DLTA_BACCR
ID DLTA_BACCR Reviewed; 504 AA.
AC Q81G39;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 01-JUN-2003, sequence version 1.
DT 03-AUG-2022, entry version 106.
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, ECO:0000269|PubMed:18847223};
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}; OrderedLocusNames=BC_1372;
OS Bacillus cereus (strain ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC
OS 15305 / NCIMB 9373 / NCTC 2599 / NRRL B-3711).
OC Bacteria; Firmicutes; Bacilli; Bacillales; Bacillaceae; Bacillus;
OC Bacillus cereus group.
OX NCBI_TaxID=226900;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 14579 / DSM 31 / CCUG 7414 / JCM 2152 / NBRC 15305 / NCIMB 9373
RC / NCTC 2599 / NRRL B-3711;
RX PubMed=12721630; DOI=10.1038/nature01582;
RA Ivanova N., Sorokin A., Anderson I., Galleron N., Candelon B., Kapatral V.,
RA Bhattacharyya A., Reznik G., Mikhailova N., Lapidus A., Chu L., Mazur M.,
RA Goltsman E., Larsen N., D'Souza M., Walunas T., Grechkin Y., Pusch G.,
RA Haselkorn R., Fonstein M., Ehrlich S.D., Overbeek R., Kyrpides N.C.;
RT "Genome sequence of Bacillus cereus and comparative analysis with Bacillus
RT anthracis.";
RL Nature 423:87-91(2003).
RN [2]
RP X-RAY CRYSTALLOGRAPHY (2.00 ANGSTROMS) IN COMPLEX WITH D-ALANYL-AMP,
RP FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, AND
RP MUTAGENESIS OF CYS-269.
RX PubMed=18847223; DOI=10.1021/bi801363b;
RA Du L., He Y., Luo Y.;
RT "Crystal structure and enantiomer selection by D-alanyl carrier protein
RT ligase DltA from Bacillus cereus.";
RL Biochemistry 47:11473-11480(2008).
RN [3]
RP X-RAY CRYSTALLOGRAPHY (1.90 ANGSTROMS) IN COMPLEX WITH ATP.
RX PubMed=19324056; DOI=10.1016/j.jmb.2009.03.040;
RA Osman K.T., Du L., He Y., Luo Y.;
RT "Crystal structure of Bacillus cereus D-alanyl carrier protein ligase
RT (DltA) in complex with ATP.";
RL J. Mol. Biol. 388:345-355(2009).
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, ECO:0000269|PubMed:18847223}.
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 ECO:0000269|PubMed:18847223};
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=1.1 mM for D-alanine {ECO:0000269|PubMed:18847223};
CC KM=14.4 mM for L-alanine {ECO:0000269|PubMed:18847223};
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; AE016877; AAP08354.1; -; Genomic_DNA.
DR RefSeq; NP_831153.1; NC_004722.1.
DR RefSeq; WP_000770505.1; NZ_CP034551.1.
DR PDB; 3DHV; X-ray; 2.00 A; A=1-504.
DR PDB; 3FCC; X-ray; 2.32 A; A=1-504.
DR PDB; 3FCE; X-ray; 1.90 A; A=1-504.
DR PDB; 4PZP; X-ray; 1.90 A; A=2-504.
DR PDBsum; 3DHV; -.
DR PDBsum; 3FCC; -.
DR PDBsum; 3FCE; -.
DR PDBsum; 4PZP; -.
DR AlphaFoldDB; Q81G39; -.
DR SMR; Q81G39; -.
DR STRING; 226900.BC_1372; -.
DR EnsemblBacteria; AAP08354; AAP08354; BC_1372.
DR KEGG; bce:BC1372; -.
DR PATRIC; fig|226900.8.peg.1346; -.
DR HOGENOM; CLU_000022_2_12_9; -.
DR OMA; VMDLYPC; -.
DR BRENDA; 6.2.1.54; 648.
DR UniPathway; UPA00556; -.
DR EvolutionaryTrace; Q81G39; -.
DR Proteomes; UP000001417; 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 DisProt; DP02664; -.
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..504
FT /note="D-alanine--D-alanyl carrier protein ligase"
FT /id="PRO_1000025526"
FT BINDING 152..153
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00593,
FT ECO:0000269|PubMed:19324056, ECO:0007744|PDB:3FCC,
FT ECO:0007744|PDB:3FCE"
FT BINDING 197
FT /ligand="D-alanine"
FT /ligand_id="ChEBI:CHEBI:57416"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00593,
FT ECO:0000269|PubMed:18847223, ECO:0007744|PDB:3DHV"
FT BINDING 292..297
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00593,
FT ECO:0000269|PubMed:18847223, ECO:0000269|PubMed:19324056,
FT ECO:0007744|PDB:3FCC, ECO:0007744|PDB:3FCE"
FT BINDING 301
FT /ligand="D-alanine"
FT /ligand_id="ChEBI:CHEBI:57416"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00593,
FT ECO:0000269|PubMed:18847223, ECO:0007744|PDB:3DHV"
FT BINDING 383
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00593,
FT ECO:0000269|PubMed:18847223, ECO:0000269|PubMed:19324056,
FT ECO:0007744|PDB:3FCC, ECO:0007744|PDB:3FCE"
FT BINDING 394..397
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00593,
FT ECO:0000269|PubMed:18847223, ECO:0000269|PubMed:19324056,
FT ECO:0007744|PDB:3FCC, ECO:0007744|PDB:3FCE"
FT BINDING 492
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00593,
FT ECO:0000269|PubMed:18847223, ECO:0000269|PubMed:19324056,
FT ECO:0007744|PDB:3FCC, ECO:0007744|PDB:3FCE"
FT BINDING 492
FT /ligand="D-alanine"
FT /ligand_id="ChEBI:CHEBI:57416"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00593,
FT ECO:0000269|PubMed:18847223, ECO:0007744|PDB:3DHV"
FT MUTAGEN 269
FT /note="C->A: Relaxes D-alanine preference, allowing the
FT enzyme to use L-alanine at the same efficiency."
FT /evidence="ECO:0000269|PubMed:18847223"
FT HELIX 3..13
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 17..22
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 25..28
FT /evidence="ECO:0007829|PDB:3FCE"
FT HELIX 29..46
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 54..60
FT /evidence="ECO:0007829|PDB:3FCE"
FT HELIX 62..73
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 78..82
FT /evidence="ECO:0007829|PDB:3FCE"
FT HELIX 87..96
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 101..106
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 114..119
FT /evidence="ECO:0007829|PDB:3FCE"
FT HELIX 121..129
FT /evidence="ECO:0007829|PDB:3FCE"
FT TURN 130..132
FT /evidence="ECO:0007829|PDB:3FCE"
FT HELIX 137..139
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 145..152
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 160..165
FT /evidence="ECO:0007829|PDB:3FCE"
FT HELIX 166..179
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 187..190
FT /evidence="ECO:0007829|PDB:3FCE"
FT HELIX 197..199
FT /evidence="ECO:0007829|PDB:3FCE"
FT HELIX 200..208
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 212..215
FT /evidence="ECO:0007829|PDB:3FCE"
FT HELIX 218..222
FT /evidence="ECO:0007829|PDB:3FCE"
FT HELIX 224..234
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 238..241
FT /evidence="ECO:0007829|PDB:3FCE"
FT HELIX 243..249
FT /evidence="ECO:0007829|PDB:3FCE"
FT TURN 257..259
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 265..268
FT /evidence="ECO:0007829|PDB:3FCE"
FT HELIX 275..284
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 289..294
FT /evidence="ECO:0007829|PDB:3FCE"
FT HELIX 297..299
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 303..307
FT /evidence="ECO:0007829|PDB:3FCE"
FT HELIX 310..315
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 322..324
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 329..333
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 335..337
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 346..352
FT /evidence="ECO:0007829|PDB:3FCE"
FT HELIX 363..369
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 370..373
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 376..388
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 391..397
FT /evidence="ECO:0007829|PDB:3FCE"
FT HELIX 398..400
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 402..404
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 407..409
FT /evidence="ECO:0007829|PDB:3FCE"
FT HELIX 411..420
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 424..434
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 437..447
FT /evidence="ECO:0007829|PDB:3FCE"
FT HELIX 455..467
FT /evidence="ECO:0007829|PDB:3FCE"
FT HELIX 472..474
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 477..481
FT /evidence="ECO:0007829|PDB:3FCE"
FT STRAND 491..493
FT /evidence="ECO:0007829|PDB:3FCE"
FT HELIX 495..503
FT /evidence="ECO:0007829|PDB:3FCE"
SQ SEQUENCE 504 AA; 56494 MW; 96BE762A25E315D2 CRC64;
MKLLEQIEKW AAETPDQTAF VWRDAKITYK QLKEDSDALA HWISSEYPDD RSPIMVYGHM
QPEMIINFLG CVKAGHAYIP VDLSIPADRV QRIAENSGAK LLLSATAVTV TDLPVRIVSE
DNLKDIFFTH KGNTPNPEHA VKGDENFYII YTSGSTGNPK GVQITYNCLV SFTKWAVEDF
NLQTGQVFLN QAPFSFDLSV MDIYPSLVTG GTLWAIDKDM IARPKDLFAS LEQSDIQVWT
STPSFAEMCL MEASFSESML PNMKTFLFCG EVLPNEVARK LIERFPKATI MNTYGPTEAT
VAVTGIHVTE EVLDQYKSLP VGYCKSDCRL LIMKEDGTIA PDGEKGEIVI VGPSVSVGYL
GSPELTEKAF TMIDGERAYK TGDAGYVENG LLFYNGRLDF QIKLHGYRME LEEIEHHLRA
CSYVEGAVIV PIKKGEKYDY LLAVVVPGEH SFEKEFKLTS AIKKELNERL PNYMIPRKFM
YQSSIPMTPN GKVDRKKLLS EVTA
