GATD_STAAC
ID GATD_STAAC Reviewed; 243 AA.
AC A0A0H2WZ38;
DT 08-MAY-2019, integrated into UniProtKB/Swiss-Prot.
DT 16-SEP-2015, sequence version 1.
DT 03-AUG-2022, entry version 35.
DE RecName: Full=Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit GatD {ECO:0000255|HAMAP-Rule:MF_02213, ECO:0000305};
DE EC=6.3.5.13 {ECO:0000250|UniProtKB:A0A0H3JN63, ECO:0000255|HAMAP-Rule:MF_02213};
DE AltName: Full=Lipid II isoglutaminyl synthase glutaminase subunit {ECO:0000255|HAMAP-Rule:MF_02213, ECO:0000305};
DE EC=3.5.1.2 {ECO:0000255|HAMAP-Rule:MF_02213, ECO:0000269|PubMed:29593310};
GN Name=gatD {ECO:0000255|HAMAP-Rule:MF_02213, ECO:0000303|PubMed:22303291};
GN OrderedLocusNames=SACOL1950 {ECO:0000312|EMBL:AAW38391.1};
OS Staphylococcus aureus (strain COL).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=93062;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=COL;
RX PubMed=15774886; DOI=10.1128/jb.187.7.2426-2438.2005;
RA Gill S.R., Fouts D.E., Archer G.L., Mongodin E.F., DeBoy R.T., Ravel J.,
RA Paulsen I.T., Kolonay J.F., Brinkac L.M., Beanan M.J., Dodson R.J.,
RA Daugherty S.C., Madupu R., Angiuoli S.V., Durkin A.S., Haft D.H.,
RA Vamathevan J.J., Khouri H., Utterback T.R., Lee C., Dimitrov G., Jiang L.,
RA Qin H., Weidman J., Tran K., Kang K.H., Hance I.R., Nelson K.E.,
RA Fraser C.M.;
RT "Insights on evolution of virulence and resistance from the complete genome
RT analysis of an early methicillin-resistant Staphylococcus aureus strain and
RT a biofilm-producing methicillin-resistant Staphylococcus epidermidis
RT strain.";
RL J. Bacteriol. 187:2426-2438(2005).
RN [2]
RP FUNCTION, PATHWAY, AND DISRUPTION PHENOTYPE.
RC STRAIN=COL;
RX PubMed=22303291; DOI=10.1371/journal.ppat.1002508;
RA Figueiredo T.A., Sobral R.G., Ludovice A.M., Almeida J.M., Bui N.K.,
RA Vollmer W., de Lencastre H., Tomasz A.;
RT "Identification of genetic determinants and enzymes involved with the
RT amidation of glutamic acid residues in the peptidoglycan of Staphylococcus
RT aureus.";
RL PLoS Pathog. 8:E1002508-E1002508(2012).
RN [3]
RP CRYSTALLIZATION.
RC STRAIN=COL;
RX PubMed=24817726; DOI=10.1107/s2053230x14007298;
RA Vieira D., Figueiredo T.A., Verma A., Sobral R.G., Ludovice A.M.,
RA de Lencastre H., Trincao J.;
RT "Purification, crystallization and preliminary X-ray diffraction analysis
RT of GatD, a glutamine amidotransferase-like protein from Staphylococcus
RT aureus peptidoglycan.";
RL Acta Crystallogr. F Struct. Biol. Commun. 70:632-635(2014).
RN [4] {ECO:0007744|PDB:5N9M}
RP X-RAY CRYSTALLOGRAPHY (1.85 ANGSTROMS) IN COMPLEX WITH GLUTAMINE, FUNCTION,
RP CATALYTIC ACTIVITY, SUBUNIT, MUTAGENESIS OF CYS-94; ARG-128 AND HIS-189,
RP AND ACTIVE SITE.
RC STRAIN=COL;
RX PubMed=29593310; DOI=10.1038/s41598-018-22986-3;
RA Leisico F., Vieira D.V., Figueiredo T.A., Silva M., Cabrita E.J.,
RA Sobral R.G., Ludovice A.M., Trincao J., Romao M.J., de Lencastre H.,
RA Santos-Silva T.;
RT "First insights of peptidoglycan amidation in Gram-positive bacteria - the
RT high-resolution crystal structure of Staphylococcus aureus glutamine
RT amidotransferase GatD.";
RL Sci. Rep. 8:5313-5313(2018).
CC -!- FUNCTION: The lipid II isoglutaminyl synthase complex catalyzes the
CC formation of alpha-D-isoglutamine in the cell wall lipid II stem
CC peptide (PubMed:22303291). The GatD subunit catalyzes the hydrolysis of
CC glutamine to glutamate and ammonia. The resulting ammonia molecule is
CC channeled to the active site of MurT (PubMed:29593310).
CC {ECO:0000269|PubMed:22303291, ECO:0000269|PubMed:29593310}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + beta-D-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-gamma-D-Glu-L-Lys-
CC D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl diphosphate + H2O + L-
CC glutamine = ADP + beta-D-GlcNAc-(1->4)-Mur2Ac(oyl-L-Ala-D-
CC isoglutaminyl-L-Lys-D-Ala-D-Ala)-di-trans,octa-cis-undecaprenyl
CC diphosphate + H(+) + L-glutamate + phosphate; Xref=Rhea:RHEA:57928,
CC ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:29985,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:58359,
CC ChEBI:CHEBI:60033, ChEBI:CHEBI:62233, ChEBI:CHEBI:456216;
CC EC=6.3.5.13; Evidence={ECO:0000250|UniProtKB:A0A0H3JN63,
CC ECO:0000255|HAMAP-Rule:MF_02213};
CC -!- CATALYTIC ACTIVITY:
CC Reaction=H2O + L-glutamine = L-glutamate + NH4(+);
CC Xref=Rhea:RHEA:15889, ChEBI:CHEBI:15377, ChEBI:CHEBI:28938,
CC ChEBI:CHEBI:29985, ChEBI:CHEBI:58359; EC=3.5.1.2;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_02213,
CC ECO:0000269|PubMed:29593310};
CC -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
CC {ECO:0000255|HAMAP-Rule:MF_02213, ECO:0000269|PubMed:22303291}.
CC -!- SUBUNIT: Forms a heterodimer with MurT. {ECO:0000255|HAMAP-
CC Rule:MF_02213, ECO:0000269|PubMed:29593310}.
CC -!- DISRUPTION PHENOTYPE: The gatD-murT double mutant shows abnormal
CC peptidoglycan composition, with decreased amidation of the glutamate
CC residue. The mutant has a normal morphology but growth rate is greatly
CC reduced. Mutant shows reduced antibiotic resistance and increased
CC sensitivity to lysozyme. {ECO:0000269|PubMed:22303291}.
CC -!- SIMILARITY: Belongs to the CobB/CobQ family. GatD subfamily.
CC {ECO:0000255|HAMAP-Rule:MF_02213, ECO:0000305}.
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DR EMBL; CP000046; AAW38391.1; -; Genomic_DNA.
DR RefSeq; WP_000544969.1; NC_002951.2.
DR PDB; 5N9M; X-ray; 1.85 A; A/B=1-243.
DR PDBsum; 5N9M; -.
DR AlphaFoldDB; A0A0H2WZ38; -.
DR SMR; A0A0H2WZ38; -.
DR EnsemblBacteria; AAW38391; AAW38391; SACOL1950.
DR KEGG; sac:SACOL1950; -.
DR HOGENOM; CLU_064047_0_0_9; -.
DR OMA; GTYMHGP; -.
DR BRENDA; 6.3.5.13; 3352.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000000530; Chromosome.
DR GO; GO:0140282; F:carbon-nitrogen ligase activity on lipid II; IEA:UniProtKB-UniRule.
DR GO; GO:0004359; F:glutaminase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0009236; P:cobalamin biosynthetic process; IEA:InterPro.
DR GO; GO:0006541; P:glutamine metabolic process; IEA:UniProtKB-KW.
DR GO; GO:0009252; P:peptidoglycan biosynthetic process; IEA:UniProtKB-UniRule.
DR GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW.
DR CDD; cd01750; GATase1_CobQ; 1.
DR Gene3D; 3.40.50.880; -; 1.
DR HAMAP; MF_02213; Lipid_II_synth_GatD; 1.
DR InterPro; IPR029062; Class_I_gatase-like.
DR InterPro; IPR033949; CobQ_GATase1.
DR InterPro; IPR011698; GATase_3.
DR InterPro; IPR043702; Lipid_II_synth_GatD.
DR Pfam; PF07685; GATase_3; 1.
DR SUPFAM; SSF52317; SSF52317; 1.
DR PROSITE; PS51274; GATASE_COBBQ; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Cell shape; Cell wall biogenesis/degradation;
KW Glutamine amidotransferase; Hydrolase; Ligase; Peptidoglycan synthesis.
FT CHAIN 1..243
FT /note="Lipid II isoglutaminyl synthase (glutamine-
FT hydrolyzing) subunit GatD"
FT /id="PRO_0000446940"
FT DOMAIN 6..197
FT /note="GATase cobBQ-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00606"
FT ACT_SITE 94
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02213,
FT ECO:0000255|PROSITE-ProRule:PRU00606,
FT ECO:0000305|PubMed:29593310"
FT ACT_SITE 189
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02213,
FT ECO:0000255|PROSITE-ProRule:PRU00606,
FT ECO:0000305|PubMed:29593310"
FT BINDING 128
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02213,
FT ECO:0000269|PubMed:29593310"
FT MUTAGEN 94
FT /note="C->A: Abolishes glutaminase activity."
FT /evidence="ECO:0000269|PubMed:29593310"
FT MUTAGEN 128
FT /note="R->A: Abolishes glutaminase activity."
FT /evidence="ECO:0000269|PubMed:29593310"
FT MUTAGEN 189
FT /note="H->A: Abolishes glutaminase activity."
FT /evidence="ECO:0000269|PubMed:29593310"
FT STRAND 2..9
FT /evidence="ECO:0007829|PDB:5N9M"
FT TURN 11..13
FT /evidence="ECO:0007829|PDB:5N9M"
FT HELIX 20..31
FT /evidence="ECO:0007829|PDB:5N9M"
FT TURN 32..34
FT /evidence="ECO:0007829|PDB:5N9M"
FT STRAND 35..43
FT /evidence="ECO:0007829|PDB:5N9M"
FT STRAND 54..58
FT /evidence="ECO:0007829|PDB:5N9M"
FT HELIX 63..73
FT /evidence="ECO:0007829|PDB:5N9M"
FT HELIX 74..76
FT /evidence="ECO:0007829|PDB:5N9M"
FT HELIX 77..86
FT /evidence="ECO:0007829|PDB:5N9M"
FT STRAND 90..93
FT /evidence="ECO:0007829|PDB:5N9M"
FT HELIX 95..98
FT /evidence="ECO:0007829|PDB:5N9M"
FT STRAND 101..105
FT /evidence="ECO:0007829|PDB:5N9M"
FT STRAND 111..113
FT /evidence="ECO:0007829|PDB:5N9M"
FT STRAND 117..119
FT /evidence="ECO:0007829|PDB:5N9M"
FT STRAND 121..137
FT /evidence="ECO:0007829|PDB:5N9M"
FT TURN 138..140
FT /evidence="ECO:0007829|PDB:5N9M"
FT STRAND 141..154
FT /evidence="ECO:0007829|PDB:5N9M"
FT STRAND 160..166
FT /evidence="ECO:0007829|PDB:5N9M"
FT STRAND 169..173
FT /evidence="ECO:0007829|PDB:5N9M"
FT STRAND 175..180
FT /evidence="ECO:0007829|PDB:5N9M"
FT STRAND 183..187
FT /evidence="ECO:0007829|PDB:5N9M"
FT TURN 190..192
FT /evidence="ECO:0007829|PDB:5N9M"
FT HELIX 193..195
FT /evidence="ECO:0007829|PDB:5N9M"
FT HELIX 197..211
FT /evidence="ECO:0007829|PDB:5N9M"
FT HELIX 223..238
FT /evidence="ECO:0007829|PDB:5N9M"
SQ SEQUENCE 243 AA; 27430 MW; 897C70CD1456A32B CRC64;
MHELTIYHFM SDKLNLYSDI GNIIALRQRA KKRNIKVNVV EINETEGITF DECDIFFIGG
GSDREQALAT KELSKIKTPL KEAIEDGMPG LTICGGYQFL GKKYITPDGT ELEGLGILDF
YTESKTNRLT GDIVIESDTF GTIVGFENHG GRTYHDFGTL GHVTFGYGNN DEDKKEGIHY
KNLLGTYLHG PILPKNYEIT DYLLEKACER KGIPFEPKEI DNEAEIQAKQ VLIDRANRQK
KSR
