3e5n Summary


Crystal strucutre of D-alanine-D-alanine ligase from Xanthomonas oryzae pv. oryzae KACC10331

The structure was published by Doan, T.N.T., Kim, J.K., Kim, H.S., et al., Kim, J.G., Lee, B.M., and Kang, L.W., in in a paper entitled "Crystal strucutre of D-alanine-D-alanine ligase from Xanthomonas oryzae pv. oryzae KACC10331" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.0 Å and deposited in 2008.

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

The PDB entry contains the structure of D-alanine-D-alanine ligase A. This molecule has the UniProt identifier Q2P8P8 (Q2P8P8_XANOM)search. The sample contained 386 residues which is 100% of the natural sequence. Out of 386 residues 340 were observed and are deposited in the PDB.

The molecule most likely forms homodimers.

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 A Q2P8P8 (1-367) (Q2P8P8_XANOM)search Xanthomonas oryzae pv. oryzae MAFF 311018search 100% 386 88%

This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
Q2P8P8 (1 - 367) D-alanine-D-alanine ligase A Xanthomonas oryzae pv. oryzae MAFF 311018

Chain Sequence family (Pfam)
A (Q2P8P8) PF01820: D-ala D-ala ligase N-terminussearch, PF07478: D-ala D-ala ligase C-terminussearch

Chain ID Molecular function (GO) Cellular component (GO) Biological process (GO)
A (Q2P8P8) ligase activitysearch manganese ion bindingsearch ATP bindingsearch metal ion bindingsearch catalytic activitysearch D-alanine-D-alanine ligase activitysearch nucleotide bindingsearch magnesium ion bindingsearch cytoplasmsearch peptidoglycan biosynthetic processsearch regulation of cell shapesearch cell wall organizationsearch

Chain InterPro annotation
A 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