GATD_STRR6
ID GATD_STRR6 Reviewed; 260 AA.
AC Q8DNZ8;
DT 08-MAY-2019, integrated into UniProtKB/Swiss-Prot.
DT 01-MAR-2003, sequence version 1.
DT 03-AUG-2022, entry version 103.
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:24044435, ECO:0000269|PubMed:30093673};
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:30093673};
GN Name=gatD {ECO:0000255|HAMAP-Rule:MF_02213, ECO:0000303|PubMed:24044435};
GN OrderedLocusNames=spr1444 {ECO:0000312|EMBL:AAL00248.1};
OS Streptococcus pneumoniae (strain ATCC BAA-255 / R6).
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
OC Streptococcus.
OX NCBI_TaxID=171101;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-255 / R6;
RX PubMed=11544234; DOI=10.1128/jb.183.19.5709-5717.2001;
RA Hoskins J., Alborn W.E. Jr., Arnold J., Blaszczak L.C., Burgett S.,
RA DeHoff B.S., Estrem S.T., Fritz L., Fu D.-J., Fuller W., Geringer C.,
RA Gilmour R., Glass J.S., Khoja H., Kraft A.R., Lagace R.E., LeBlanc D.J.,
RA Lee L.N., Lefkowitz E.J., Lu J., Matsushima P., McAhren S.M., McHenney M.,
RA McLeaster K., Mundy C.W., Nicas T.I., Norris F.H., O'Gara M., Peery R.B.,
RA Robertson G.T., Rockey P., Sun P.-M., Winkler M.E., Yang Y.,
RA Young-Bellido M., Zhao G., Zook C.A., Baltz R.H., Jaskunas S.R.,
RA Rosteck P.R. Jr., Skatrud P.L., Glass J.I.;
RT "Genome of the bacterium Streptococcus pneumoniae strain R6.";
RL J. Bacteriol. 183:5709-5717(2001).
RN [2]
RP FUNCTION, CATALYTIC ACTIVITY, AND PATHWAY.
RC STRAIN=ATCC BAA-255 / R6;
RX PubMed=24044435; DOI=10.1021/cb400575t;
RA Zapun A., Philippe J., Abrahams K.A., Signor L., Roper D.I., Breukink E.,
RA Vernet T.;
RT "In vitro reconstitution of peptidoglycan assembly from the Gram-positive
RT pathogen Streptococcus pneumoniae.";
RL ACS Chem. Biol. 8:2688-2696(2013).
RN [3] {ECO:0007744|PDB:6FQB}
RP X-RAY CRYSTALLOGRAPHY (3.00 ANGSTROMS) IN COMPLEX WITH MURT AND GLUTAMINE,
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, SUBUNIT,
RP DISRUPTION PHENOTYPE, AND ACTIVE SITE.
RX PubMed=30093673; DOI=10.1038/s41467-018-05602-w;
RA Morlot C., Straume D., Peters K., Hegnar O.A., Simon N., Villard A.M.,
RA Contreras-Martel C., Leisico F., Breukink E., Gravier-Pelletier C.,
RA Le Corre L., Vollmer W., Pietrancosta N., Havarstein L.S., Zapun A.;
RT "Structure of the essential peptidoglycan amidotransferase MurT/GatD
RT complex from Streptococcus pneumoniae.";
RL Nat. Commun. 9:3180-3180(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:24044435, PubMed:30093673). 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:30093673). {ECO:0000269|PubMed:24044435,
CC ECO:0000269|PubMed:30093673}.
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:24044435, ECO:0000269|PubMed:30093673};
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:30093673};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=78 uM for L-glutamine {ECO:0000269|PubMed:30093673};
CC -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
CC {ECO:0000255|HAMAP-Rule:MF_02213, ECO:0000269|PubMed:24044435}.
CC -!- SUBUNIT: Forms a heterodimer with MurT. {ECO:0000255|HAMAP-
CC Rule:MF_02213, ECO:0000269|PubMed:30093673}.
CC -!- DISRUPTION PHENOTYPE: Severe depletion of GatD/MurT produces a high
CC proportion of aberrant cells, elongated or bulging.
CC {ECO:0000269|PubMed:30093673}.
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; AE007317; AAL00248.1; -; Genomic_DNA.
DR PIR; C95185; C95185.
DR PIR; C98052; C98052.
DR RefSeq; NP_359037.1; NC_003098.1.
DR RefSeq; WP_000263194.1; NC_003098.1.
DR PDB; 6FQB; X-ray; 3.00 A; E/F/G/H=1-260.
DR PDBsum; 6FQB; -.
DR AlphaFoldDB; Q8DNZ8; -.
DR SMR; Q8DNZ8; -.
DR STRING; 171101.spr1444; -.
DR EnsemblBacteria; AAL00248; AAL00248; spr1444.
DR GeneID; 60234380; -.
DR KEGG; spr:spr1444; -.
DR PATRIC; fig|171101.6.peg.1560; -.
DR eggNOG; COG3442; Bacteria.
DR HOGENOM; CLU_064047_1_0_9; -.
DR OMA; GTYMHGP; -.
DR BRENDA; 6.3.5.13; 1960.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000000586; 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;
KW Reference proteome.
FT CHAIN 1..260
FT /note="Lipid II isoglutaminyl synthase (glutamine-
FT hydrolyzing) subunit GatD"
FT /id="PRO_0000446942"
FT DOMAIN 16..214
FT /note="GATase cobBQ-type"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00606"
FT ACT_SITE 107
FT /note="Nucleophile"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02213,
FT ECO:0000255|PROSITE-ProRule:PRU00606,
FT ECO:0000305|PubMed:30093673"
FT ACT_SITE 206
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02213,
FT ECO:0000255|PROSITE-ProRule:PRU00606,
FT ECO:0000305|PubMed:30093673"
FT BINDING 142
FT /ligand="substrate"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_02213,
FT ECO:0000269|PubMed:30093673"
FT STRAND 3..7
FT /evidence="ECO:0007829|PDB:6FQB"
FT STRAND 14..22
FT /evidence="ECO:0007829|PDB:6FQB"
FT TURN 23..26
FT /evidence="ECO:0007829|PDB:6FQB"
FT TURN 30..33
FT /evidence="ECO:0007829|PDB:6FQB"
FT HELIX 34..45
FT /evidence="ECO:0007829|PDB:6FQB"
FT STRAND 48..55
FT /evidence="ECO:0007829|PDB:6FQB"
FT TURN 63..65
FT /evidence="ECO:0007829|PDB:6FQB"
FT STRAND 67..71
FT /evidence="ECO:0007829|PDB:6FQB"
FT HELIX 76..85
FT /evidence="ECO:0007829|PDB:6FQB"
FT HELIX 86..89
FT /evidence="ECO:0007829|PDB:6FQB"
FT HELIX 90..98
FT /evidence="ECO:0007829|PDB:6FQB"
FT STRAND 102..106
FT /evidence="ECO:0007829|PDB:6FQB"
FT HELIX 108..113
FT /evidence="ECO:0007829|PDB:6FQB"
FT STRAND 114..118
FT /evidence="ECO:0007829|PDB:6FQB"
FT STRAND 124..126
FT /evidence="ECO:0007829|PDB:6FQB"
FT STRAND 130..132
FT /evidence="ECO:0007829|PDB:6FQB"
FT STRAND 134..136
FT /evidence="ECO:0007829|PDB:6FQB"
FT STRAND 143..151
FT /evidence="ECO:0007829|PDB:6FQB"
FT TURN 152..155
FT /evidence="ECO:0007829|PDB:6FQB"
FT STRAND 156..165
FT /evidence="ECO:0007829|PDB:6FQB"
FT STRAND 167..169
FT /evidence="ECO:0007829|PDB:6FQB"
FT STRAND 177..183
FT /evidence="ECO:0007829|PDB:6FQB"
FT STRAND 191..203
FT /evidence="ECO:0007829|PDB:6FQB"
FT HELIX 209..212
FT /evidence="ECO:0007829|PDB:6FQB"
FT HELIX 214..229
FT /evidence="ECO:0007829|PDB:6FQB"
FT HELIX 238..241
FT /evidence="ECO:0007829|PDB:6FQB"
FT HELIX 243..245
FT /evidence="ECO:0007829|PDB:6FQB"
SQ SEQUENCE 260 AA; 29193 MW; F995B9DF214BD3A8 CRC64;
MVYTSLSSKD GNYPYQLNIA HLYGNLMNTY GDNGNILMLK YVAEKLGAHV TVDIVSLHDD
FDENHYDIAF FGGGQDFEQS IIADDLPAKK ESIDNYIQND GVVLAICGGF QLLGQYYVEA
SGKRIEGLGV MGHYTLNQTN NRFIGDIKIH NEDFDETYYG FENHQGRTFL SDDQKPLGQV
VYGNGNNEEK VGEGVHYKNV FGSYFHGPIL SRNANLAYRL VTTALKKKYG QDIQLPAYED
ILSQEIAEEY SDVKSKADFS
