GATD_STAAN
ID GATD_STAAN Reviewed; 243 AA.
AC A0A0H3JN63;
DT 08-MAY-2019, integrated into UniProtKB/Swiss-Prot.
DT 16-SEP-2015, sequence version 1.
DT 03-AUG-2022, entry version 34.
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:0000255|HAMAP-Rule:MF_02213, ECO:0000269|PubMed:22291598, ECO:0000269|PubMed:30154570};
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:22291598};
GN Name=gatD {ECO:0000255|HAMAP-Rule:MF_02213, ECO:0000303|PubMed:22291598};
GN OrderedLocusNames=SA1707 {ECO:0000312|EMBL:BAB42977.1};
OS Staphylococcus aureus (strain N315).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=158879;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=N315;
RX PubMed=11418146; DOI=10.1016/s0140-6736(00)04403-2;
RA Kuroda M., Ohta T., Uchiyama I., Baba T., Yuzawa H., Kobayashi I., Cui L.,
RA Oguchi A., Aoki K., Nagai Y., Lian J.-Q., Ito T., Kanamori M.,
RA Matsumaru H., Maruyama A., Murakami H., Hosoyama A., Mizutani-Ui Y.,
RA Takahashi N.K., Sawano T., Inoue R., Kaito C., Sekimizu K., Hirakawa H.,
RA Kuhara S., Goto S., Yabuzaki J., Kanehisa M., Yamashita A., Oshima K.,
RA Furuya K., Yoshino C., Shiba T., Hattori M., Ogasawara N., Hayashi H.,
RA Hiramatsu K.;
RT "Whole genome sequencing of meticillin-resistant Staphylococcus aureus.";
RL Lancet 357:1225-1240(2001).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, PATHWAY,
RP SUBUNIT, DISRUPTION PHENOTYPE, ACTIVE SITE, AND MUTAGENESIS OF CYS-94.
RC STRAIN=N315;
RX PubMed=22291598; DOI=10.1371/journal.ppat.1002509;
RA Muench D., Roemer T., Lee S.H., Engeser M., Sahl H.G., Schneider T.;
RT "Identification and in vitro analysis of the GatD/MurT enzyme-complex
RT catalyzing lipid II amidation in Staphylococcus aureus.";
RL PLoS Pathog. 8:E1002509-E1002509(2012).
RN [3] {ECO:0007744|PDB:6GS2, ECO:0007744|PDB:6H5E}
RP X-RAY CRYSTALLOGRAPHY (2.04 ANGSTROMS) IN COMPLEXES WITH MURT, FUNCTION,
RP CATALYTIC ACTIVITY, SUBUNIT, DOMAIN, ACTIVE SITE, AND MUTAGENESIS OF
RP CYS-94.
RX PubMed=30154570; DOI=10.1038/s41598-018-31098-x;
RA Noldeke E.R., Muckenfuss L.M., Niemann V., Muller A., Stork E., Zocher G.,
RA Schneider T., Stehle T.;
RT "Structural basis of cell wall peptidoglycan amidation by the GatD/MurT
RT complex of Staphylococcus aureus.";
RL Sci. Rep. 8:12953-12953(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:22291598, PubMed:30154570). The GatD subunit catalyzes
CC the hydrolysis of glutamine to glutamate and ammonia. The resulting
CC ammonia molecule is channeled to the active site of MurT
CC (PubMed:22291598). {ECO:0000269|PubMed:22291598,
CC ECO:0000269|PubMed:30154570}.
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:0000255|HAMAP-Rule:MF_02213,
CC ECO:0000269|PubMed:22291598, ECO:0000269|PubMed:30154570};
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:22291598};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC pH dependence:
CC Optimum pH is 7.5-7.8 for isoglutaminyl synthase activity.
CC {ECO:0000269|PubMed:22291598};
CC -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
CC {ECO:0000255|HAMAP-Rule:MF_02213, ECO:0000269|PubMed:22291598}.
CC -!- SUBUNIT: Forms a heterodimer with MurT. {ECO:0000255|HAMAP-
CC Rule:MF_02213, ECO:0000269|PubMed:22291598,
CC ECO:0000269|PubMed:30154570}.
CC -!- DOMAIN: The GatD/MurT complex has an open, boomerang-shaped
CC conformation in which GatD is docked onto one end of MurT. Both
CC proteins contribute to the catalytic triad.
CC {ECO:0000269|PubMed:30154570}.
CC -!- DISRUPTION PHENOTYPE: The gatD-murT double mutant displays
CC susceptibility to diverse carbapenem and cephalosporin beta-lactam
CC antibiotics and shows increased susceptibility to plectasin.
CC {ECO:0000269|PubMed:22291598}.
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; BA000018; BAB42977.1; -; Genomic_DNA.
DR RefSeq; WP_000544969.1; NC_002745.2.
DR PDB; 6GS2; X-ray; 2.04 A; A/C=1-243.
DR PDB; 6H5E; X-ray; 2.14 A; A/C=1-243.
DR PDBsum; 6GS2; -.
DR PDBsum; 6H5E; -.
DR AlphaFoldDB; A0A0H3JN63; -.
DR SMR; A0A0H3JN63; -.
DR EnsemblBacteria; BAB42977; BAB42977; BAB42977.
DR KEGG; sau:SA1707; -.
DR HOGENOM; CLU_064047_0_0_9; -.
DR OMA; GTYMHGP; -.
DR BRENDA; 6.3.5.13; 3352.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000000751; Chromosome.
DR GO; GO:0140282; F:carbon-nitrogen ligase activity on lipid II; IDA:CACAO.
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_0000446941"
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:22291598, ECO:0000305|PubMed:30154570"
FT ACT_SITE 189
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02213,
FT ECO:0000255|PROSITE-ProRule:PRU00606"
FT BINDING 128
FT /ligand="substrate"
FT /evidence="ECO:0000250|UniProtKB:A0A0H2WZ38,
FT ECO:0000255|HAMAP-Rule:MF_02213"
FT MUTAGEN 94
FT /note="C->G,S: Cannot use glutamine. Abolishes amidation of
FT lipid II."
FT /evidence="ECO:0000269|PubMed:22291598,
FT ECO:0000269|PubMed:30154570"
FT STRAND 3..9
FT /evidence="ECO:0007829|PDB:6GS2"
FT TURN 10..13
FT /evidence="ECO:0007829|PDB:6H5E"
FT HELIX 17..31
FT /evidence="ECO:0007829|PDB:6GS2"
FT TURN 32..34
FT /evidence="ECO:0007829|PDB:6GS2"
FT STRAND 36..43
FT /evidence="ECO:0007829|PDB:6GS2"
FT STRAND 54..58
FT /evidence="ECO:0007829|PDB:6GS2"
FT HELIX 63..73
FT /evidence="ECO:0007829|PDB:6GS2"
FT HELIX 74..76
FT /evidence="ECO:0007829|PDB:6GS2"
FT HELIX 77..85
FT /evidence="ECO:0007829|PDB:6GS2"
FT STRAND 90..93
FT /evidence="ECO:0007829|PDB:6GS2"
FT HELIX 95..98
FT /evidence="ECO:0007829|PDB:6GS2"
FT STRAND 101..105
FT /evidence="ECO:0007829|PDB:6GS2"
FT STRAND 111..113
FT /evidence="ECO:0007829|PDB:6GS2"
FT STRAND 117..119
FT /evidence="ECO:0007829|PDB:6GS2"
FT STRAND 121..136
FT /evidence="ECO:0007829|PDB:6GS2"
FT STRAND 138..140
FT /evidence="ECO:0007829|PDB:6GS2"
FT STRAND 142..154
FT /evidence="ECO:0007829|PDB:6GS2"
FT STRAND 160..166
FT /evidence="ECO:0007829|PDB:6GS2"
FT STRAND 169..173
FT /evidence="ECO:0007829|PDB:6GS2"
FT STRAND 175..180
FT /evidence="ECO:0007829|PDB:6GS2"
FT STRAND 183..186
FT /evidence="ECO:0007829|PDB:6GS2"
FT TURN 193..195
FT /evidence="ECO:0007829|PDB:6GS2"
FT HELIX 197..211
FT /evidence="ECO:0007829|PDB:6GS2"
FT HELIX 223..243
FT /evidence="ECO:0007829|PDB:6GS2"
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
