 |
PDBsum entry 1acp
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
Fatty acid synthesis protein
|
PDB id
|
|
|
|
1acp
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
Contents |
 |
|
|
|
|
|
|
|
|
* Residue conservation analysis
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
|
|
|
|
|
|
| |
|
|
Proteins
8:377-385
(1990)
|
|
PubMed id:
|
|
|
|
|
|
| |
|
Refinement of the NMR structures for acyl carrier protein with scalar coupling data.
|
|
Y.Kim,
J.H.Prestegard.
|
|
|
|
|
| |
ABSTRACT
|
|
|
|
| |
|
|
Structure determination of small proteins using NMR data is most commonly
pursued by combining NOE derived distance constraints with inherent constraints
based on chemical bonding. Ideally, one would make use of a variety of
experimental observations, not just distance constraints. Here, coupling
constant constraints have been added to molecular mechanics and molecular
dynamics protocols for structure determination in the form of a psuedoenergy
function that is minimized in a search for an optimum molecular conformation.
Application is made to refinement of a structure for a 77 amino acid protein
involved in fatty acid synthesis, Escherichia coli acyl carrier protein (ACP).
54 3JHN alpha coupling constants, 12 coupling constants for stereospecifically
assigned side chain protons, and 450 NOE distance constraints were used to
calculate the 3-D structure of ACP. A three-step protocol for a molecular
dynamics calculation is described, in analogy to the protocol previously used in
molecular mechanics calculations. The structures calculated with the molecular
mechanics approach and the molecular dynamics approach using a rigid model for
the protein show similar molecular energies and similar agreement with
experimental distance and coupling constant constraints. The molecular dynamics
approach shows some advantage in overcoming local minimum problems, but only
when a two-state averaging model for the protein was used, did molecular
energies drop significantly.
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
 |
 |
 |
|
Literature references that cite this PDB file's key reference
|
|
|
| |
PubMed id
|
|
Reference
|
|
|
|
|
|
A.W.Barb,
J.R.Cort,
J.Seetharaman,
S.Lew,
H.W.Lee,
T.Acton,
R.Xiao,
M.A.Kennedy,
L.Tong,
G.T.Montelione,
and
J.H.Prestegard
(2011).
Structures of domains I and IV from YbbR are representative of a widely distributed protein family.
|
| |
Protein Sci,
20,
396-405.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
A.Koglin,
and
C.T.Walsh
(2009).
Structural insights into nonribosomal peptide enzymatic assembly lines.
|
| |
Nat Prod Rep,
26,
987.
|
|
|
|
|
|
|
B.N.Wu,
Y.M.Zhang,
C.O.Rock,
and
J.J.Zheng
(2009).
Structural modification of acyl carrier protein by butyryl group.
|
| |
Protein Sci,
18,
240-246.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
J.L.Meier,
and
M.D.Burkart
(2009).
The chemical biology of modular biosynthetic enzymes.
|
| |
Chem Soc Rev,
38,
2012-2045.
|
|
|
|
|
|
|
E.Płoskoń,
C.J.Arthur,
S.E.Evans,
C.Williams,
J.Crosby,
T.J.Simpson,
and
M.P.Crump
(2008).
A mammalian type I fatty acid synthase acyl carrier protein domain does not sequester acyl chains.
|
| |
J Biol Chem,
283,
518-528.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
A.H.Williams,
and
C.R.Raetz
(2007).
Structural basis for the acyl chain selectivity and mechanism of UDP-N-acetylglucosamine acyltransferase.
|
| |
Proc Natl Acad Sci U S A,
104,
13543-13550.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
A.Misra,
S.K.Sharma,
N.Surolia,
and
A.Surolia
(2007).
Self-acylation properties of type II fatty acid biosynthesis acyl carrier protein.
|
| |
Chem Biol,
14,
775-783.
|
|
|
|
|
|
|
D.M.Byers,
and
H.Gong
(2007).
Acyl carrier protein: structure-function relationships in a conserved multifunctional protein family.
|
| |
Biochem Cell Biol,
85,
649-662.
|
|
|
|
|
|
|
H.Donato,
N.I.Krupenko,
Y.Tsybovsky,
and
S.A.Krupenko
(2007).
10-formyltetrahydrofolate dehydrogenase requires a 4'-phosphopantetheine prosthetic group for catalysis.
|
| |
J Biol Chem,
282,
34159-34166.
|
|
|
|
|
|
|
R.P.Barnwal,
A.K.Rout,
K.V.Chary,
and
H.S.Atreya
(2007).
Rapid measurement of 3J(H N-H alpha) and 3J(N-H beta) coupling constants in polypeptides.
|
| |
J Biomol NMR,
39,
259-263.
|
|
|
|
|
|
|
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.
|
| |
Chem Biol,
13,
409-419.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
G.A.Zornetzer,
B.G.Fox,
and
J.L.Markley
(2006).
Solution structures of spinach acyl carrier protein with decanoate and stearate.
|
| |
Biochemistry,
45,
5217-5227.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
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.
|
| |
Protein Sci,
15,
1030-1041.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
S.Chattopadhyay,
N.K.Sinha,
S.Banerjee,
D.Roy,
D.Chattopadhyay,
and
S.Roy
(2006).
Small cationic protein from a marine turtle has beta-defensin-like fold and antibacterial and antiviral activity.
|
| |
Proteins,
64,
524-531.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.Thomas,
and
J.E.Cronan
(2005).
The enigmatic acyl carrier protein phosphodiesterase of Escherichia coli: genetic and enzymological characterization.
|
| |
J Biol Chem,
280,
34675-34683.
|
|
|
|
|
|
|
S.B.Nabuurs,
E.Krieger,
C.A.Spronk,
A.J.Nederveen,
G.Vriend,
and
G.W.Vuister
(2005).
Definition of a new information-based per-residue quality parameter.
|
| |
J Biomol NMR,
33,
123-134.
|
|
|
|
|
|
|
S.W.White,
J.Zheng,
Y.M.Zhang,
and
Rock
(2005).
The structural biology of type II fatty acid biosynthesis.
|
| |
Annu Rev Biochem,
74,
791-831.
|
|
|
|
|
|
|
M.M.Rosenblatt,
J.Wang,
and
K.S.Suslick
(2003).
De novo designed cyclic-peptide heme complexes.
|
| |
Proc Natl Acad Sci U S A,
100,
13140-13145.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
P.Ruchala,
B.Picur,
M.Lisowski,
T.Cierpicki,
Z.Wieczorek,
and
I.Z.Siemion
(2003).
Synthesis, conformation, and immunosuppressive activity of CLX and its analogues.
|
| |
Biopolymers,
70,
497-511.
|
|
|
|
|
|
|
A.Roujeinikova,
C.Baldock,
W.J.Simon,
J.Gilroy,
P.J.Baker,
A.R.Stuitje,
D.W.Rice,
J.B.Rafferty,
and
A.R.Slabas
(2002).
Crystallization and preliminary X-ray crystallographic studies on acyl-(acyl carrier protein) from Escherichia coli.
|
| |
Acta Crystallogr D Biol Crystallogr,
58,
330-332.
|
|
|
|
|
|
|
H.C.Wong,
G.Liu,
Y.M.Zhang,
C.O.Rock,
and
J.Zheng
(2002).
The solution structure of acyl carrier protein from Mycobacterium tuberculosis.
|
| |
J Biol Chem,
277,
15874-15880.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
S.Kar,
K.Sakaguchi,
Y.Shimohigashi,
S.Samaddar,
R.Banerjee,
G.Basu,
V.Swaminathan,
T.K.Kundu,
and
S.Roy
(2002).
Effect of phosphorylation on the structure and fold of transactivation domain of p53.
|
| |
J Biol Chem,
277,
15579-15585.
|
|
|
|
|
|
|
T.Cierpicki,
J.Bania,
and
J.Otlewski
(2000).
NMR solution structure of Apis mellifera chymotrypsin/cathepsin G inhibitor-1 (AMCI-1): structural similarity with Ascaris protease inhibitors.
|
| |
Protein Sci,
9,
976-984.
|
|
|
PDB code:
|
|
|
|
|
|
|
|
J.Dreier,
A.N.Shah,
and
C.Khosla
(1999).
Kinetic analysis of the actinorhodin aromatic polyketide synthase.
|
| |
J Biol Chem,
274,
25108-25112.
|
|
|
|
|
|
|
T.J.Wyckoff,
and
C.R.Raetz
(1999).
The active site of Escherichia coli UDP-N-acetylglucosamine acyltransferase. Chemical modification and site-directed mutagenesis.
|
| |
J Biol Chem,
274,
27047-27055.
|
|
|
|
|
|
|
A.T.Brünger,
P.D.Adams,
and
L.M.Rice
(1997).
New applications of simulated annealing in X-ray crystallography and solution NMR.
|
| |
Structure,
5,
325-336.
|
|
|
|
|
|
|
C.A.Townsend
(1997).
Structural studies of natural product biosynthetic proteins.
|
| |
Chem Biol,
4,
721-730.
|
|
|
|
|
|
|
L.Tang,
A.C.Weissborn,
and
E.P.Kennedy
(1997).
Domains of Escherichia coli acyl carrier protein important for membrane-derived-oligosaccharide biosynthesis.
|
| |
J Bacteriol,
179,
3697-3705.
|
|
|
|
|
|
|
C.O.Rock,
and
J.E.Cronan
(1996).
Escherichia coli as a model for the regulation of dissociable (type II) fatty acid biosynthesis.
|
| |
Biochim Biophys Acta,
1302,
1.
|
|
|
|
|
|
|
D.Bassolino-Klimas,
R.Tejero,
S.R.Krystek,
W.J.Metzler,
G.T.Montelione,
and
R.E.Bruccoleri
(1996).
Simulated annealing with restrained molecular dynamics using a flexible restraint potential: theory and evaluation with simulated NMR constraints.
|
| |
Protein Sci,
5,
593-603.
|
|
|
|
|
|
|
D.H.Keating,
and
J.E.Cronan
(1996).
An isoleucine to valine substitution in Escherichia coli acyl carrier protein results in a functional protein of decreased molecular radius at elevated pH.
|
| |
J Biol Chem,
271,
15905-15910.
|
|
|
|
|
|
|
D.V.Debabov,
M.P.Heaton,
Q.Zhang,
K.D.Stewart,
R.H.Lambalot,
and
F.C.Neuhaus
(1996).
The D-Alanyl carrier protein in Lactobacillus casei: cloning, sequencing, and expression of dltC.
|
| |
J Bacteriol,
178,
3869-3876.
|
|
|
|
|
|
|
M.Nilges
(1996).
Structure calculation from NMR data.
|
| |
Curr Opin Struct Biol,
6,
617-623.
|
|
|
|
|
|
|
Z.Shen,
and
D.M.Byers
(1996).
Isolation of Vibrio harveyi acyl carrier protein and the fabG, acpP, and fabF genes involved in fatty acid biosynthesis.
|
| |
J Bacteriol,
178,
571-573.
|
|
|
|
|
|
|
D.Frishman,
and
P.Argos
(1995).
Knowledge-based protein secondary structure assignment.
|
| |
Proteins,
23,
566-579.
|
|
|
|
|
|
|
L.A.Horvath,
J.M.Sturtevant,
and
J.H.Prestegard
(1994).
Kinetics and thermodynamics of thermal denaturation in acyl carrier protein.
|
| |
Protein Sci,
3,
103-108.
|
|
|
|
|
|
|
A.T.Brünger,
and
M.Nilges
(1993).
Computational challenges for macromolecular structure determination by X-ray crystallography and solution NMR-spectroscopy.
|
| |
Q Rev Biophys,
26,
49.
|
|
|
|
|
|
|
K.Magnuson,
S.Jackowski,
C.O.Rock,
and
J.E.Cronan
(1993).
Regulation of fatty acid biosynthesis in Escherichia coli.
|
| |
Microbiol Rev,
57,
522-542.
|
|
|
|
|
|
|
R.C.Hoffman,
S.J.Horvath,
and
R.E.Klevit
(1993).
Structures of DNA-binding mutant zinc finger domains: implications for DNA binding.
|
| |
Protein Sci,
2,
951-965.
|
|
|
PDB codes:
|
|
|
|
|
|
|
|
P.Schmieder,
and
H.Kessler
(1992).
Determination of the phi angle in a peptide backbone by NMR spectroscopy with a combination of homonuclear and heteronuclear coupling constants.
|
| |
Biopolymers,
32,
435-440.
|
|
|
|
|
|
|
P.Schmieder,
M.Kurz,
and
H.Kessler
(1991).
Determination of heteronuclear long-range couplings to heteronuclei in natural abundance by two- and three-dimensional NMR spectroscopy.
|
| |
J Biomol NMR,
1,
403-420.
|
|
|
|
|
|
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.
|
|
Links
