_EC 6.3.2.4 D-alanine--D-alanine ligase. 33 PDB entries  
EC 6.-.-.- Ligases. [1,580 PDB entries]
EC 6.3.-.- Forming carbon-nitrogen bonds. [793 PDB entries]
EC 6.3.2.- Acid--amino-acid ligases (peptide synthases). [329 PDB entries]
EC 6.3.2.4 D-alanine--D-alanine ligase. [33 PDB entries]    
1ehi

Pathway: Peptidoglycan Biosynthesis (Part 1)
Reaction: Atp + 2 D-alanine = adp + phosphate + D-alanyl-D-alanine.
 


ATP
+
2 × D-alanine
=
ADP
+
phosphate
+
D-alanyl-D-alanine
Molecule diagrams generated from .mol files obtained from the KEGG ftp site.

Other name(s): Alanine:alanine ligase (ADP-forming). Alanylalanine synthetase. D-Ala-D-Ala synthetase. D-alanyl-D-alanine synthetase. D-alanylalanine synthetase.
Comments: Involved with Ec 6.3.2.7 or Ec 6.3.2.13, Ec 6.3.2.8, Ec 6.3.2.9 and Ec 6.3.2.10 in the synthesis of a cell-wall peptide.
Links:   [IntEnz]   [ExPASy]   [KEGG]  

There are 33 PDB entries in enzyme class E.C.6.3.2.4

  PDB code Protein
1ehi
D-alanine:d-lactate ligase (lmddl2) of vancomycin-resistant leuconostoc mesenteroides
Source: Leuconostoc mesenteroides. Organism_taxid: 1245. Atcc: 8293. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B (360 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
1iov
Complex of d-ala:d-ala ligase with adp and a phosphoryl phosphonate
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: enzyme provided by c.T. Walsh, harvard med school. See zawadzke et al. Biochem. 30, p. 1673, 1991.
Chain: A (306 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
Bound ligand:   Het Group ADP corresponds to enzyme product ADP
1iow
Complex of y216f d-ala:d-ala ligase with adp and a phosphoryl phosphinate
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli str. K12 substr. W3110. Expression_system_taxid: 316407. Other_details: enzyme provided by c.T. Walsh, harvard med school. See shi and walsh, biochem. 34, p. 2768, 1995.
Chain: A (306 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
Bound ligand:   Het Group ADP corresponds to enzyme product ADP
2dln
Vancomycin resistance: structure of d-alanine:d-alanine ligase at 2.3 angstroms resolution
Source: Escherichia coli. Organism_taxid: 562
Chain: A (306 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
Bound ligand:   Het Group ADP corresponds to enzyme product ADP
2fb9
Crystal structure of the apo form of d-alanine: d-alanine li from thermus caldophilus: a basis for the substrate-induced conformational changes
Source: Thermus caldophilus. Organism_taxid: 272. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chain: A (322 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
2i80
Allosteric inhibition of staphylococcus aureus d-alanine:d-a ligase revealed by crystallographic studies
Source: Staphylococcus aureus. Organism_taxid: 1280. Strain: strain col. Gene: ddl, ddla. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B (345 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
2i87
Allosteric inhibition of staphylococcus aureus d-alanine:d-a ligase revealed by crystallographic studies
Source: Staphylococcus aureus subsp. Aureus. Organism_taxid: 93062. Strain: col. Gene: ddl. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B (345 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
2i8c
Allosteric inhibition of staphylococcus aureus d-alanine:d-a ligase revealed by crystallographic studies
Source: Staphylococcus aureus subsp. Aureus. Organism_taxid: 93062. Strain: col. Gene: ddl. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B (345 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
Bound ligand:   Het Group ADP corresponds to enzyme product ADP
2pvp
Crystal structure of d-alanine-d-alanine ligase from helicob pylori
Source: Helicobacter pylori. Organism_taxid: 102617. Strain: ss1. Gene: ddl. Expressed in: escherichia coli bl21. Expression_system_taxid: 511693.
Chains: A, B (329 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
2yzg
Crystal structure of d-ala:d-ala ligase from thermus thermop
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C (319 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
2yzm
Structure of d-alanine:d-alanine ligase with substrate from thermophilus hb8
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C (319 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
Bound ligand:   Het Group DAL corresponds to enzyme reactant D-alanine
2yzn
Crystal structure of d-alanine:d-alanine ligase with amppnp thermus thermophilus hb8.
Source: Thermus thermophilus. Organism_taxid: 300852. Strain: hb8. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C (317 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
Bound ligand:   Het Group ANP is 81.25% similar to enzyme product ADP
2zdg
Crystal structure of d-alanine:d-alanine ligase with adp from thermus thermophius hb8
Source: Thermus thermophilus. Strain: hb8. Expressed in: escherichia coli.
Chains: A, B, C, D (302 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
Bound ligand:   Het Group ADP corresponds to enzyme product ADP
2zdh
Crystal structure of d-alanine:d-alanine ligase with adp and d-alanine from thermus thermophius hb8
Source: Thermus thermophilus. Strain: hb8. Expressed in: escherichia coli.
Chains: A, B, C, D (319 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
Bound ligands:   Het Group DAL corresponds to enzyme reactant D-alanine
  Het Group ADP corresponds to enzyme product ADP
2zdq
Crystal structure of d-alanine:d-alanine ligase with atp and d-alanine:d-alanine from thermus thermophius hb8
Source: Thermus thermophilus. Strain: hb8. Expressed in: escherichia coli.
Chains: A, B (319 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
Bound ligands:   Het Group ATP corresponds to enzyme reactant ATP
  Het Group DAL corresponds to enzyme reactant D-alanine
3e5n
Crystal strucutre of d-alanine-d-alanine ligase from xanthomonas oryzae pv. Oryzae kacc10331
Source: Xanthomonas oryzae pv. Oryzae. Organism_taxid: 342109. Strain: maff 311018. Gene: xoo0324. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chain: A (340 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
3i12
The crystal structure of the d-alanyl-alanine synthetase a f salmonella enterica subsp. Enterica serovar typhimurium str
Source: Salmonella typhimurium. Organism_taxid: 90371. Strain: lt2'. Gene: ddla, stm0380. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D (360 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
Bound ligand:   Het Group ADP corresponds to enzyme product ADP
3k3p
Crystal structure of the apo form of d-alanine:d-alanine lig from streptococcus mutans
Source: Streptococcus mutans. Organism_taxid: 1309. Strain: ua159. Gene: ddl. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B (317 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
3lwb
Crystal structure of apo d-alanine:d-alanine ligase (ddl) fr mycobacterium tuberculosis
Source: Mycobacterium tuberculosis. Organism_taxid: 1773. Gene: ddl, ddla, mt3059, mtcy349.06, rv2981c. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B (323 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
3n8d
Crystal structure of staphylococcus aureus vrsa-9 d-ala:d-al
Source: Staphylococcus aureus. Organism_taxid: 1280. Strain: vrsa-9. Gene: ddl. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Chains: A, B (329 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
Bound ligand:   Het Group ANP is 81.00% similar to enzyme product ADP
3q1k
The crystal structure of the d-alanyl-alanine synthetase a f salmonella enterica typhimurium complexed with adp
Source: Salmonella enterica subsp. Enterica se typhimurium. Organism_taxid: 90371. Strain: lt2. Gene: ddl, ddla, stm0380. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D (357 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
Bound ligands:   Het Group GOL is 50.00% similar to enzyme reactant D-alanine
  Het Group ADP corresponds to enzyme product ADP
3r23
Crystal structure of d-alanine--d-alanine ligase from bacill anthracis
Source: Bacillus anthracis. Anthrax,anthrax bacterium. Organism_taxid: 198094. Strain: ames. Gene: bas2435, ba_2610, ddl, ddlb, gbaa_2610. Expressed in: escherichia coli. Expression_system_taxid: 511693.
Chains: A, B (304 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
Bound ligand:   Het Group EDO is 42.86% similar to enzyme reactant D-alanine
3r5f
Crystal structure of d-alanine-d-alnine ligase from xanthomo pv. Oryzae with atp
Source: Xanthomonas oryzae pv. Oryzae. Organism_taxid: 291331. Strain: kacc10331. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chain: A (343 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
Bound ligand:   Het Group ATP corresponds to enzyme reactant ATP
3r5x
Crystal structure of d-alanine--d-alanine ligase from bacill anthracis complexed with atp
Source: Bacillus anthracis. Anthrax,anthrax bacterium. Organism_taxid: 1392. Strain: ames. Gene: bas2435, ba_2610, ddl, ddlb, gbaa_2610. Expressed in: escherichia coli. Expression_system_taxid: 511693.
Chains: A, B, C, D (302 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
Bound ligands:   Het Group ATP corresponds to enzyme reactant ATP
  Het Group ACY is 66.67% similar to enzyme reactant D-alanine
3rfc
Crystal structure of d-alanine-d-alanine ligase a from xanth oryzae pathovar oryzae with adp
Source: Xanthomonas oryzae pv. Oryzae. Organism_taxid: 342109. Strain: maff 311018. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chain: A (344 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
Bound ligand:   Het Group ADP corresponds to enzyme product ADP
3tqt
Structure of the d-alanine-d-alanine ligase from coxiella bu
Source: Coxiella burnetii. Organism_taxid: 227377. Strain: rsa493. Gene: ddl, cbu_1338. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Chains: A, B (348 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
3v4z
D-alanine--d-alanine ligase from yersinia pestis
Source: Yersinia pestis. Organism_taxid: 214092. Strain: co92. Gene: ddl, ddlb, y3624, ypo0557, yp_3627. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B (293 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
4eg0
Crystal structure of d-alanine--d-alanine ligase from burkho ambifaria
Source: Burkholderia ambifaria. Organism_taxid: 398577. Strain: mc40-6. Gene: ddl, bammc406_0490. Expressed in: escherichia coli. Expression_system_taxid: 562
Chains: A, B (288 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
Bound ligand:   Het Group EDO is 42.86% similar to enzyme reactant D-alanine
4egj
Crystal structure of d-alanine-d-alanine ligase from burkhol xenovorans
Source: Burkholderia xenovorans. Organism_taxid: 266265. Strain: lb400. Gene: bxeno_a3907, bxe_a0488, ddl. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Chains: A, B, C, D (285 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
4egq
Crystal structure of d-alanine-d-alanine ligase b from burkh pseudomallei
Source: Burkholderia pseudomallei. Organism_taxid: 320372. Strain: 1710b. Gene: burps1710b_3542, ddl. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B, C, D (288 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
4fu0
Crystal structure of vang d-ala:d-ser ligase from enterococc faecalis
Source: Enterococcus faecalis. Organism_taxid: 1351. Strain: bm4518. Gene: ddl7, vang. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chains: A, B (343 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
Bound ligand:   Het Group ADP corresponds to enzyme product ADP
4l1k
Crystal structure of d-alanine-d-alnine ligase from xanthomo pv. Oryzae with amppnp
Source: Xanthomonas oryzae pv. Oryzae. Organism_taxid: 291331. Strain: kacc10331. Gene: ddl, ddla, xoo0352. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chain: A (340 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
Bound ligand:   Het Group ANP is 81.25% similar to enzyme product ADP
4me6
Crystal structure of d-alanine-d-alanine ligase a from xanth oryzae pathovar oryzae with adp
Source: Xanthomonas oryzae pv. Oryzae. Organism_taxid: 291331. Strain: kacc10331. Gene: ddla, ddl, xoo0352. Expressed in: escherichia coli. Expression_system_taxid: 562.
Chain: A (337 residues) CATH domains: 3.40.50.20 3.30.470.20 3.30.1490.20
Bound ligand:   Het Group ADP corresponds to enzyme product ADP