1DV5

TERTIARY STRUCTURE OF APO-D-ALANYL CARRIER PROTEIN


Experimental Data Snapshot

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 30 
  • Selection Criteria: target function 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history


Literature

Biosynthesis of D-alanyl-lipoteichoic acid: the tertiary structure of apo-D-alanyl carrier protein.

Volkman, B.F.Zhang, Q.Debabov, D.V.Rivera, E.Kresheck, G.C.Neuhaus, F.C.

(2001) Biochemistry 40: 7964-7972

  • Primary Citation of Related Structures:  
    1DV5, 1HQB

  • PubMed Abstract: 
  • The D-alanylation of lipoteichoic acid (LTA) allows the Gram-positive organism to modulate its surface charge, regulate ligand binding, and control the electromechanical properties of the cell wall. The incorporation of D-alanine into LTA requires the D-alanine:D-alanyl carrier protein ligase (AMP-forming) (Dcl) and the carrier protein (Dcp) ...

    The D-alanylation of lipoteichoic acid (LTA) allows the Gram-positive organism to modulate its surface charge, regulate ligand binding, and control the electromechanical properties of the cell wall. The incorporation of D-alanine into LTA requires the D-alanine:D-alanyl carrier protein ligase (AMP-forming) (Dcl) and the carrier protein (Dcp). The high-resolution solution structure of the 81-residue (8.9 kDa) Dcp has been determined by multidimensional heteronuclear NMR. An ensemble of 30 structures was calculated using the torsion angle dynamics approach of DYANA. These calculations utilized 3288 NOEs containing 1582 unique nontrivial NOE distance constraints. Superposition of residues 4-81 on the mean structure yields average atomic rmsd values of 0.43 +/- 0.08 and 0.86 +/- 0.09 A for backbone and non-hydrogen atoms, respectively. The solution structure is composed of three alpha-helices in a bundle with additional short 3(10)- and alpha-helices in intervening loops. Comparisons of the three-dimensional structure with the acyl carrier proteins involved in fatty acid, polyketide, and nonribosomal peptide syntheses support the conclusion that Dcp is a homologue in this family. While there is conservation of the three-helix bundle fold, Dcp has a higher enthalpy of unfolding and no apparent divalent metal binding site(s), features that distinguish it from the fatty acid synthase acyl carrier protein of Escherichia coli. This three-dimensional structure also provides insights into the D-alanine ligation site recognized by Dcl, as well as the site which may bind the poly(glycerophosphate) acceptor moiety of membrane-associated LTA.


    Related Citations: 
    • The D-Alanyl Carrier Protein in Lactobacillus casei: Cloning, Sequencing and Expression of dltC
      Debabov, D.V., Heaton, M.P., Zhang, Q., Stewart, K.D., Lambalot, R.H., Neuhaus, F.C.
      (1996) J Bacteriol 178: 3869

    Organizational Affiliation

    Department of Biochemistry and National Magnetic Resonance Facility at Madison, University of Wisconsin-Madison, Madison, Wisconsin 53706-1544, USA. bvolkman@mcw.edu



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
APO-D-ALANYL CARRIER PROTEINA80Lacticaseibacillus caseiMutation(s): 0 
UniProt
Find proteins for P55153 (Lactobacillus rhamnosus)
Explore P55153 
Go to UniProtKB:  P55153
Protein Feature View
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: SOLUTION NMR
  • Conformers Calculated: 50 
  • Conformers Submitted: 30 
  • Selection Criteria: target function 
  • OLDERADO: 1DV5 Olderado

Structure Validation

View Full Validation Report




Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2001-08-01
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2019-11-06
    Changes: Atomic model, Data collection, Database references, Derived calculations