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Transport protein
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PDB id
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1hqb
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Contents |
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* Residue conservation analysis
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Enzyme class:
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E.C.6.1.1.13
- D-alanine--poly(phosphoribitol) ligase.
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Reaction:
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ATP + D-alanine + poly(ribitol phosphate) = AMP + diphosphate + O-D- alanyl-poly(ribitol phosphate)
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ATP
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+
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D-alanine
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+
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poly(ribitol phosphate)
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=
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AMP
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+
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diphosphate
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+
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O-D- alanyl-poly(ribitol phosphate)
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Molecule diagrams generated from .mol files obtained from the
KEGG ftp site
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Gene Ontology (GO) functional annotation
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Biological process
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cell wall organization
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3 terms
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Biochemical function
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nucleotide binding
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6 terms
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DOI no:
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Biochemistry
40:7964-7972
(2001)
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PubMed id:
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Biosynthesis of D-alanyl-lipoteichoic acid: the tertiary structure of apo-D-alanyl carrier protein.
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B.F.Volkman,
Q.Zhang,
D.V.Debabov,
E.Rivera,
G.C.Kresheck,
F.C.Neuhaus.
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ABSTRACT
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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.
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Literature references that cite this PDB file's key reference
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PubMed id
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Reference
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H.Barreteau,
A.Kovac,
A.Boniface,
M.Sova,
S.Gobec,
and
D.Blanot
(2008).
Cytoplasmic steps of peptidoglycan biosynthesis.
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FEMS Microbiol Rev, 32,
168-207.
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H.Yonus,
P.Neumann,
S.Zimmermann,
J.J.May,
M.A.Marahiel,
and
M.T.Stubbs
(2008).
Crystal structure of DltA. Implications for the reaction mechanism of non-ribosomal peptide synthetase adenylation domains.
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J Biol Chem, 283,
32484-32491.
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PDB codes:
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K.J.Weissman,
and
R.Müller
(2008).
Protein-protein interactions in multienzyme megasynthetases.
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Chembiochem, 9,
826-848.
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A.C.Mercer,
and
M.D.Burkart
(2007).
The ubiquitous carrier protein--a window to metabolite biosynthesis.
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Nat Prod Rep, 24,
750-773.
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D.M.Byers,
and
H.Gong
(2007).
Acyl carrier protein: structure-function relationships in a conserved multifunctional protein family.
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Biochem Cell Biol, 85,
649-662.
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M.Perea Vélez,
T.L.Verhoeven,
C.Draing,
S.Von Aulock,
M.Pfitzenmaier,
A.Geyer,
I.Lambrichts,
C.Grangette,
B.Pot,
J.Vanderleyden,
and
S.C.De Keersmaecker
(2007).
Functional analysis of D-alanylation of lipoteichoic acid in the probiotic strain Lactobacillus rhamnosus GG.
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Appl Environ Microbiol, 73,
3595-3604.
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V.Y.Alekseyev,
C.W.Liu,
D.E.Cane,
J.D.Puglisi,
and
C.Khosla
(2007).
Solution structure and proposed domain domain recognition interface of an acyl carrier protein domain from a modular polyketide synthase.
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Protein Sci, 16,
2093-2107.
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PDB codes:
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E.J.Drake,
D.A.Nicolai,
and
A.M.Gulick
(2006).
Structure of the EntB multidomain nonribosomal peptide synthetase and functional analysis of its interaction with the EntE adenylation domain.
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Chem Biol, 13,
409-419.
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PDB code:
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M.A.Johnson,
W.Peti,
T.Herrmann,
I.A.Wilson,
and
K.Wüthrich
(2006).
Solution structure of Asl1650, an acyl carrier protein from Anabaena sp. PCC 7120 with a variant phosphopantetheinylation-site sequence.
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Protein Sci, 15,
1030-1041.
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PDB codes:
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S.Srisailam,
J.A.Lukin,
A.Yee,
A.Semesi,
and
C.H.Arrowsmith
(2006).
Solution structure of acyl carrier protein from Nitrosomonas europaea.
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Proteins, 64,
800-803.
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PDB code:
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S.W.White,
J.Zheng,
Y.M.Zhang,
and
Rock
(2005).
The structural biology of type II fatty acid biosynthesis.
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| |
Annu Rev Biochem, 74,
791-831.
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F.C.Neuhaus,
and
J.Baddiley
(2003).
A continuum of anionic charge: structures and functions of D-alanyl-teichoic acids in gram-positive bacteria.
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| |
Microbiol Mol Biol Rev, 67,
686-723.
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The most recent references are shown first.
Citation data come partly from CiteXplore and partly
from an automated harvesting procedure. Note that this is likely to be
only a partial list as not all journals are covered by
either method. However, we are continually building up the citation data
so more and more references will be included with time.
Where a reference describes a PDB structure, the PDB
codes are
shown on the right.
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Links
