ID DDL_STAA8 Reviewed; 356 AA.
AC Q2FWH3;
DT 15-JAN-2008, integrated into UniProtKB/Swiss-Prot.
DT 21-MAR-2006, sequence version 1.
DT 27-MAR-2024, entry version 111.
DE RecName: Full=D-alanine--D-alanine ligase {ECO:0000255|HAMAP-Rule:MF_00047};
DE EC=6.3.2.4 {ECO:0000255|HAMAP-Rule:MF_00047};
DE AltName: Full=D-Ala-D-Ala ligase {ECO:0000255|HAMAP-Rule:MF_00047};
DE AltName: Full=D-alanylalanine synthetase {ECO:0000255|HAMAP-Rule:MF_00047};
GN Name=ddl {ECO:0000255|HAMAP-Rule:MF_00047};
GN OrderedLocusNames=SAOUHSC_02318;
OS Staphylococcus aureus (strain NCTC 8325 / PS 47).
OC Bacteria; Bacillota; Bacilli; Bacillales; Staphylococcaceae;
OC Staphylococcus.
OX NCBI_TaxID=93061;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=NCTC 8325 / PS 47;
RA Gillaspy A.F., Worrell V., Orvis J., Roe B.A., Dyer D.W., Iandolo J.J.;
RT "The Staphylococcus aureus NCTC 8325 genome.";
RL (In) Fischetti V., Novick R., Ferretti J., Portnoy D., Rood J. (eds.);
RL Gram positive pathogens, 2nd edition, pp.381-412, ASM Press, Washington
RL D.C. (2006).
CC -!- FUNCTION: Cell wall formation. {ECO:0000255|HAMAP-Rule:MF_00047}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP + 2 D-alanine = ADP + D-alanyl-D-alanine + H(+) +
CC phosphate; Xref=Rhea:RHEA:11224, ChEBI:CHEBI:15378,
CC ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:57416,
CC ChEBI:CHEBI:57822, ChEBI:CHEBI:456216; EC=6.3.2.4;
CC Evidence={ECO:0000255|HAMAP-Rule:MF_00047};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
CC Note=Binds 2 magnesium or manganese ions per subunit. {ECO:0000250};
CC -!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
CC {ECO:0000255|HAMAP-Rule:MF_00047}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00047}.
CC -!- SIMILARITY: Belongs to the D-alanine--D-alanine ligase family.
CC {ECO:0000255|HAMAP-Rule:MF_00047}.
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DR EMBL; CP000253; ABD31352.1; -; Genomic_DNA.
DR RefSeq; WP_000159631.1; NZ_LS483365.1.
DR RefSeq; YP_500797.1; NC_007795.1.
DR PDB; 7U9K; X-ray; 2.00 A; A/B=1-356.
DR PDBsum; 7U9K; -.
DR AlphaFoldDB; Q2FWH3; -.
DR SMR; Q2FWH3; -.
DR STRING; 93061.SAOUHSC_02318; -.
DR PaxDb; 1280-SAXN108_2328; -.
DR GeneID; 3920943; -.
DR KEGG; sao:SAOUHSC_02318; -.
DR PATRIC; fig|93061.5.peg.2101; -.
DR eggNOG; COG1181; Bacteria.
DR HOGENOM; CLU_039268_0_0_9; -.
DR OrthoDB; 9813261at2; -.
DR UniPathway; UPA00219; -.
DR PRO; PR:Q2FWH3; -.
DR Proteomes; UP000008816; Chromosome.
DR GO; GO:0005829; C:cytosol; IBA:GO_Central.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0008716; F:D-alanine-D-alanine ligase activity; IBA:GO_Central.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
DR GO; GO:0009252; P:peptidoglycan biosynthetic process; IBA:GO_Central.
DR GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW.
DR Gene3D; 3.40.50.20; -; 1.
DR Gene3D; 3.30.1490.20; ATP-grasp fold, A domain; 1.
DR Gene3D; 3.30.470.20; ATP-grasp fold, B domain; 1.
DR HAMAP; MF_00047; Dala_Dala_lig; 1.
DR InterPro; IPR011761; ATP-grasp.
DR InterPro; IPR013815; ATP_grasp_subdomain_1.
DR InterPro; IPR000291; D-Ala_lig_Van_CS.
DR InterPro; IPR005905; D_ala_D_ala.
DR InterPro; IPR011095; Dala_Dala_lig_C.
DR InterPro; IPR011127; Dala_Dala_lig_N.
DR InterPro; IPR016185; PreATP-grasp_dom_sf.
DR NCBIfam; TIGR01205; D_ala_D_alaTIGR; 1.
DR PANTHER; PTHR23132; D-ALANINE--D-ALANINE LIGASE; 1.
DR PANTHER; PTHR23132:SF25; D-ALANINE--D-ALANINE LIGASE A; 1.
DR Pfam; PF07478; Dala_Dala_lig_C; 1.
DR Pfam; PF01820; Dala_Dala_lig_N; 1.
DR PIRSF; PIRSF039102; Ddl/VanB; 1.
DR SUPFAM; SSF56059; Glutathione synthetase ATP-binding domain-like; 1.
DR SUPFAM; SSF52440; PreATP-grasp domain; 1.
DR PROSITE; PS50975; ATP_GRASP; 1.
DR PROSITE; PS00843; DALA_DALA_LIGASE_1; 1.
DR PROSITE; PS00844; DALA_DALA_LIGASE_2; 1.
PE 1: Evidence at protein level;
KW 3D-structure; ATP-binding; Cell shape; Cell wall biogenesis/degradation;
KW Cytoplasm; Ligase; Magnesium; Manganese; Metal-binding; Nucleotide-binding;
KW Peptidoglycan synthesis; Reference proteome.
FT CHAIN 1..356
FT /note="D-alanine--D-alanine ligase"
FT /id="PRO_1000030494"
FT DOMAIN 134..339
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 167..222
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 293
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 306
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 306
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 308
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT STRAND 4..11
FT /evidence="ECO:0007829|PDB:7U9K"
FT HELIX 17..30
FT /evidence="ECO:0007829|PDB:7U9K"
FT TURN 33..35
FT /evidence="ECO:0007829|PDB:7U9K"
FT STRAND 36..43
FT /evidence="ECO:0007829|PDB:7U9K"
FT STRAND 49..52
FT /evidence="ECO:0007829|PDB:7U9K"
FT HELIX 62..65
FT /evidence="ECO:0007829|PDB:7U9K"
FT HELIX 75..80
FT /evidence="ECO:0007829|PDB:7U9K"
FT STRAND 89..93
FT /evidence="ECO:0007829|PDB:7U9K"
FT TURN 98..100
FT /evidence="ECO:0007829|PDB:7U9K"
FT STRAND 101..103
FT /evidence="ECO:0007829|PDB:7U9K"
FT HELIX 104..112
FT /evidence="ECO:0007829|PDB:7U9K"
FT STRAND 116..118
FT /evidence="ECO:0007829|PDB:7U9K"
FT HELIX 121..128
FT /evidence="ECO:0007829|PDB:7U9K"
FT HELIX 130..140
FT /evidence="ECO:0007829|PDB:7U9K"
FT STRAND 147..151
FT /evidence="ECO:0007829|PDB:7U9K"
FT HELIX 152..169
FT /evidence="ECO:0007829|PDB:7U9K"
FT STRAND 172..180
FT /evidence="ECO:0007829|PDB:7U9K"
FT STRAND 188..192
FT /evidence="ECO:0007829|PDB:7U9K"
FT HELIX 193..204
FT /evidence="ECO:0007829|PDB:7U9K"
FT STRAND 208..214
FT /evidence="ECO:0007829|PDB:7U9K"
FT STRAND 219..230
FT /evidence="ECO:0007829|PDB:7U9K"
FT STRAND 237..239
FT /evidence="ECO:0007829|PDB:7U9K"
FT STRAND 242..245
FT /evidence="ECO:0007829|PDB:7U9K"
FT HELIX 248..252
FT /evidence="ECO:0007829|PDB:7U9K"
FT STRAND 259..262
FT /evidence="ECO:0007829|PDB:7U9K"
FT HELIX 267..283
FT /evidence="ECO:0007829|PDB:7U9K"
FT STRAND 288..296
FT /evidence="ECO:0007829|PDB:7U9K"
FT STRAND 302..310
FT /evidence="ECO:0007829|PDB:7U9K"
FT HELIX 318..325
FT /evidence="ECO:0007829|PDB:7U9K"
FT HELIX 330..349
FT /evidence="ECO:0007829|PDB:7U9K"
SQ SEQUENCE 356 AA; 40231 MW; 65822883958DC645 CRC64;
MTKENICIVF GGKSAEHEVS ILTAQNVLNA IDKDKYHVDI IYITNDGDWR KQNNITAEIK
STDELHLENG EALEISQLLK ESSSGQPYDA VFPLLHGPNG EDGTIQGLFE VLDVPYVGNG
VLSAASSMDK LVMKQLFEHR GLPQLPYISF LRSEYEKYEH NILKLVNDKL NYPVFVKPAN
LGSSVGISKC NNEAELKEGI KEAFQFDRKL VIEQGVNARE IEVAVLGNDY PEATWPGEVV
KDVAFYDYKS KYKDGKVQLQ IPADLDEDVQ LTLRNMALEA FKATDCSGLV RADFFVTEDN
QIYINETNAM PGFTAFSMYP KLWENMGLSY PELITKLIEL AKERHQDKQK NKYKID
//
