3v4z Summary


D-alanine--D-alanine ligase from Yersinia pestis

A publication describing this structure is not available. The depositing authors are Osipiuk, J.search; Nocek, B.search; Mulligan, R.search; Papazisi, L.search; Anderson, W.F.search; Joachimiak, A.search; Center for Structural Genomics of Infectious Diseases (CSGID)search

This crystal structure was determined using X-ray diffraction at a resolution of 2.69 Å and deposited in 2011.

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.

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 Q8ZIE7 (1-306) (DDL_YERPE)search Yersinia pestissearch 100% 309 94%
B D-alanine--D-alanine ligase Q8ZIE7 (1-306) (DDL_YERPE)search Yersinia pestissearch 100% 309 94%

This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
Q8ZIE7 (1 - 306) D-alanine--D-alanine ligase Yersinia pestis CO92

Chain Sequence family (Pfam)
A, B (Q8ZIE7) PF01820: D-ala D-ala ligase N-terminussearch, PF07478: D-ala D-ala ligase C-terminussearch

Chain ID Biological process (GO) Molecular function (GO) Cellular component (GO)
A, B (Q8ZIE7) peptidoglycan biosynthetic processsearch cell wall organizationsearch regulation of cell shapesearch nucleotide bindingsearch metal ion bindingsearch ATP bindingsearch D-alanine-D-alanine ligase activitysearch catalytic activitysearch ligase activitysearch manganese ion bindingsearch magnesium ion bindingsearch cytoplasmsearch

Chain InterPro annotation
A, B 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