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D-alanine--D-alanine ligase (EC 6.3.2.4) (D-Ala-D-Ala ligase) (D-alanine:D-alanine ligase) (D-alanylalanine synthetase)

 DDL_MYCTU               Reviewed;         373 AA.
P9WP31; L0TBF6; P95114;
16-APR-2014, integrated into UniProtKB/Swiss-Prot.
16-APR-2014, sequence version 1.
28-FEB-2018, entry version 27.
RecName: Full=D-alanine--D-alanine ligase {ECO:0000255|HAMAP-Rule:MF_00047};
EC=6.3.2.4 {ECO:0000255|HAMAP-Rule:MF_00047, ECO:0000269|PubMed:20956591, ECO:0000269|PubMed:23286234};
AltName: Full=D-Ala-D-Ala ligase {ECO:0000255|HAMAP-Rule:MF_00047};
AltName: Full=D-alanine:D-alanine ligase {ECO:0000303|PubMed:20956591, ECO:0000303|PubMed:23286234};
AltName: Full=D-alanylalanine synthetase {ECO:0000255|HAMAP-Rule:MF_00047};
Name=ddl {ECO:0000255|HAMAP-Rule:MF_00047,
ECO:0000303|PubMed:20956591, ECO:0000303|PubMed:23286234};
Synonyms=ddlA; OrderedLocusNames=Rv2981c; ORFNames=MTCY349.06;
Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv).
Bacteria; Actinobacteria; Corynebacteriales; Mycobacteriaceae;
Mycobacterium; Mycobacterium tuberculosis complex.
NCBI_TaxID=83332;
[1]
NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
STRAIN=ATCC 25618 / H37Rv;
PubMed=9634230; DOI=10.1038/31159;
Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C.M.,
Harris D.E., Gordon S.V., Eiglmeier K., Gas S., Barry C.E. III,
Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T.,
Connor R., Davies R.M., Devlin K., Feltwell T., Gentles S., Hamlin N.,
Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S.,
Murphy L.D., Oliver S., Osborne J., Quail M.A., Rajandream M.A.,
Rogers J., Rutter S., Seeger K., Skelton S., Squares S., Squares R.,
Sulston J.E., Taylor K., Whitehead S., Barrell B.G.;
"Deciphering the biology of Mycobacterium tuberculosis from the
complete genome sequence.";
Nature 393:537-544(1998).
[2]
IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
STRAIN=ATCC 25618 / H37Rv;
PubMed=21969609; DOI=10.1074/mcp.M111.011627;
Kelkar D.S., Kumar D., Kumar P., Balakrishnan L., Muthusamy B.,
Yadav A.K., Shrivastava P., Marimuthu A., Anand S., Sundaram H.,
Kingsbury R., Harsha H.C., Nair B., Prasad T.S., Chauhan D.S.,
Katoch K., Katoch V.M., Kumar P., Chaerkady R., Ramachandran S.,
Dash D., Pandey A.;
"Proteogenomic analysis of Mycobacterium tuberculosis by high
resolution mass spectrometry.";
Mol. Cell. Proteomics 10:M111.011627-M111.011627(2011).
[3]
FUNCTION, CATALYTIC ACTIVITY, BIOPHYSICOCHEMICAL PROPERTIES, ENZYME
REGULATION, KINETIC MECHANISM, AND PATHWAY.
PubMed=23286234; DOI=10.1111/febs.12108;
Prosser G.A., de Carvalho L.P.;
"Kinetic mechanism and inhibition of Mycobacterium tuberculosis D-
alanine:D-alanine ligase by the antibiotic D-cycloserine.";
FEBS J. 280:1150-1166(2013).
[4]
X-RAY CRYSTALLOGRAPHY (2.10 ANGSTROMS), FUNCTION, CATALYTIC ACTIVITY,
ENZYME REGULATION, SUBUNIT, AND PATHWAY.
STRAIN=H37Rv;
PubMed=20956591; DOI=10.1128/AAC.00558-10;
Bruning J.B., Murillo A.C., Chacon O., Barletta R.G.,
Sacchettini J.C.;
"Structure of the Mycobacterium tuberculosis D-alanine:D-alanine
ligase, a target of the antituberculosis drug D-cycloserine.";
Antimicrob. Agents Chemother. 55:291-301(2011).
-!- FUNCTION: Catalyzes the ATP-driven ligation of two D-alanine
molecules to form the D-alanyl-D-alanine dipeptide. This molecule
is a key building block in peptidoglycan biosynthesis.
{ECO:0000255|HAMAP-Rule:MF_00047, ECO:0000269|PubMed:20956591,
ECO:0000269|PubMed:23286234}.
-!- CATALYTIC ACTIVITY: ATP + 2 D-alanine = ADP + phosphate + D-
alanyl-D-alanine. {ECO:0000255|HAMAP-Rule:MF_00047,
ECO:0000269|PubMed:20956591, ECO:0000269|PubMed:23286234}.
-!- COFACTOR:
Name=Mg(2+); Xref=ChEBI:CHEBI:18420; Evidence={ECO:0000250};
Name=Mn(2+); Xref=ChEBI:CHEBI:29035; Evidence={ECO:0000250};
Note=Binds 2 magnesium or manganese ions per subunit.
{ECO:0000250};
-!- ENZYME REGULATION: Is inhibited by the antituberculous drug D-
cycloserine (DCS), which is a structural analog of D-alanine
(PubMed:20956591, PubMed:23286234). Is activated by K(+)
(PubMed:23286234). {ECO:0000269|PubMed:20956591,
ECO:0000269|PubMed:23286234}.
-!- BIOPHYSICOCHEMICAL PROPERTIES:
Kinetic parameters:
KM=0.075 mM for D-Ala (first D-Ala binding site) (at pH 7.3)
{ECO:0000269|PubMed:23286234};
KM=3.6 mM for D-Ala (second D-Ala binding site) (at pH 7.3)
{ECO:0000269|PubMed:23286234};
KM=0.31 mM for ATP (at pH 7.3) {ECO:0000269|PubMed:23286234};
Note=kcat is 9.7 sec(-1) (at pH 7.3).
{ECO:0000269|PubMed:23286234};
-!- PATHWAY: Cell wall biogenesis; peptidoglycan biosynthesis.
{ECO:0000255|HAMAP-Rule:MF_00047, ECO:0000305|PubMed:20956591,
ECO:0000305|PubMed:23286234}.
-!- SUBUNIT: Homodimer. {ECO:0000305|PubMed:20956591}.
-!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000255|HAMAP-Rule:MF_00047}.
-!- MISCELLANEOUS: Follows an ordered ter-ter mechanism. ATP is the
first substrate to bind and is necessary for subsequent binding of
D-alanine or DCS. ADP is the final product to dissociate.
{ECO:0000269|PubMed:23286234}.
-!- SIMILARITY: Belongs to the D-alanine--D-alanine ligase family.
{ECO:0000255|HAMAP-Rule:MF_00047}.
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EMBL; AL123456; CCP45786.1; -; Genomic_DNA.
PIR; B70673; B70673.
RefSeq; NP_217497.1; NC_000962.3.
RefSeq; WP_003912011.1; NZ_KK339370.1.
PDB; 3LWB; X-ray; 2.10 A; A/B=1-373.
PDBsum; 3LWB; -.
ProteinModelPortal; P9WP31; -.
SMR; P9WP31; -.
STRING; 83332.Rv2981c; -.
ChEMBL; CHEMBL2030; -.
PaxDb; P9WP31; -.
EnsemblBacteria; CCP45786; CCP45786; Rv2981c.
GeneID; 888415; -.
KEGG; mtu:Rv2981c; -.
TubercuList; Rv2981c; -.
eggNOG; ENOG4105CPF; Bacteria.
eggNOG; COG1181; LUCA.
KO; K01921; -.
OMA; YETKYTE; -.
PhylomeDB; P9WP31; -.
BioCyc; MetaCyc:G185E-7236-MONOMER; -.
UniPathway; UPA00219; -.
PRO; PR:P9WP31; -.
Proteomes; UP000001584; Chromosome.
GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
GO; GO:0005886; C:plasma membrane; IDA:MTBBASE.
GO; GO:0005524; F:ATP binding; IEA:UniProtKB-KW.
GO; GO:0008716; F:D-alanine-D-alanine ligase activity; IDA:MTBBASE.
GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
GO; GO:0071555; P:cell wall organization; IEA:UniProtKB-KW.
GO; GO:0040007; P:growth; IMP:MTBBASE.
GO; GO:0009252; P:peptidoglycan biosynthetic process; IDA:MTBBASE.
GO; GO:0008360; P:regulation of cell shape; IEA:UniProtKB-KW.
Gene3D; 3.30.1490.20; -; 1.
HAMAP; MF_00047; Dala_Dala_lig; 1.
InterPro; IPR011761; ATP-grasp.
InterPro; IPR013815; ATP_grasp_subdomain_1.
InterPro; IPR000291; D-Ala_lig_Van_CS.
InterPro; IPR005905; D_ala_D_ala.
InterPro; IPR011095; Dala_Dala_lig_C.
InterPro; IPR011127; Dala_Dala_lig_N.
InterPro; IPR016185; PreATP-grasp_dom_sf.
Pfam; PF07478; Dala_Dala_lig_C; 1.
Pfam; PF01820; Dala_Dala_lig_N; 1.
PIRSF; PIRSF039102; Ddl/VanB; 1.
SUPFAM; SSF52440; SSF52440; 1.
TIGRFAMs; TIGR01205; D_ala_D_alaTIGR; 1.
PROSITE; PS50975; ATP_GRASP; 1.
PROSITE; PS00843; DALA_DALA_LIGASE_1; 1.
PROSITE; PS00844; DALA_DALA_LIGASE_2; 1.
1: Evidence at protein level;
3D-structure; ATP-binding; Cell shape;
Cell wall biogenesis/degradation; Complete proteome; Cytoplasm;
Ligase; Magnesium; Manganese; Metal-binding; Nucleotide-binding;
Peptidoglycan synthesis; Reference proteome.
CHAIN 1 373 D-alanine--D-alanine ligase.
/FTId=PRO_0000177844.
DOMAIN 156 363 ATP-grasp. {ECO:0000255|HAMAP-
Rule:MF_00047}.
NP_BIND 184 239 ATP. {ECO:0000255|HAMAP-Rule:MF_00047}.
METAL 318 318 Magnesium or manganese 1.
{ECO:0000255|HAMAP-Rule:MF_00047}.
METAL 330 330 Magnesium or manganese 1.
{ECO:0000255|HAMAP-Rule:MF_00047}.
METAL 330 330 Magnesium or manganese 2.
{ECO:0000255|HAMAP-Rule:MF_00047}.
METAL 332 332 Magnesium or manganese 2.
{ECO:0000255|HAMAP-Rule:MF_00047}.
STRAND 11 18 {ECO:0000244|PDB:3LWB}.
HELIX 26 37 {ECO:0000244|PDB:3LWB}.
TURN 40 42 {ECO:0000244|PDB:3LWB}.
STRAND 43 50 {ECO:0000244|PDB:3LWB}.
STRAND 56 59 {ECO:0000244|PDB:3LWB}.
HELIX 103 108 {ECO:0000244|PDB:3LWB}.
STRAND 111 115 {ECO:0000244|PDB:3LWB}.
HELIX 126 134 {ECO:0000244|PDB:3LWB}.
STRAND 138 141 {ECO:0000244|PDB:3LWB}.
HELIX 143 150 {ECO:0000244|PDB:3LWB}.
HELIX 152 161 {ECO:0000244|PDB:3LWB}.
STRAND 169 172 {ECO:0000244|PDB:3LWB}.
HELIX 181 187 {ECO:0000244|PDB:3LWB}.
STRAND 191 197 {ECO:0000244|PDB:3LWB}.
TURN 200 203 {ECO:0000244|PDB:3LWB}.
STRAND 205 207 {ECO:0000244|PDB:3LWB}.
HELIX 210 212 {ECO:0000244|PDB:3LWB}.
HELIX 213 221 {ECO:0000244|PDB:3LWB}.
STRAND 225 231 {ECO:0000244|PDB:3LWB}.
STRAND 234 244 {ECO:0000244|PDB:3LWB}.
STRAND 250 252 {ECO:0000244|PDB:3LWB}.
STRAND 256 259 {ECO:0000244|PDB:3LWB}.
STRAND 266 271 {ECO:0000244|PDB:3LWB}.
HELIX 273 277 {ECO:0000244|PDB:3LWB}.
STRAND 283 287 {ECO:0000244|PDB:3LWB}.
HELIX 292 308 {ECO:0000244|PDB:3LWB}.
STRAND 313 322 {ECO:0000244|PDB:3LWB}.
STRAND 325 334 {ECO:0000244|PDB:3LWB}.
HELIX 342 349 {ECO:0000244|PDB:3LWB}.
HELIX 354 367 {ECO:0000244|PDB:3LWB}.
SEQUENCE 373 AA; 39710 MW; FD7838E8B7526B53 CRC64;
MSANDRRDRR VRVAVVFGGR SNEHAISCVS AGSILRNLDS RRFDVIAVGI TPAGSWVLTD
ANPDALTITN RELPQVKSGS GTELALPADP RRGGQLVSLP PGAGEVLESV DVVFPVLHGP
YGEDGTIQGL LELAGVPYVG AGVLASAVGM DKEFTKKLLA ADGLPVGAYA VLRPPRSTLH
RQECERLGLP VFVKPARGGS SIGVSRVSSW DQLPAAVARA RRHDPKVIVE AAISGRELEC
GVLEMPDGTL EASTLGEIRV AGVRGREDSF YDFATKYLDD AAELDVPAKV DDQVAEAIRQ
LAIRAFAAID CRGLARVDFF LTDDGPVINE INTMPGFTTI SMYPRMWAAS GVDYPTLLAT
MIETTLARGV GLH


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