR11113:SF14; PTHR11113:SF14; 1.
DR Pfam; PF01979; Amidohydro_1; 1.
DR PIRSF; PIRSF038994; NagA; 1.
DR SUPFAM; SSF51338; SSF51338; 1.
DR SUPFAM; SSF51556; SSF51556; 1.
DR TIGRFAMs; TIGR00221; nagA; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Carbohydrate metabolism; Hydrolase; Metal-binding; Nickel;
KW Reference proteome.
FT CHAIN 1..378
FT /note="N-acetylglucosamine-6-phosphate deacetylase"
FT /id="PRO_0000170918"
FT ACT_SITE 270
FT /note="Proton donor/acceptor"
FT /evidence="ECO:0000250|UniProtKB:P0AF18"
FT BINDING 128
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 139..140
FT /ligand="substrate"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 192
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 213
FT /ligand="a divalent metal cation"
FT /ligand_id="ChEBI:CHEBI:60240"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 216..217
FT /ligand="substrate"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 224
FT /ligand="substrate"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 245..248
FT /ligand="substrate"
FT /evidence="ECO:0000269|Ref.3"
FT BINDING 303..305
FT /ligand="substrate"
FT /evidence="ECO:0000269|Ref.3"
FT CONFLICT 79
FT /note="T -> I (in Ref. 1; BAA22834)"
FT /evidence="ECO:0000305"
FT STRAND 2..10
FT /evidence="ECO:0007829|PDB:3IV8"
FT STRAND 15..24
FT /evidence="ECO:0007829|PDB:3IV8"
FT STRAND 27..33
FT /evidence="ECO:0007829|PDB:3IV8"
FT HELIX 34..36
FT /evidence="ECO:0007829|PDB:3IV8"
FT STRAND 42..53
FT /evidence="ECO:0007829|PDB:3IV8"
FT STRAND 55..60
FT /evidence="ECO:0007829|PDB:3IV8"
FT TURN 68..70
FT /evidence="ECO:0007829|PDB:3IV8"
FT HELIX 74..86
FT /evidence="ECO:0007829|PDB:3IV8"
FT STRAND 89..98
FT /evidence="ECO:0007829|PDB:3IV8"
FT HELIX 101..117
FT /evidence="ECO:0007829|PDB:3IV8"
FT STRAND 119..122
FT /evidence="ECO:0007829|PDB:3IV8"
FT STRAND 125..128
FT /evidence="ECO:0007829|PDB:3IV8"
FT HELIX 134..136
FT /evidence="ECO:0007829|PDB:3IV8"
FT TURN 142..144
FT /evidence="ECO:0007829|PDB:3IV8"
FT HELIX 150..158
FT /evidence="ECO:0007829|PDB:3IV8"
FT TURN 159..161
FT /evidence="ECO:0007829|PDB:3IV8"
FT STRAND 162..168
FT /evidence="ECO:0007829|PDB:3IV8"
FT HELIX 170..172
FT /evidence="ECO:0007829|PDB:3EGJ"
FT HELIX 175..183
FT /evidence="ECO:0007829|PDB:3IV8"
FT STRAND 187..190
FT /evidence="ECO:0007829|PDB:3IV8"
FT HELIX 197..205
FT /evidence="ECO:0007829|PDB:3IV8"
FT STRAND 210..213
FT /evidence="ECO:0007829|PDB:3IV8"
FT STRAND 216..218
FT /evidence="ECO:0007829|PDB:3IV8"
FT HELIX 227..234
FT /evidence="ECO:0007829|PDB:3IV8"
FT STRAND 239..243
FT /evidence="ECO:0007829|PDB:3IV8"
FT STRAND 245..249
FT /evidence="ECO:0007829|PDB:3IV8"
FT HELIX 251..261
FT /evidence="ECO:0007829|PDB:3IV8"
FT HELIX 262..264
FT /evidence="ECO:0007829|PDB:3IV8"
FT STRAND 265..268
FT /evidence="ECO:0007829|PDB:3IV8"
FT TURN 273..276
FT /evidence="ECO:0007829|PDB:3IV8"
FT STRAND 280..286
FT /evidence="ECO:0007829|PDB:3IV8"
FT STRAND 288..292
FT /evidence="ECO:0007829|PDB:3IV8"
FT STRAND 295..297
FT /evidence="ECO:0007829|PDB:3IV8"
FT TURN 299..301
FT /evidence="ECO:0007829|PDB:3EGJ"
FT HELIX 310..319
FT /evidence="ECO:0007829|PDB:3IV8"
FT HELIX 325..332
FT /evidence="ECO:0007829|PDB:3IV8"
FT HELIX 334..340
FT /evidence="ECO:0007829|PDB:3IV8"
FT TURN 343..345
FT /evidence="ECO:0007829|PDB:3IV8"
FT STRAND 346..348
FT /evidence="ECO:0007829|PDB:3IV8"
FT STRAND 357..360
FT /evidence="ECO:0007829|PDB:3IV8"
FT STRAND 366..371
FT /evidence="ECO:0007829|PDB:3IV8"
FT STRAND 374..377
FT /evidence="ECO:0007829|PDB:3IV8"
SQ SEQUENCE 378 AA; 40956 MW; 34906344A3F92A0F CRC64;
MYALTNCKIY TGNDVLVKHA VIINGDKIEA VCPIESLPSE MNVVDLNGAN LSPGFIDLQL
NGCGGVMFND EITAETIDTM HKANLKSGCT SFLPTLITSS DENMRQAIAA AREYQAKYPN
QSLGLHLEGP YLNVMKKGIH SVDFIRPSDD TMIDTICANS DVIAKVTLAP ENNKPEHIEK
LVKAGIVVSI GHTNATYSEA RKSFESGITF ATHLFNAMTP MVGREPGVVG AIYDTPEVYA
GIIADGFHVD YANIRIAHKI KGEKLVLVTD ATAPAGAEMD YFIFVGKKVY YRDGKCVDEN
GTLGGSALTM IEAVQNTVEH VGIALDEALR MATLYPAKAI GVDEKLGRIK KGMIANLTVF
DRDFNVKATV VNGQYEQN
