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
15422
15570
57416
16761
26078
16576
57822
PubChem 888
5957
71080
7311725
6022
1004
22486802
20112020
5460362
6992112
1ehiA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1ehiB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1iovA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1iowA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2dlnA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1ehiA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_MG Unbound Unbound Bound:ADP Unbound Unbound Unbound Analogue:PHY
1ehiB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1iovA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:3x_MG Unbound Unbound Bound:ADP Unbound Unbound Unbound Analogue:POB
1iowA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_MG Unbound Unbound Bound:ADP Unbound Unbound Unbound Analogue:PHY
2dlnA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Bound:2x_MG Unbound Unbound Bound:ADP Unbound Unbound Unbound Analogue:PHY
1ehiA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1ehiB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1iovA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
1iowA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain Unbound Unbound Unbound Unbound Unbound Unbound Unbound Unbound
2dlnA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 16
1ehiB01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 416
1iovA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 15
1iowA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 15
2dlnA01 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain GLU 15
1ehiA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 260;;ARG 301 ASP 303(Magnesium-1);GLU 316(Magnesium-1 & -2);ASN 318(Magnesium-2) GLY 322
1ehiB02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain ; ;ARG 701 ASP 703(Magnesium-1);GLU 716(Magnesium-1 & -2);ASN 718(Magnesium-2) GLY 722 invisible 645-666
1iovA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 215;TYR 216;ARG 255 ASP 257(Magnesium-1);GLU 270(Magnesium-1 & -2);ASN 272(Magnesium-2) GLY 276
1iowA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 215;;ARG 255 ASP 257(Magnesium-1);GLU 270(Magnesium-1 & -2);ASN 272(Magnesium-2) GLY 276 mutant Y216F
2dlnA02 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain LYS 215;TYR 216;ARG 255 ASP 257(Magnesium-1);GLU 270(Magnesium-1 & -2);ASN 272(Magnesium-2) GLY 276
1ehiA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 186
1ehiB03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 586
1iovA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 150
1iowA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain SER 150
2dlnA03 Pdbj logo s Rasmollogo id Rasmollogo chain Mmcif id Mmcif chain 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