4egj Summary

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Crystal structure of D-alanine-D-alanine ligase from Burkholderia xenovorans

The structure was published by Baugh, L., Gallagher, L.A., Patrapuvich, R., et al., Stewart, L.J., Manoil, C., and Van Voorhis, W.C., in 2013 in a paper entitled "Combining functional and structural genomics to sample the essential Burkholderia structome." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.3 Å and deposited in 2012.

The experimental data on which the structure is based was also deposited.

This PDB entry contains multiple copies of the structure of D-alanine--D-alanine ligase.

The molecule has more than one probable quaternary state observed. For more details see the quaternary structure page.

The following tables show cross-reference information to other databases (to obtain a list of all PDB entries sharing the same property or classification, click on the magnifying glass icon):


Chain Name UniProt Name of source organism % of UniProt sequence present in the sample Residues in the sample molecules % of residues observed
A D-alanine--D-alanine ligase Q13TZ4 (1-313) (DDL_BURXL)search Burkholderia xenovorans LB400search 100% 334 85%
B D-alanine--D-alanine ligase Q13TZ4 (1-313) (DDL_BURXL)search Burkholderia xenovorans LB400search 100% 334 85%
C D-alanine--D-alanine ligase Q13TZ4 (1-313) (DDL_BURXL)search Burkholderia xenovorans LB400search 100% 334 85%
D D-alanine--D-alanine ligase Q13TZ4 (1-313) (DDL_BURXL)search Burkholderia xenovorans LB400search 100% 334 85%


This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
Q13TZ4 (1 - 313) D-alanine--D-alanine ligase Burkholderia xenovorans LB400

Chain Sequence family (Pfam)
A, B, C, D (Q13TZ4) PF01820: D-ala D-ala ligase N-terminussearch, PF07478: D-ala D-ala ligase C-terminussearch

Chain ID Cellular component (GO) Molecular function (GO) Biological process (GO)
A, B, C, D (Q13TZ4) cytoplasmsearch magnesium ion bindingsearch ATP bindingsearch metal ion bindingsearch D-alanine-D-alanine ligase activitysearch catalytic activitysearch ligase activitysearch nucleotide bindingsearch manganese ion bindingsearch peptidoglycan biosynthetic processsearch regulation of cell shapesearch cell wall organizationsearch

Chain InterPro annotation
A, B, C, D D-alanine--D-alanine ligase/VANA/B/C, conserved sitesearch D-alanine--D-alanine ligasesearch D-alanine--D-alanine ligase, C-terminalsearch D-alanine--D-alanine ligase, N-terminal domainsearch ATP-grasp foldsearch ATP-grasp fold, subdomain 1search ATP-grasp fold, subdomain 2search Pre-ATP-grasp domainsearch