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PDBsum entry 1y8b

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protein links
Transferase PDB id
1y8b
Jmol
Contents
Protein chain
723 a.a. *
* Residue conservation analysis
PDB id:
1y8b
Name: Transferase
Title: Solution nmr-derived global fold of malate synthase g from e.Coli
Structure: Malate synthase g. Chain: a. Synonym: msg. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Gene: glcb, glc. Expressed in: escherichia coli. Expression_system_taxid: 562.
NMR struc: 10 models
Authors: V.Tugarinov,W.-Y.Choy,V.Y.Orekhov,L.E.Kay
Key ref:
V.Tugarinov et al. (2005). Solution NMR-derived global fold of a monomeric 82-kDa enzyme. Proc Natl Acad Sci U S A, 102, 622-627. PubMed id: 15637152 DOI: 10.1073/pnas.0407792102
Date:
10-Dec-04     Release date:   11-Jan-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P37330  (MASZ_ECOLI) -  Malate synthase G
Seq:
Struc:
 
Seq:
Struc:
723 a.a.
723 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Enzyme reactions 
   Enzyme class: E.C.2.3.3.9  - Malate synthase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]

      Pathway:
Glyoxylate Cycle
      Reaction: Acetyl-CoA + H2O + glyoxylate = (S)-malate + CoA
Acetyl-CoA
+ H(2)O
+ glyoxylate
= (S)-malate
+ CoA
Molecule diagrams generated from .mol files obtained from the KEGG ftp site
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   1 term 
  Biological process     glyoxylate cycle   3 terms 
  Biochemical function     catalytic activity     4 terms  

 

 
    reference    
 
 
DOI no: 10.1073/pnas.0407792102 Proc Natl Acad Sci U S A 102:622-627 (2005)
PubMed id: 15637152  
 
 
Solution NMR-derived global fold of a monomeric 82-kDa enzyme.
V.Tugarinov, W.Y.Choy, V.Y.Orekhov, L.E.Kay.
 
  ABSTRACT  
 
The size of proteins that can be studied by solution NMR spectroscopy has increased significantly because of recent developments in methodology. Important experiments include those that make use of approaches that increase the lifetimes of NMR signals or that define the orientation of internuclear bond vectors with respect to a common molecular frame. The advances in NMR techniques are strongly coupled to isotope labeling methods that increase sensitivity and reduce the complexity of NMR spectra. We show that these developments can be exploited in structural studies of high-molecular-weight, single-polypeptide proteins, and we present the solution global fold of the monomeric 723-residue (82-kDa) enzyme malate synthase G from Escherichia coli, which has been extensively characterized by NMR in the past several years.
 
  Selected figure(s)  
 
Figure 1.
Fig. 1. Representative planes from 4D NOE data sets. (a)F[1](1H)--F[2](13C) plane from the 4D CH[3]--CH[3] NOESY spectrum showing correlations to L433 1. (b) The correlation involving L577 1 can be assigned despite the fact that this residue is in a very crowded region of the 2D 1H--13C correlation map. (c)F[3](15N)--F[4](1HN) plane from the HN--HN 4D data set showing correlations to Lys 206 HN. (d)F[3](15N)--F[4](1HN) plane from the methyl--HN 4D matrix, showing NOEs between I200 1 and proximal amide protons.
Figure 2.
Fig. 2. Comparison of x-ray and NMR-derived structures of MSG. (a) Ribbon diagrams of the x-ray structure of MSG (Left, PDB ID code 1D8C [PDB] ; ref. 17) and the lowest energy NMR structure (Right) calculated on the basis of 1,531 NOE, 1,101 dihedral angle, 415 residual dipolar couplings, and 300 carbonyl-shift restraints. (b) Ribbon representations of MSG (Left shows x-ray structure, and Right shows the lowest-energy NMR structure) are shown with the C carbons of residues that either contact or are proximal to glyoxylate (D270, E272, R338, E427, F453, L454, D455, and D631) in the active site of the protein, indicated with red spheres. The image was prepared by using MOLMOL (39).
 
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21214860 A.H.Kwan, M.Mobli, P.R.Gooley, G.F.King, and J.P.Mackay (2011).
Macromolecular NMR spectroscopy for the non-spectroscopist.
  FEBS J, 278, 687-703.  
20806263 D.Latek, and A.Kolinski (2011).
CABS-NMR--De novo tool for rapid global fold determination from chemical shifts, residual dipolar couplings and sparse methyl-methyl NOEs.
  J Comput Chem, 32, 536-544.  
19957200 C.Guo, and V.Tugarinov (2010).
Selective 1H- 13C NMR spectroscopy of methyl groups in residually protonated samples of large proteins.
  J Biomol NMR, 46, 127-133.  
20633347 D.Sheppard, R.Sprangers, and V.Tugarinov (2010).
Experimental approaches for NMR studies of side-chain dynamics in high-molecular-weight proteins.
  Prog Nucl Magn Reson Spectrosc, 56, 1.  
20838855 G.Jaipuria, A.Thakur, P.D'Silva, and H.S.Atreya (2010).
High-resolution methyl edited GFT NMR experiments for protein resonance assignments and structure determination.
  J Biomol NMR, 48, 137-145.  
20195256 S.I.O'Donoghue, D.S.Goodsell, A.S.Frangakis, F.Jossinet, R.A.Laskowski, M.Nilges, H.R.Saibil, A.Schafferhans, R.C.Wade, E.Westhof, and A.J.Olson (2010).
Visualization of macromolecular structures.
  Nat Methods, 7, S42-S55.  
  20160991 B.R.Donald, and J.Martin (2009).
Automated NMR Assignment and Protein Structure Determination using Sparse Dipolar Coupling Constraints.
  Prog Nucl Magn Reson Spectrosc, 55, 101-127.  
19002386 C.Guo, and V.Tugarinov (2009).
Identification of HN-methyl NOEs in large proteins using simultaneous amide-methyl TROSY-based detection.
  J Biomol NMR, 43, 21-30.  
19522502 G.M.Clore, and J.Iwahara (2009).
Theory, practice, and applications of paramagnetic relaxation enhancement for the characterization of transient low-population states of biological macromolecules and their complexes.
  Chem Rev, 109, 4108-4139.  
  20161395 H.J.Kim, S.C.Howell, W.D.Van Horn, Y.H.Jeon, and C.R.Sanders (2009).
Recent Advances in the Application of Solution NMR Spectroscopy to Multi-Span Integral Membrane Proteins.
  Prog Nucl Magn Reson Spectrosc, 55, 335-360.  
19115043 I.Ayala, R.Sounier, N.Usé, P.Gans, and J.Boisbouvier (2009).
An efficient protocol for the complete incorporation of methyl-protonated alanine in perdeuterated protein.
  J Biomol NMR, 43, 111-119.  
19684068 M.F.Dunn, J.A.Ramírez-Trujillo, and I.Hernández-Lucas (2009).
Major roles of isocitrate lyase and malate synthase in bacterial and fungal pathogenesis.
  Microbiology, 155, 3166-3175.  
19359484 N.Popovych, S.R.Tzeng, M.Tonelli, R.H.Ebright, and C.G.Kalodimos (2009).
Structural basis for cAMP-mediated allosteric control of the catabolite activator protein.
  Proc Natl Acad Sci U S A, 106, 6927-6932.
PDB code: 2wc2
19288066 N.Sibille, X.Hanoulle, F.Bonachera, D.Verdegem, I.Landrieu, J.M.Wieruszeski, and G.Lippens (2009).
Selective backbone labelling of ILV methyl labelled proteins.
  J Biomol NMR, 43, 219-227.  
19548092 Y.Shen, F.Delaglio, G.Cornilescu, and A.Bax (2009).
TALOS+: a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts.
  J Biomol NMR, 44, 213-223.  
18008171 A.Grishaev, V.Tugarinov, L.E.Kay, J.Trewhella, and A.Bax (2008).
Refined solution structure of the 82-kDa enzyme malate synthase G from joint NMR and synchrotron SAXS restraints.
  J Biomol NMR, 40, 95.
PDB code: 2jqx
18411193 I.G.Muñoz, F.J.Blanco, and G.Montoya (2008).
On the relevance of defining protein structures in cancer research.
  Clin Transl Oncol, 10, 204-212.  
18714089 J.R.Lohman, A.C.Olson, and S.J.Remington (2008).
Atomic resolution structures of Escherichia coli and Bacillus anthracis malate synthase A: comparison with isoform G and implications for structure-based drug discovery.
  Protein Sci, 17, 1935-1945.
PDB codes: 3cux 3cuz 3cv1 3cv2
18761469 J.Shin, W.Lee, and W.Lee (2008).
Structural proteomics by NMR spectroscopy.
  Expert Rev Proteomics, 5, 589-601.  
18762867 S.C.Shih, I.Stoica, and N.K.Goto (2008).
Investigation of the utility of selective methyl protonation for determination of membrane protein structures.
  J Biomol NMR, 42, 49-58.  
18937031 S.Ohki, K.Dohi, A.Tamai, M.Takeuchi, and M.Mori (2008).
Stable-isotope labeling using an inducible viral infection system in suspension-cultured plant cells.
  J Biomol NMR, 42, 271-277.  
18305193 W.Zhao, Y.Zhang, C.Cui, Q.Li, and J.Wang (2008).
An efficient on-column expressed protein ligation strategy: application to segmental triple labeling of human apolipoprotein E3.
  Protein Sci, 17, 736-747.  
17328009 M.Fischer, K.Kloiber, J.Häusler, K.Ledolter, R.Konrat, and W.Schmid (2007).
Synthesis of a 13C-methyl-group-labeled methionine precursor as a useful tool for simplifying protein structural analysis by NMR spectroscopy.
  Chembiochem, 8, 610-612.  
17554497 M.Matzapetakis, P.Turano, E.C.Theil, and I.Bertini (2007).
13C- 13C NOESY spectra of a 480 kDa protein: solution NMR of ferritin.
  J Biomol NMR, 38, 237-242.  
17209543 M.P.Foster, C.A.McElroy, and C.D.Amero (2007).
Solution NMR of large molecules and assemblies.
  Biochemistry, 46, 331-340.  
18041839 R.L.Isaacson, P.J.Simpson, M.Liu, E.Cota, X.Zhang, P.Freemont, and S.Matthews (2007).
A new labeling method for methyl transverse relaxation-optimized spectroscopy NMR spectra of alanine residues.
  J Am Chem Soc, 129, 15428-15429.  
17762877 R.Sprangers, A.Velyvis, and L.E.Kay (2007).
Solution NMR of supramolecular complexes: providing new insights into function.
  Nat Methods, 4, 697-703.  
16826539 C.R.Sanders, and F.Sönnichsen (2006).
Solution NMR of membrane proteins: practice and challenges.
  Magn Reson Chem, 44, S24-S40.  
16877713 D.M.Anstrom, and S.J.Remington (2006).
The product complex of M. tuberculosis malate synthase revisited.
  Protein Sci, 15, 2002-2007.
PDB code: 2gq3
16826537 D.Staunton, R.Schlinkert, G.Zanetti, S.A.Colebrook, and I.D.Campbell (2006).
Cell-free expression and selective isotope labelling in protein NMR.
  Magn Reson Chem, 44, S2-S9.  
16689638 K.Mitra, and J.Frank (2006).
Ribosome dynamics: insights from atomic structure modeling into cryo-electron microscopy maps.
  Annu Rev Biophys Biomol Struct, 35, 299-317.  
17406304 V.Tugarinov, V.Kanelis, and L.E.Kay (2006).
Isotope labeling strategies for the study of high-molecular-weight proteins by solution NMR spectroscopy.
  Nat Protoc, 1, 749-754.  
17060917 Y.Xu, Y.Zheng, J.S.Fan, and D.Yang (2006).
A new strategy for structure determination of large proteins in solution without deuteration.
  Nat Methods, 3, 931-937.
PDB codes: 2h25 2h35
16258829 C.Tang, J.Iwahara, and G.M.Clore (2005).
Accurate determination of leucine and valine side-chain conformations using U-[15N/13C/2H]/[1H-(methine/methyl)-Leu/Val] isotope labeling, NOE pattern recognition, and methine Cgamma-Hgamma/Cbeta-Hbeta residual dipolar couplings: application to the 34-kDa enzyme IIA(chitobiose).
  J Biomol NMR, 33, 105-121.  
16222555 J.E.Ollerenshaw, V.Tugarinov, N.R.Skrynnikov, and L.E.Kay (2005).
Comparison of 13CH3, 13CH2D, and 13CHD2 methyl labeling strategies in proteins.
  J Biomol NMR, 33, 25-41.  
16075427 V.Tugarinov, and L.E.Kay (2005).
Methyl groups as probes of structure and dynamics in NMR studies of high-molecular-weight proteins.
  Chembiochem, 6, 1567-1577.  
16270364 Y.Wang, I.Filippov, C.Richter, R.Luo, and R.W.Kriwacki (2005).
Solution NMR studies of an intrinsically unstructured protein within a dilute, 75 kDa eukaryotic protein assembly; probing the practical limits for efficiently assigning polypeptide backbone resonances.
  Chembiochem, 6, 2242-2246.  
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 code is shown on the right.