2pvp Summary

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Crystal structure of D-Alanine-D-Alanine Ligase from Helicobacter pylori

The structure was published by Wu, D., Zhang, L., Kong, Y., et al., Ding, J., Jiang, H., and Shen, X., in 2008 in a paper entitled "Enzymatic characterization and crystal structure analysis of the D-alanine-D-alanine ligase from Helicobacter pylori." (abstract).

This crystal structure was determined using X-ray diffraction at a resolution of 2.4 Å and deposited in 2007.

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 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 Q2N4T5 (1-347) (Q2N4T5_HELPX)search Helicobacter pylorisearch 100% 367 89%
B D-alanine-D-alanine ligase Q2N4T5 (1-347) (Q2N4T5_HELPX)search Helicobacter pylorisearch 100% 367 89%


This entry contains 1 unique UniProt protein:

UniProt accession Name Organism PDB
Q2N4T5 (1 - 347) D-alanine-D-alanine ligase Helicobacter pylori SS1

Chain Structural classification (CATH) Sequence family (Pfam)
A, B (Q2N4T5) ATP-grasp fold, A domainsearch PF01820: D-ala D-ala ligase N-terminussearch, PF07478: D-ala D-ala ligase C-terminussearch

Chain ID Molecular function (GO) Biological process (GO) Cellular component (GO)
A, B (Q2N4T5) metal ion bindingsearch magnesium ion bindingsearch ATP bindingsearch nucleotide bindingsearch catalytic activitysearch D-alanine-D-alanine ligase activitysearch manganese ion bindingsearch ligase activitysearch regulation of cell shapesearch cell wall organizationsearch peptidoglycan biosynthetic processsearch 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