3rfc Summary


Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ADP

The structure was published by Doan, T.T.N., Kim, J.K., Ahn, Y.J., and Kang, L.W., in in a paper entitled "Crystal structure of D-alanine-D-alanine ligase A from Xanthomonas oryzae pathovar oryzae with ADP" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.1 Å and deposited in 2011.

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

The PDB entry contains the structure of D-alanine--D-alanine ligase 1. This molecule has the UniProt identifier Q2P8P8 (Q2P8P8_XANOM)search. The sample contained 384 residues which is 100% of the natural sequence. Out of 384 residues 344 were observed and are deposited in the PDB.

It also contains one or more heterogenic compounds (e.g., ligands, co-factors, ions, modified amino acids, etc.); see here for a complete list.

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 1 Q2P8P8 (1-367) (Q2P8P8_XANOM)search Xanthomonas oryzae pv. oryzae MAFF 311018search 100% 384 89%

This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
Q2P8P8 (1 - 367) D-alanine--D-alanine ligase 1 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) ATP bindingsearch D-alanine-D-alanine ligase activitysearch ligase activitysearch catalytic activitysearch nucleotide bindingsearch manganese ion bindingsearch metal ion 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