2fb9 Summary


Crystal structure of the Apo form of D-alanine: D-alanine ligase (Ddl) from Thermus caldophilus: a basis for the substrate-induced conformational changes

The structure was published by Lee, J.H., Na, Y., Song, H.E., et al., Kang, G.B., Lee, D.S., and Eom, S.H., in 2006 in a paper entitled "Crystal structure of the apo form of D-alanine: D-alanine ligase (Ddl) from Thermus caldophilus: A basis for the substrate-induced conformational changes" (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 1.9 Å and deposited in 2005.

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

The PDB entry contains the structure of D-alanine:D-alanine ligase. This molecule has the UniProt identifier Q3T920 (Q3T920_THECA)search. The sample contained 322 residues which is 100% of the natural sequence. Out of 322 residues 322 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 Q3T920 (1-319) (Q3T920_THECA)search Thermus caldophilussearch 100% 322 100%

This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
Q3T920 (1 - 319) D-alanine:D-alanine ligase Thermus caldophilus

Chain Structural classification (CATH) Sequence family (Pfam)
A (Q3T920) Rossmann foldsearch, ATP-grasp fold, B domainsearch, ATP-grasp fold, A domainsearch 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 (Q3T920) cytoplasmsearch ATP bindingsearch D-alanine-D-alanine ligase activitysearch metal ion bindingsearch catalytic activitysearch magnesium ion bindingsearch manganese ion bindingsearch nucleotide bindingsearch ligase activitysearch peptidoglycan biosynthetic processsearch regulation of cell shapesearch

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