DDL_THET8
ID DDL_THET8 Reviewed; 319 AA.
AC Q5SHZ3;
DT 10-JUN-2008, integrated into UniProtKB/Swiss-Prot.
DT 21-DEC-2004, sequence version 1.
DT 03-AUG-2022, 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}; OrderedLocusNames=TTHA1587;
OS Thermus thermophilus (strain ATCC 27634 / DSM 579 / HB8).
OC Bacteria; Deinococcus-Thermus; Deinococci; Thermales; Thermaceae; Thermus.
OX NCBI_TaxID=300852;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC 27634 / DSM 579 / HB8;
RA Masui R., Kurokawa K., Nakagawa N., Tokunaga F., Koyama Y., Shibata T.,
RA Oshima T., Yokoyama S., Yasunaga T., Kuramitsu S.;
RT "Complete genome sequence of Thermus thermophilus HB8.";
RL Submitted (NOV-2004) to the EMBL/GenBank/DDBJ databases.
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}.
CC ---------------------------------------------------------------------------
CC Copyrighted by the UniProt Consortium, see https://www.uniprot.org/terms
CC Distributed under the Creative Commons Attribution (CC BY 4.0) License
CC ---------------------------------------------------------------------------
DR EMBL; AP008226; BAD71410.1; -; Genomic_DNA.
DR RefSeq; WP_011228789.1; NC_006461.1.
DR RefSeq; YP_144853.1; NC_006461.1.
DR PDB; 2FB9; X-ray; 1.90 A; A=1-319.
DR PDB; 2YZG; X-ray; 2.30 A; A/B/C=1-319.
DR PDB; 2YZM; X-ray; 2.21 A; A/B/C=1-319.
DR PDB; 2YZN; X-ray; 2.60 A; A/B/C=1-319.
DR PDB; 2ZDG; X-ray; 2.20 A; A/B/C/D=1-319.
DR PDB; 2ZDH; X-ray; 1.90 A; A/B/C/D=1-319.
DR PDB; 2ZDQ; X-ray; 2.30 A; A/B=1-319.
DR PDB; 6U1C; X-ray; 2.20 A; A/B/C/D=1-319.
DR PDB; 6U1D; X-ray; 1.90 A; A/B=1-319.
DR PDB; 6U1E; X-ray; 2.10 A; A/B=1-319.
DR PDB; 6U1F; X-ray; 2.30 A; A/B=1-319.
DR PDB; 6U1G; X-ray; 2.40 A; A/B=1-319.
DR PDB; 6U1H; X-ray; 2.20 A; A/B/C/D=1-319.
DR PDB; 6U1I; X-ray; 2.30 A; A/B/C/D=1-319.
DR PDB; 6U1J; X-ray; 2.20 A; A/B/C/D=1-319.
DR PDB; 6U1K; X-ray; 1.67 A; A/B/C/D=1-319.
DR PDBsum; 2FB9; -.
DR PDBsum; 2YZG; -.
DR PDBsum; 2YZM; -.
DR PDBsum; 2YZN; -.
DR PDBsum; 2ZDG; -.
DR PDBsum; 2ZDH; -.
DR PDBsum; 2ZDQ; -.
DR PDBsum; 6U1C; -.
DR PDBsum; 6U1D; -.
DR PDBsum; 6U1E; -.
DR PDBsum; 6U1F; -.
DR PDBsum; 6U1G; -.
DR PDBsum; 6U1H; -.
DR PDBsum; 6U1I; -.
DR PDBsum; 6U1J; -.
DR PDBsum; 6U1K; -.
DR AlphaFoldDB; Q5SHZ3; -.
DR SMR; Q5SHZ3; -.
DR STRING; 300852.55772969; -.
DR EnsemblBacteria; BAD71410; BAD71410; BAD71410.
DR GeneID; 3168507; -.
DR KEGG; ttj:TTHA1587; -.
DR PATRIC; fig|300852.9.peg.1557; -.
DR eggNOG; COG1181; Bacteria.
DR HOGENOM; CLU_039268_0_0_0; -.
DR OMA; NTTPGMT; -.
DR PhylomeDB; Q5SHZ3; -.
DR BRENDA; 6.3.2.4; 2305.
DR UniPathway; UPA00219; -.
DR EvolutionaryTrace; Q5SHZ3; -.
DR Proteomes; UP000000532; Chromosome.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
DR GO; GO:0008716; F:D-alanine-D-alanine ligase activity; IEA:UniProtKB-UniRule.
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; IEA:UniProtKB-UniRule.
DR GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW.
DR Gene3D; 3.30.1490.20; -; 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 Pfam; PF07478; Dala_Dala_lig_C; 1.
DR Pfam; PF01820; Dala_Dala_lig_N; 1.
DR PIRSF; PIRSF039102; Ddl/VanB; 1.
DR SUPFAM; SSF52440; SSF52440; 1.
DR TIGRFAMs; TIGR01205; D_ala_D_alaTIGR; 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..319
FT /note="D-alanine--D-alanine ligase"
FT /id="PRO_0000341188"
FT DOMAIN 120..315
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 147..198
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 270
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 282
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 282
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 284
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT STRAND 3..8
FT /evidence="ECO:0007829|PDB:6U1K"
FT HELIX 14..27
FT /evidence="ECO:0007829|PDB:6U1K"
FT STRAND 32..37
FT /evidence="ECO:0007829|PDB:6U1K"
FT STRAND 43..45
FT /evidence="ECO:0007829|PDB:6U1H"
FT HELIX 46..55
FT /evidence="ECO:0007829|PDB:6U1K"
FT HELIX 71..73
FT /evidence="ECO:0007829|PDB:6U1K"
FT STRAND 75..80
FT /evidence="ECO:0007829|PDB:6U1K"
FT TURN 84..86
FT /evidence="ECO:0007829|PDB:6U1K"
FT STRAND 87..89
FT /evidence="ECO:0007829|PDB:6U1K"
FT HELIX 90..98
FT /evidence="ECO:0007829|PDB:6U1K"
FT STRAND 102..104
FT /evidence="ECO:0007829|PDB:6U1K"
FT HELIX 107..114
FT /evidence="ECO:0007829|PDB:6U1K"
FT HELIX 118..125
FT /evidence="ECO:0007829|PDB:6U1K"
FT STRAND 133..137
FT /evidence="ECO:0007829|PDB:6U1K"
FT STRAND 150..154
FT /evidence="ECO:0007829|PDB:6U1K"
FT TURN 159..162
FT /evidence="ECO:0007829|PDB:6U1K"
FT STRAND 164..166
FT /evidence="ECO:0007829|PDB:6U1K"
FT HELIX 169..171
FT /evidence="ECO:0007829|PDB:6U1K"
FT HELIX 172..179
FT /evidence="ECO:0007829|PDB:6U1K"
FT TURN 180..182
FT /evidence="ECO:0007829|PDB:6U1K"
FT STRAND 184..190
FT /evidence="ECO:0007829|PDB:6U1K"
FT STRAND 196..207
FT /evidence="ECO:0007829|PDB:6U1K"
FT STRAND 209..217
FT /evidence="ECO:0007829|PDB:6U1K"
FT STRAND 219..222
FT /evidence="ECO:0007829|PDB:6U1K"
FT HELIX 225..229
FT /evidence="ECO:0007829|PDB:6U1K"
FT TURN 231..233
FT /evidence="ECO:0007829|PDB:6U1K"
FT STRAND 234..239
FT /evidence="ECO:0007829|PDB:6U1K"
FT HELIX 244..260
FT /evidence="ECO:0007829|PDB:6U1K"
FT STRAND 265..274
FT /evidence="ECO:0007829|PDB:6U1K"
FT STRAND 277..286
FT /evidence="ECO:0007829|PDB:6U1K"
FT HELIX 294..301
FT /evidence="ECO:0007829|PDB:6U1K"
FT HELIX 306..319
FT /evidence="ECO:0007829|PDB:6U1K"
SQ SEQUENCE 319 AA; 34666 MW; 85E6F0AA367A13AF CRC64;
MRVLLIAGGV SPEHEVSLLS AEGVLRHIPF PTDLAVIAQD GRWLLGEKAL TALEAKAAPE
GEHPFPPPLS WERYDVVFPL LHGRFGEDGT VQGFLELLGK PYVGAGVAAS ALCMDKDLSK
RVLAQAGVPV VPWVAVRKGE PPVVPFDPPF FVKPANTGSS VGISRVERFQ DLEAALALAF
RYDEKAVVEK ALSPVRELEV GVLGNVFGEA SPVGEVRYEA PFYDYETKYT PGRAELLIPA
PLDPGTQETV QELALKAYKV LGVRGMARVD FFLAEGELYL NELNTIPGFT PTSMYPRLFE
AGGVAYPELL RRLVELALT
