DDL_PARXL
ID DDL_PARXL Reviewed; 313 AA.
AC Q13TZ4;
DT 10-JUN-2008, integrated into UniProtKB/Swiss-Prot.
DT 22-AUG-2006, sequence version 1.
DT 03-AUG-2022, entry version 113.
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=Bxeno_A3907;
GN ORFNames=Bxe_A0488;
OS Paraburkholderia xenovorans (strain LB400).
OC Bacteria; Proteobacteria; Betaproteobacteria; Burkholderiales;
OC Burkholderiaceae; Paraburkholderia.
OX NCBI_TaxID=266265;
RN [1]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=LB400;
RX PubMed=17030797; DOI=10.1073/pnas.0606924103;
RA Chain P.S.G., Denef V.J., Konstantinidis K.T., Vergez L.M., Agullo L.,
RA Reyes V.L., Hauser L., Cordova M., Gomez L., Gonzalez M., Land M., Lao V.,
RA Larimer F., LiPuma J.J., Mahenthiralingam E., Malfatti S.A., Marx C.J.,
RA Parnell J.J., Ramette A., Richardson P., Seeger M., Smith D., Spilker T.,
RA Sul W.J., Tsoi T.V., Ulrich L.E., Zhulin I.B., Tiedje J.M.;
RT "Burkholderia xenovorans LB400 harbors a multi-replicon, 9.73-Mbp genome
RT shaped for versatility.";
RL Proc. Natl. Acad. Sci. U.S.A. 103:15280-15287(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; CP000270; ABE32445.1; -; Genomic_DNA.
DR RefSeq; WP_011489915.1; NZ_CP008760.1.
DR PDB; 4EGJ; X-ray; 2.30 A; A/B/C/D=1-313.
DR PDBsum; 4EGJ; -.
DR AlphaFoldDB; Q13TZ4; -.
DR SMR; Q13TZ4; -.
DR STRING; 266265.Bxe_A0488; -.
DR EnsemblBacteria; ABE32445; ABE32445; Bxe_A0488.
DR KEGG; bxb:DR64_2664; -.
DR KEGG; bxe:Bxe_A0488; -.
DR PATRIC; fig|266265.5.peg.4128; -.
DR eggNOG; COG1181; Bacteria.
DR OMA; NTTPGMT; -.
DR OrthoDB; 764798at2; -.
DR UniPathway; UPA00219; -.
DR Proteomes; UP000001817; Chromosome 1.
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..313
FT /note="D-alanine--D-alanine ligase"
FT /id="PRO_0000341080"
FT DOMAIN 108..308
FT /note="ATP-grasp"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 138..193
FT /ligand="ATP"
FT /ligand_id="ChEBI:CHEBI:30616"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 262
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 275
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 275
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT BINDING 277
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000255|HAMAP-Rule:MF_00047"
FT HELIX 6..9
FT /evidence="ECO:0007829|PDB:4EGJ"
FT STRAND 11..15
FT /evidence="ECO:0007829|PDB:4EGJ"
FT HELIX 23..39
FT /evidence="ECO:0007829|PDB:4EGJ"
FT STRAND 43..47
FT /evidence="ECO:0007829|PDB:4EGJ"
FT TURN 49..51
FT /evidence="ECO:0007829|PDB:4EGJ"
FT HELIX 56..59
FT /evidence="ECO:0007829|PDB:4EGJ"
FT STRAND 64..67
FT /evidence="ECO:0007829|PDB:4EGJ"
FT HELIX 72..74
FT /evidence="ECO:0007829|PDB:4EGJ"
FT HELIX 78..86
FT /evidence="ECO:0007829|PDB:4EGJ"
FT STRAND 89..92
FT /evidence="ECO:0007829|PDB:4EGJ"
FT HELIX 95..101
FT /evidence="ECO:0007829|PDB:4EGJ"
FT HELIX 104..113
FT /evidence="ECO:0007829|PDB:4EGJ"
FT STRAND 121..125
FT /evidence="ECO:0007829|PDB:4EGJ"
FT HELIX 130..141
FT /evidence="ECO:0007829|PDB:4EGJ"
FT STRAND 143..149
FT /evidence="ECO:0007829|PDB:4EGJ"
FT HELIX 164..166
FT /evidence="ECO:0007829|PDB:4EGJ"
FT HELIX 167..174
FT /evidence="ECO:0007829|PDB:4EGJ"
FT TURN 175..177
FT /evidence="ECO:0007829|PDB:4EGJ"
FT STRAND 179..185
FT /evidence="ECO:0007829|PDB:4EGJ"
FT STRAND 189..198
FT /evidence="ECO:0007829|PDB:4EGJ"
FT STRAND 206..208
FT /evidence="ECO:0007829|PDB:4EGJ"
FT STRAND 228..231
FT /evidence="ECO:0007829|PDB:4EGJ"
FT HELIX 236..251
FT /evidence="ECO:0007829|PDB:4EGJ"
FT TURN 252..254
FT /evidence="ECO:0007829|PDB:4EGJ"
FT STRAND 257..266
FT /evidence="ECO:0007829|PDB:4EGJ"
FT STRAND 271..279
FT /evidence="ECO:0007829|PDB:4EGJ"
FT HELIX 287..294
FT /evidence="ECO:0007829|PDB:4EGJ"
FT HELIX 299..308
FT /evidence="ECO:0007829|PDB:4EGJ"
SQ SEQUENCE 313 AA; 33535 MW; DDBB5D2E458BD6D3 CRC64;
MSSIDPKQFG KVAVLLGGNS AEREVSLNSG RLVLQGLRDA GIDAHPFDPA ERPLAALKEE
GFVRAFNALH GGYGENGQIQ GALDFYGIRY TGSGVLGSAL GLDKFRTKLV WQQLGIPTPP
FEAVLRGDDY EARAKEIVAK LGLPLFVKPA SEGSSVAVIK VKSADALPAA LIEAVKFDRI
VVVEKSIEGG GEYTACIAGN LDLPVIRIVP AGEFYDYHAK YIANDTQYLI PCGLTADEEA
RLKVLARRAF DVLGCTDWGR ADFMLDADGN PYFLEVNTAP GMTDHSLPPK AARAVGISYQ
ELVVAVLALT LKD
