DB code: T00108

CATH domain 3.40.50.20 : Rossmann fold Catalytic domain
3.30.470.20 : D-amino Acid Aminotransferase; Chain A, domain 1 Catalytic domain
3.30.1490.20 : Dna Ligase; domain 1 Catalytic domain
E.C. 6.3.2.4
CSA 2dln
M-CSA 2dln
MACiE

CATH domain Related DB codes (homologues)
3.30.1490.20 : Dna Ligase; domain 1 T00082 M00035 M00037 T00107
3.30.470.20 : D-amino Acid Aminotransferase; Chain A, domain 1 T00082 D00298 M00035 M00037 M00051 T00107
3.40.50.20 : Rossmann fold T00082 M00037 T00107

Uniprot Enzyme Name
UniprotKB Protein name Synonyms RefSeq Pfam
P07862 D-alanine--D-alanine ligase B
EC 6.3.2.4
D-alanylalanine synthetase B
D-Ala-D-Ala ligase B
NP_414634.1 (Protein)
NC_000913.2 (DNA/RNA sequence)
YP_488397.1 (Protein)
NC_007779.1 (DNA/RNA sequence)
PF07478 (Dala_Dala_lig_C)
PF01820 (Dala_Dala_lig_N)
[Graphical View]
P71454
D-Ala-D-Ala ligase2
PF07478 (Dala_Dala_lig_C)
PF01820 (Dala_Dala_lig_N)
[Graphical View]

KEGG enzyme name
D-alanine---D-alanine ligase
MurE synthetase [ambiguous]
alanine:alanine ligase (ADP-forming)
alanylalanine synthetase

UniprotKB: Accession Number Entry name Activity Subunit Subcellular location Cofactor
P07862 DDLB_ECOLI ATP + 2 D-alanine = ADP + phosphate + D- alanyl-D-alanine. Monomer. Cytoplasm. Binds 2 magnesium or manganese ions per subunit (By similarity).
P71454 P71454_LEUME

KEGG Pathways
Map code Pathways E.C.
MAP00473 D-Alanine metabolism
MAP00550 Peptidoglycan biosynthesis

Compound table
Cofactors Substrates Products Intermediates
KEGG-id C00305 C00002 C00133 C00008 C00009 C00993 C12021
E.C.
Compound Magnesium ATP D-Alanine ADP Orthophosphate D-Alanyl-D-alanine D-alanyl acylphosphate Tetrahedral transition-state
Type divalent metal (Ca2+, Mg2+) amine group,nucleotide amino acids amine group,nucleotide phosphate group/phosphate ion amino acids,amide group,amine group,carboxyl group
ChEBI 18420
 18420
 		15422
 15422
 		15570
 57416
 15570
 57416
 		16761
 16761
 		26078
 26078
 		16576
 57822
 16576
 57822
PubChem 888
 888
 		5957
 5957
 		71080
 7311725
 71080
 7311725
 		6022
 6022
 		1004
 22486802
 1004
 22486802
 		20112020
 5460362
 6992112
 20112020
 5460362
 6992112
1ehiA01 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1ehiB01 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1iovA01 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1iowA01 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2dlnA01 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1ehiA02 Bound:2x_MG Unbound Unbound Bound:ADP Unbound Unbound Unbound Analogue:PHY
1ehiB02 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1iovA02 Bound:3x_MG Unbound Unbound Bound:ADP Unbound Unbound Unbound Analogue:POB
1iowA02 Bound:2x_MG Unbound Unbound Bound:ADP Unbound Unbound Unbound Analogue:PHY
2dlnA02 Bound:2x_MG Unbound Unbound Bound:ADP Unbound Unbound Unbound Analogue:PHY
1ehiA03 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1ehiB03 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1iovA03 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1iowA03 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2dlnA03 Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound

Reference for Active-site residues
resource references E.C.
PDB;1iov, 1iow, 2dln & Swiss-prot;P07862 & literature [7], [8], [14]

Active-site residues
PDB Catalytic residues Cofactor-binding residues Modified residues Main-chain involved in catalysis Comment
1ehiA01 GLU 16
1ehiB01 GLU 416
1iovA01 GLU 15
1iowA01 GLU 15
2dlnA01 GLU 15
1ehiA02 LYS 260;;ARG 301 ASP 303(Magnesium-1);GLU 316(Magnesium-1 & -2);ASN 318(Magnesium-2) GLY 322
1ehiB02 ; ;ARG 701 ASP 703(Magnesium-1);GLU 716(Magnesium-1 & -2);ASN 718(Magnesium-2) GLY 722 invisible 645-666
1iovA02 LYS 215;TYR 216;ARG 255 ASP 257(Magnesium-1);GLU 270(Magnesium-1 & -2);ASN 272(Magnesium-2) GLY 276
1iowA02 LYS 215;;ARG 255 ASP 257(Magnesium-1);GLU 270(Magnesium-1 & -2);ASN 272(Magnesium-2) GLY 276 mutant Y216F
2dlnA02 LYS 215;TYR 216;ARG 255 ASP 257(Magnesium-1);GLU 270(Magnesium-1 & -2);ASN 272(Magnesium-2) GLY 276
1ehiA03 SER 186
1ehiB03 SER 586
1iovA03 SER 150
1iowA03 SER 150
2dlnA03 SER 150

References for Catalytic Mechanism
References Sections No. of steps in catalysis
[1]
Fig.4, Fig.5, p.3714
[2]
Scheme II
[4]
Fig.1, p.5774
[7]
Fig.5, Fig.6, p.441 3
[8]
Scheme 1, Scheme 2, p.2773-2776 4
[9]
Scheme I 3
[10]
Eq.(11), Eq.(12), p.10469-10470
[14]
p.2536-2537
[15]
[25]
Fig.1, p.466, p.467-468 2

References
[1]
Resource
Comments
Medline ID
PubMed ID 3044448
Journal Biochemistry
Year 1988
Volume 27
Pages 3709-14
Authors Duncan K, Walsh CT
Title ATP-dependent inactivation and slow binding inhibition of Salmonella typhimurium D-alanine:D-alanine ligase (ADP) by (aminoalkyl)phosphinate and aminophosphonate analogues of D-alanine.
Related PDB
Related UniProtKB
[2]
Resource
Comments
Medline ID
PubMed ID 2562853
Journal J Med Chem
Year 1989
Volume 32
Pages 165-70
Authors Greenlee WJ, Springer JP, Patchett AA
Title Synthesis of an analogue of tabtoxinine as a potential inhibitor of D-alanine:D-alanine ligase (ADP forming).
Related PDB
Related UniProtKB
[3]
Resource
Comments
Medline ID
PubMed ID 2648004
Journal J Mol Biol
Year 1989
Volume 205
Pages 461-3
Authors Knox JR, Liu HS, Walsh CT, Zawadzke LE
Title D-alanine-D-alanine ligase (ADP) from Salmonella typhimurium. Overproduction, purification, crystallization and preliminary X-ray analysis.
Related PDB
Related UniProtKB
[4]
Resource
Comments
Medline ID
PubMed ID 2200515
Journal Biochemistry
Year 1990
Volume 29
Pages 5767-75
Authors McDermott AE, Creuzet F, Griffin RG, Zawadzke LE, Ye QZ, Walsh CT
Title Rotational resonance determination of the structure of an enzyme-inhibitor complex: phosphorylation of an (aminoalkyl)phosphinate inhibitor of D-alanyl-D-alanine ligase by ATP.
Related PDB
Related UniProtKB
[5]
Resource
Comments
Medline ID
PubMed ID 1540152
Journal Biochem Biophys Res Commun
Year 1992
Volume 182
Pages 1040-6
Authors Peters JM, Dalrymple BP, Jorgensen WK
Title Sequence of a putative glutathione synthetase II gene and flanking regions from Anaplasma centrale.
Related PDB
Related UniProtKB
[6]
Resource
Comments
Medline ID
PubMed ID 8251948
Journal Protein Sci
Year 1993
Volume 2
Pages 1765-9
Authors Wright GD, Walsh CT
Title Identification of a common protease-sensitive region in D-alanyl-D-alanine and D-alanyl-D-lactate ligases and photoaffinity labeling with 8-azido ATP.
Related PDB
Related UniProtKB
[7]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.3 ANGSTROMS).
Medline ID 95025939
PubMed ID 7939684
Journal Science
Year 1994
Volume 266
Pages 439-43
Authors Fan C, Moews PC, Walsh CT, Knox JR
Title Vancomycin resistance: structure of D-alanine:D-alanine ligase at 2.3 A resolution.
Related PDB 2dln
Related UniProtKB P07862
[8]
Resource
Comments
Medline ID
PubMed ID 7893688
Journal Biochemistry
Year 1995
Volume 34
Pages 2768-76
Authors Shi Y, Walsh CT
Title Active site mapping of Escherichia coli D-Ala-D-Ala ligase by structure-based mutagenesis.
Related PDB
Related UniProtKB
[9]
Resource
Comments
Medline ID
PubMed ID 7862655
Journal Proc Natl Acad Sci U S A
Year 1995
Volume 92
Pages 1172-6
Authors Fan C, Moews PC, Shi Y, Walsh CT, Knox JR
Title A common fold for peptide synthetases cleaving ATP to ADP: glutathione synthetase and D-alanine:d-alanine ligase of Escherichia coli.
Related PDB
Related UniProtKB
[10]
Resource
Comments
Medline ID
PubMed ID 8756703
Journal Biochemistry
Year 1996
Volume 35
Pages 10464-71
Authors Park IS, Lin CH, Walsh CT
Title Gain of D-alanyl-D-lactate or D-lactyl-D-alanine synthetase activities in three active-site mutants of the Escherichia coli D-alanyl-D-alanine ligase B.
Related PDB
Related UniProtKB
[11]
Resource
Comments
Medline ID
PubMed ID 8662022
Journal J Mol Evol
Year 1996
Volume 42
Pages 706-12
Authors Evers S, Casadewall B, Charles M, Dutka-Malen S, Galimand M, Courvalin P
Title Evolution of structure and substrate specificity in D-alanine:D-alanine ligases and related enzymes.
Related PDB
Related UniProtKB
[12]
Resource
Comments
Medline ID
PubMed ID 8564538
Journal Nat Struct Biol
Year 1996
Volume 3
Pages 128-32
Authors Artymiuk PJ, Poirrette AR, Rice DW, Willett P
Title Biotin carboxylase comes into the fold.
Related PDB
Related UniProtKB
[13]
Resource
Comments
Medline ID
PubMed ID 9010922
Journal Protein Eng
Year 1996
Volume 9
Pages 1083-92
Authors Matsuda K, Mizuguchi K, Nishioka T, Kato H, Go N, Oda J
Title Crystal structure of glutathione synthetase at optimal pH: domain architecture and structural similarity with other proteins.
Related PDB
Related UniProtKB
[14]
Resource
Comments X-RAY CRYSTALLOGRAPHY (2.2 ANGSTROMS).
Medline ID 97207065
PubMed ID 9054558
Journal Biochemistry
Year 1997
Volume 36
Pages 2531-8
Authors Fan C, Park IS, Walsh CT, Knox JR
Title D-alanine:D-alanine ligase: phosphonate and phosphinate intermediates with wild type and the Y216F mutant.
Related PDB 1iov 1iow
Related UniProtKB P07862
[15]
Resource
Comments
Medline ID
PubMed ID 9083053
Journal J Biol Chem
Year 1997
Volume 272
Pages 9210-4
Authors Park IS, Walsh CT
Title D-Alanyl-D-lactate and D-alanyl-D-alanine synthesis by D-alanyl-D-alanine ligase from vancomycin-resistant Leuconostoc mesenteroides. Effects of a phenylalanine 261 to tyrosine mutation.
Related PDB
Related UniProtKB
[16]
Resource
Comments
Medline ID
PubMed ID 9463376
Journal EMBO J
Year 1998
Volume 17
Pages 977-84
Authors Esser L, Wang CR, Hosaka M, Smagula CS, Sudhof TC, Deisenhofer J
Title Synapsin I is structurally similar to ATP-utilizing enzymes.
Related PDB
Related UniProtKB
[17]
Resource
Comments
Medline ID
PubMed ID 10082373
Journal Protein Sci
Year 1998
Volume 7
Pages 1768-71
Authors Denessiouk KA, Lehtonen JV, Johnson MS
Title Enzyme-mononucleotide interactions: three different folds share common structural elements for ATP recognition.
Related PDB
Related UniProtKB
[18]
Resource
Comments
Medline ID
PubMed ID 9605318
Journal Protein Sci
Year 1998
Volume 7
Pages 1136-46
Authors Denessiouk KA, Lehtonen JV, Korpela T, Johnson MS
Title Two "unrelated" families of ATP-dependent enzymes share extensive structural similarities about their cofactor binding sites.
Related PDB
Related UniProtKB
[19]
Resource
Comments
Medline ID
PubMed ID 9551557
Journal Structure
Year 1998
Volume 6
Pages 363-76
Authors Levdikov VM, Barynin VV, Grebenko AI, Melik-Adamyan WR, Lamzin VS, Wilson KS
Title The structure of SAICAR synthase: an enzyme in the de novo pathway of purine nucleotide biosynthesis.
Related PDB
Related UniProtKB
[20]
Resource
Comments
Medline ID
PubMed ID 10074467
Journal Chem Biol
Year 1999
Volume 6
Pages 177-87
Authors Lessard IA, Walsh CT
Title Mutational analysis of active-site residues of the enterococcal D-ala-D-Ala dipeptidase VanX and comparison with Escherichia coli D-ala-D-Ala ligase and D-ala-D-Ala carboxypeptidase VanY.
Related PDB
Related UniProtKB
[21]
Resource
Comments
Medline ID
PubMed ID 10065705
Journal Protein Eng
Year 1999
Volume 12
Pages 11-4
Authors Kinoshita K, Sadanami K, Kidera A, Go N
Title Structural motif of phosphate-binding site common to various protein superfamilies: all-against-all structural comparison of protein-mononucleotide complexes.
Related PDB
Related UniProtKB
[22]
Resource
Comments
Medline ID
PubMed ID 10903933
Journal Chem Biol
Year 2000
Volume 7
Pages 505-14
Authors Healy VL, Mullins LS, Li X, Hall SE, Raushel FM, Walsh CT
Title D-Ala-D-X ligases: evaluation of D-alanyl phosphate intermediate by MIX, PIX and rapid quench studies.
Related PDB
Related UniProtKB
[23]
Resource
Comments
Medline ID
PubMed ID 10937441
Journal J Mol Microbiol Biotechnol
Year 2000
Volume 2
Pages 321-30
Authors Prevost M, Van Belle D, Tulkens PM, Courvalin P, Van Bambeke F
Title Modeling of Enterococcus faecalis D-alanine:D-alanine ligase: structure-based study of the active site in the wild-type enzyme and in glycopeptide-dependent mutants.
Related PDB
Related UniProtKB
[24]
Resource
Comments
Medline ID
PubMed ID 10713991
Journal Proteins
Year 2000
Volume 38
Pages 310-26
Authors Denessiouk KA, Johnson MS
Title When fold is not important: a common structural framework for adenine and AMP binding in 12 unrelated protein families.
Related PDB
Related UniProtKB
[25]
Resource
Comments X-ray crystallography
Medline ID
PubMed ID 10801495
Journal Structure Fold Des
Year 2000
Volume 8
Pages 463-70
Authors Kuzin AP, Sun T, Jorczak-Baillass J, Healy VL, Walsh CT, Knox JR
Title Enzymes of vancomycin resistance: the structure of D-alanine-D-lactate ligase of naturally resistant Leuconostoc mesenteroides.
Related PDB 1ehi
Related UniProtKB
[26]
Resource
Comments
Medline ID
PubMed ID 11274474
Journal Protein Sci
Year 2001
Volume 10
Pages 836-44
Authors Gholizadeh Y, Prevost M, Van Bambeke F, Casadewall B, Tulkens PM, Courvalin P
Title Sequencing of the ddl gene and modeling of the mutated D-alanine:D-alanine ligase in glycopeptide-dependent strains of Enterococcus faecium.
Related PDB
Related UniProtKB

Comments
This enzyme is homologous to Glutathione synthetase (Swiss-prot;P04425, T00107 in EzCatDB).
This enzyme catalyzes the following reactions (see [7], [8]):
(A) Transfer of phosphate group from ATP to carboxyl oxygen of D-alanine, forming an intermediate, D-alanyl acylphosphate:
(B) Transfer of acyl group from D-alanyl acylphosphate to amine group of the second D-alanine substrate, releasing inorganic phosphate:

Created Updated
2004-08-01 2009-02-26