DLTA_STRP1
ID DLTA_STRP1 Reviewed; 512 AA.
AC Q99ZA6; Q48Y81;
DT 08-NOV-2002, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2001, sequence version 1.
DT 03-AUG-2022, entry version 132.
DE RecName: Full=D-alanine--D-alanyl carrier protein ligase {ECO:0000255|HAMAP-Rule:MF_00593};
DE Short=DCL {ECO:0000255|HAMAP-Rule:MF_00593};
DE EC=6.2.1.54 {ECO:0000255|HAMAP-Rule:MF_00593};
DE AltName: Full=D-alanine--poly(phosphoribitol) ligase subunit 1 {ECO:0000255|HAMAP-Rule:MF_00593};
DE AltName: Full=D-alanine-activating enzyme {ECO:0000255|HAMAP-Rule:MF_00593};
DE Short=DAE {ECO:0000255|HAMAP-Rule:MF_00593};
GN Name=dltA {ECO:0000255|HAMAP-Rule:MF_00593};
GN OrderedLocusNames=SPy_1312, M5005_Spy1073;
OS Streptococcus pyogenes serotype M1.
OC Bacteria; Firmicutes; Bacilli; Lactobacillales; Streptococcaceae;
OC Streptococcus.
OX NCBI_TaxID=301447;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 700294 / SF370 / Serotype M1;
RX PubMed=11296296; DOI=10.1073/pnas.071559398;
RA Ferretti J.J., McShan W.M., Ajdic D.J., Savic D.J., Savic G., Lyon K.,
RA Primeaux C., Sezate S., Suvorov A.N., Kenton S., Lai H.S., Lin S.P.,
RA Qian Y., Jia H.G., Najar F.Z., Ren Q., Zhu H., Song L., White J., Yuan X.,
RA Clifton S.W., Roe B.A., McLaughlin R.E.;
RT "Complete genome sequence of an M1 strain of Streptococcus pyogenes.";
RL Proc. Natl. Acad. Sci. U.S.A. 98:4658-4663(2001).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-947 / MGAS5005 / Serotype M1;
RX PubMed=16088826; DOI=10.1086/432514;
RA Sumby P., Porcella S.F., Madrigal A.G., Barbian K.D., Virtaneva K.,
RA Ricklefs S.M., Sturdevant D.E., Graham M.R., Vuopio-Varkila J., Hoe N.P.,
RA Musser J.M.;
RT "Evolutionary origin and emergence of a highly successful clone of serotype
RT M1 group A Streptococcus involved multiple horizontal gene transfer
RT events.";
RL J. Infect. Dis. 192:771-782(2005).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (2.60 ANGSTROMS) OF 3-512 IN COMPLEX WITH ATP.
RA Ramagopal U.A., Toro R., Burley S.K., Almo S.C.;
RT "Structure of probable D-alanine-poly(phosphoribitol) ligase subunit-1 from
RT Streptococcus pyogenes with ATP.";
RL Submitted (JAN-2010) to the PDB data bank.
CC -!- FUNCTION: Catalyzes the first step in the D-alanylation of lipoteichoic
CC acid (LTA), the activation of D-alanine and its transfer onto the D-
CC alanyl carrier protein (Dcp) DltC. In an ATP-dependent two-step
CC reaction, forms a high energy D-alanyl-AMP intermediate, followed by
CC transfer of the D-alanyl residue as a thiol ester to the
CC phosphopantheinyl prosthetic group of the Dcp. D-alanylation of LTA
CC plays an important role in modulating the properties of the cell wall
CC in Gram-positive bacteria, influencing the net charge of the cell wall.
CC {ECO:0000255|HAMAP-Rule:MF_00593}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + D-alanine + holo-[D-alanyl-carrier protein] = AMP + D-
CC alanyl-[D-alanyl-carrier protein] + diphosphate;
CC Xref=Rhea:RHEA:55132, Rhea:RHEA-COMP:14102, Rhea:RHEA-COMP:14103,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:33019, ChEBI:CHEBI:57416,
CC ChEBI:CHEBI:64479, ChEBI:CHEBI:138620, ChEBI:CHEBI:456215;
CC EC=6.2.1.54; Evidence={ECO:0000255|HAMAP-Rule:MF_00593};
CC -!- PATHWAY: Cell wall biogenesis; lipoteichoic acid biosynthesis.
CC {ECO:0000255|HAMAP-Rule:MF_00593}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00593}.
CC -!- SIMILARITY: Belongs to the ATP-dependent AMP-binding enzyme family.
CC DltA subfamily. {ECO:0000255|HAMAP-Rule:MF_00593}.
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DR EMBL; AE004092; AAK34156.1; -; Genomic_DNA.
DR EMBL; CP000017; AAZ51691.1; -; Genomic_DNA.
DR RefSeq; NP_269435.1; NC_002737.2.
DR PDB; 3LGX; X-ray; 2.60 A; A/B/C/D=3-512.
DR PDBsum; 3LGX; -.
DR AlphaFoldDB; Q99ZA6; -.
DR SMR; Q99ZA6; -.
DR STRING; 1314.HKU360_01052; -.
DR PaxDb; Q99ZA6; -.
DR EnsemblBacteria; AAK34156; AAK34156; SPy_1312.
DR KEGG; spy:SPy_1312; -.
DR KEGG; spz:M5005_Spy1073; -.
DR PATRIC; fig|160490.10.peg.1149; -.
DR HOGENOM; CLU_000022_2_12_9; -.
DR OMA; VMDLYPC; -.
DR UniPathway; UPA00556; -.
DR EvolutionaryTrace; Q99ZA6; -.
DR PHI-base; PHI:8561; -.
DR Proteomes; UP000000750; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0047473; F:D-alanine [D-alanyl carrier protein] ligase activity; IEA:UniProtKB-UniRule.
DR GO; GO:0070395; P:lipoteichoic acid biosynthetic process; IEA:UniProtKB-UniRule.
DR CDD; cd05945; DltA; 1.
DR Gene3D; 3.30.300.30; -; 1.
DR Gene3D; 3.40.50.12780; -; 1.
DR HAMAP; MF_00593; DltA; 1.
DR InterPro; IPR010071; AA_adenyl_domain.
DR InterPro; IPR025110; AMP-bd_C.
DR InterPro; IPR045851; AMP-bd_C_sf.
DR InterPro; IPR020845; AMP-binding_CS.
DR InterPro; IPR000873; AMP-dep_Synth/Lig.
DR InterPro; IPR042099; ANL_N_sf.
DR InterPro; IPR010072; DltA.
DR InterPro; IPR044507; DltA-like.
DR Pfam; PF00501; AMP-binding; 1.
DR Pfam; PF13193; AMP-binding_C; 1.
DR TIGRFAMs; TIGR01733; AA-adenyl-dom; 1.
DR TIGRFAMs; TIGR01734; D-ala-DACP-lig; 1.
DR PROSITE; PS00455; AMP_BINDING; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Cytoplasm; Ligase; Nucleotide-binding;
KW Reference proteome.
FT CHAIN 1..512
FT /note="D-alanine--D-alanyl carrier protein ligase"
FT /id="PRO_0000213165"
FT BINDING 152..153
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00593,
FT ECO:0000269|Ref.3, ECO:0007744|PDB:3LGX"
FT BINDING 199
FT /ligand="D-alanine"
FT /ligand_id="ChEBI:CHEBI:57416"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00593"
FT BINDING 294..299
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00593,
FT ECO:0000269|Ref.3, ECO:0007744|PDB:3LGX"
FT BINDING 303
FT /ligand="D-alanine"
FT /ligand_id="ChEBI:CHEBI:57416"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00593"
FT BINDING 385
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00593,
FT ECO:0000269|Ref.3, ECO:0007744|PDB:3LGX"
FT BINDING 397..400
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00593,
FT ECO:0000269|Ref.3, ECO:0007744|PDB:3LGX"
FT BINDING 499
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00593,
FT ECO:0000269|Ref.3, ECO:0007744|PDB:3LGX"
FT BINDING 499
FT /ligand="D-alanine"
FT /ligand_id="ChEBI:CHEBI:57416"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00593"
FT CONFLICT 65
FT /note="D -> N (in Ref. 2; AAZ51691)"
FT /evidence="ECO:0000305"
FT HELIX 5..15
FT /evidence="ECO:0007829|PDB:3LGX"
FT TURN 16..18
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 19..24
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 27..30
FT /evidence="ECO:0007829|PDB:3LGX"
FT HELIX 31..47
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 56..60
FT /evidence="ECO:0007829|PDB:3LGX"
FT HELIX 64..75
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 80..84
FT /evidence="ECO:0007829|PDB:3LGX"
FT HELIX 89..99
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 102..108
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 115..121
FT /evidence="ECO:0007829|PDB:3LGX"
FT HELIX 122..131
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 145..152
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 160..165
FT /evidence="ECO:0007829|PDB:3LGX"
FT HELIX 166..178
FT /evidence="ECO:0007829|PDB:3LGX"
FT TURN 180..182
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 189..191
FT /evidence="ECO:0007829|PDB:3LGX"
FT HELIX 199..201
FT /evidence="ECO:0007829|PDB:3LGX"
FT HELIX 202..211
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 214..216
FT /evidence="ECO:0007829|PDB:3LGX"
FT HELIX 220..222
FT /evidence="ECO:0007829|PDB:3LGX"
FT HELIX 226..234
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 239..243
FT /evidence="ECO:0007829|PDB:3LGX"
FT HELIX 245..251
FT /evidence="ECO:0007829|PDB:3LGX"
FT TURN 259..261
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 267..270
FT /evidence="ECO:0007829|PDB:3LGX"
FT HELIX 277..286
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 291..296
FT /evidence="ECO:0007829|PDB:3LGX"
FT HELIX 299..301
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 305..310
FT /evidence="ECO:0007829|PDB:3LGX"
FT HELIX 312..317
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 324..326
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 332..335
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 348..354
FT /evidence="ECO:0007829|PDB:3LGX"
FT HELIX 365..371
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 372..375
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 378..389
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 395..400
FT /evidence="ECO:0007829|PDB:3LGX"
FT HELIX 401..403
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 407..409
FT /evidence="ECO:0007829|PDB:3LGX"
FT HELIX 414..422
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 427..436
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 442..451
FT /evidence="ECO:0007829|PDB:3LGX"
FT HELIX 462..472
FT /evidence="ECO:0007829|PDB:3LGX"
FT TURN 474..476
FT /evidence="ECO:0007829|PDB:3LGX"
FT TURN 479..481
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 484..488
FT /evidence="ECO:0007829|PDB:3LGX"
FT STRAND 498..500
FT /evidence="ECO:0007829|PDB:3LGX"
FT HELIX 502..507
FT /evidence="ECO:0007829|PDB:3LGX"
SQ SEQUENCE 512 AA; 56987 MW; 330928DC894A6146 CRC64;
MIKDMIDSIE QFAQTQADFP VYDCLGERRT YGQLKRDSDS IAAFIDSLAL LAKSPVLVFG
AQTYDMLATF VALTKSGHAY IPVDVHSAPE RILAIIEIAK PSLIIAIEEF PLTIEGISLV
SLSEIESAKL AEMPYERTHS VKGDDNYYII FTSGTTGQPK GVQISHDNLL SFTNWMIEDA
AFDVPKQPQM LAQPPYSFDL SVMYWAPTLA LGGTLFALPK ELVADFKQLF TTIAQLPVGI
WTSTPSFADM AMLSDDFCQA KMPALTHFYF DGEELTVSTA RKLFERFPSA KIINAYGPTE
ATVALSAIEI TREMVDNYTR LPIGYPKPDS PTYIIDEDGK ELSSGEQGEI IVTGPAVSKG
YLNNPEKTAE AFFTFKGQPA YHTGDIGSLT EDNILLYGGR LDFQIKYAGY RIELEDVSQQ
LNQSPMVASA VAVPRYNKEH KVQNLLAYIV VKDGVKERFD RELELTKAIK ASVKDHMMSY
MMPSKFLYRD SLPLTPNGKI DIKTLINEVN NR
