spacer
spacer

PDBsum entry 2akb
Go to PDB code: 
protein links
Immune system PDB id
2akb

 

 

 

 

Loading ...

 
JSmol PyMol  
Contents
Protein chain
77 a.a.
Theoretical model
PDB id:
2akb
Name: Immune system
Title: Circumsporozoite protein
Structure: Circumsporozoite protein. Chain: a. Fragment: residues 336-412. Synonym: cs
Source: Plasmodium falciparum. Malaria parasite p. Falciparum
Authors: R.Muthuvijayakumar
Key ref: K.Diederichs and G.E.Schulz (1991). The refined structure of the complex between adenylate kinase from beef heart mitochondrial matrix and its substrate AMP at 1.85 A resolution. J Mol Biol, 217, 541-549. PubMed id: 1994037
Date:
03-Aug-05     Release date:   23-Aug-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P02893  (CSP_PLAFA) -  Circumsporozoite protein from Plasmodium falciparum
Seq:
Struc: 		412 a.a.
77 a.a.
Key:    PfamA domain  Secondary structure

 

 
J Mol Biol 217:541-549 (1991)
PubMed id: 1994037  
 
 
The refined structure of the complex between adenylate kinase from beef heart mitochondrial matrix and its substrate AMP at 1.85 A resolution.
K.Diederichs, G.E.Schulz.
 
  ABSTRACT  
 
The crystal structure of the complex between adenylate kinase from bovine mitochondrial matrix and its substrate AMP has been refined at 1.85 A resolution (1 A = 0.1 nm). Based on 42,519 independent reflections of better than 10 A resolution, a final R-factor of 18.9% was obtained with a model obeying standard geometry within 0.016 A in bond lengths and 3.2 degrees in bond angles. There are two enzyme: substrate complexes in the asymmetric unit, each consisting of 226 amino acid residues, one AMP and one sulfate ion. A superposition of the two full-length polypeptides revealed deviations that can be described as small relative movements of three domains. Best superpositions of individual domains yielded a residual overall root-mean-square deviation of 0.3 A for the backbone atoms and 0.5 A for the sidechains. The final model contains 381 solvent molecules in the asymmetric unit, 2 x 72 = 144 of which occupy corresponding positions in both complexes.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
21081091 J.B.Brokaw, and J.W.Chu (2010).
On the roles of substrate binding and hinge unfolding in conformational changes of adenylate kinase.
  Biophys J, 99, 3420-3429.  
19706894 A.Korkut, and W.A.Hendrickson (2009).
Computation of conformational transitions in proteins by virtual atom molecular mechanics as validated in application to adenylate kinase.
  Proc Natl Acad Sci U S A, 106, 15673-15678.  
19180449 K.S.Keating, S.C.Flores, M.B.Gerstein, and L.A.Kuhn (2009).
StoneHinge: hinge prediction by network analysis of individual protein structures.
  Protein Sci, 18, 359-371.  
19751742 O.Beckstein, E.J.Denning, J.R.Perilla, and T.B.Woolf (2009).
Zipping and unzipping of adenylate kinase: atomistic insights into the ensemble of open<-->closed transitions.
  J Mol Biol, 394, 160-176.  
19130895 R.Liu, A.L.Ström, J.Zhai, J.Gal, S.Bao, W.Gong, and H.Zhu (2009).
Enzymatically inactive adenylate kinase 4 interacts with mitochondrial ADP/ATP translocase.
  Int J Biochem Cell Biol, 41, 1371-1380.  
17998210 P.C.Whitford, S.Gosavi, and J.N.Onuchic (2008).
Conformational Transitions in Adenylate Kinase: ALLOSTERIC COMMUNICATION REDUCES MISLIGATION.
  J Biol Chem, 283, 2042-2048.  
17959599 A.Mukhopadhyay, C.S.Yang, B.Wei, and H.Weiner (2007).
Precursor Protein Is Readily Degraded in Mitochondrial Matrix Space if the Leader Is Not Processed by Mitochondrial Processing Peptidase.
  J Biol Chem, 282, 37266-37275.  
17299745 C.Snow, G.Qi, and S.Hayward (2007).
Essential dynamics sampling study of adenylate kinase: comparison to citrate synthase and implication for the hinge and shear mechanisms of domain motions.
  Proteins, 67, 325-337.  
  16880539 B.Dhaliwal, J.Ren, M.Lockyer, I.Charles, A.R.Hawkins, and D.K.Stammers (2006).
Structure of Staphylococcus aureus cytidine monophosphate kinase in complex with cytidine 5'-monophosphate.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 62, 710-715.
PDB code: 2h92
15229886 N.Fernandez-Fuentes, A.Hermoso, J.Espadaler, E.Querol, F.X.Aviles, and B.Oliva (2004).
Classification of common functional loops of kinase super-families.
  Proteins, 56, 539-555.  
12952559 B.E.Shakhnovich, J.M.Harvey, S.Comeau, D.Lorenz, C.DeLisi, and E.Shakhnovich (2003).
ELISA: structure-function inferences based on statistically significant and evolutionarily inspired observations.
  BMC Bioinformatics, 4, 34.  
12045196 R.Schricker, M.Angermayr, G.Strobel, S.Klinke, D.Korber, and W.Bandlow (2002).
Redundant mitochondrial targeting signals in yeast adenylate kinase.
  J Biol Chem, 277, 28757-28764.  
11123913 I.M.Li de La Sierra, J.Gallay, M.Vincent, T.Bertrand, P.Briozzo, O.Bârzu, and A.M.Gilles (2000).
Substrate-induced fit of the ATP binding site of cytidine monophosphate kinase from Escherichia coli: time-resolved fluorescence of 3'-anthraniloyl-2'-deoxy-ADP and molecular modeling.
  Biochemistry, 39, 15870-15878.  
10215863 A.R.Van Rompay, M.Johansson, and A.Karlsson (1999).
Identification of a novel human adenylate kinase. cDNA cloning, expression analysis, chromosome localization and characterization of the recombinant protein.
  Eur J Biochem, 261, 509-517.  
10398370 H.Munier-Lehmann, S.Burlacu-Miron, C.T.Craescu, H.H.Mantsch, and C.P.Schultz (1999).
A new subfamily of short bacterial adenylate kinases with the Mycobacterium tuberculosis enzyme as a model: A predictive and experimental study.
  Proteins, 36, 238-248.  
10497207 P.J.Haney, M.Stees, and J.Konisky (1999).
Analysis of thermal stabilizing interactions in mesophilic and thermophilic adenylate kinases from the genus Methanococcus.
  J Biol Chem, 274, 28453-28458.  
9548738 D.H.Harrison, J.A.Runquist, A.Holub, and H.M.Miziorko (1998).
The crystal structure of phosphoribulokinase from Rhodobacter sphaeroides reveals a fold similar to that of adenylate kinase.
  Biochemistry, 37, 5074-5085.
PDB code: 1a7j
9485466 L.V.Mello, D.M.van Aalten, and J.B.Findlay (1998).
Dynamic properties of the guanine nucleotide binding protein alpha subunit and comparison of its guanosine triphosphate hydrolase domain with that of ras p21.
  Biochemistry, 37, 3137-3142.  
9715904 M.B.Berry, and G.N.Phillips (1998).
Crystal structures of Bacillus stearothermophilus adenylate kinase with bound Ap5A, Mg2+ Ap5A, and Mn2+ Ap5A reveal an intermediate lid position and six coordinate octahedral geometry for bound Mg2+ and Mn2+.
  Proteins, 32, 276-288.
PDB codes: 1zin 1zio 1zip
9862805 P.Briozzo, B.Golinelli-Pimpaneau, A.M.Gilles, J.F.Gaucher, S.Burlacu-Miron, H.Sakamoto, J.Janin, and O.Bârzu (1998).
Structures of escherichia coli CMP kinase alone and in complex with CDP: a new fold of the nucleoside monophosphate binding domain and insights into cytosine nucleotide specificity.
  Structure, 6, 1517-1527.
PDB codes: 1cke 2cmk
9095194 K.Diederichs, and P.A.Karplus (1997).
Improved R-factors for diffraction data analysis in macromolecular crystallography.
  Nat Struct Biol, 4, 269-275.  
  8670851 A.Teplyakov, P.Sebastiao, G.Obmolova, A.Perrakis, G.S.Brush, M.J.Bessman, and K.S.Wilson (1996).
Crystal structure of bacteriophage T4 deoxynucleotide kinase with its substrates dGMP and ATP.
  EMBO J, 15, 3487-3497.
PDB codes: 1dek 1del
8805593 C.D.Mol, J.M.Harris, E.M.McIntosh, and J.A.Tainer (1996).
Human dUTP pyrophosphatase: uracil recognition by a beta hairpin and active sites formed by three separate subunits.
  Structure, 4, 1077-1092.
PDB codes: 1q5h 1q5u
8805521 C.W.Müller, G.J.Schlauderer, J.Reinstein, and G.E.Schulz (1996).
Adenylate kinase motions during catalysis: an energetic counterweight balancing substrate binding.
  Structure, 4, 147-156.
PDB code: 4ake
8703943 K.Scheffzek, W.Kliche, L.Wiesmüller, and J.Reinstein (1996).
Crystal structure of the complex of UMP/CMP kinase from Dictyostelium discoideum and the bisubstrate inhibitor P1-(5'-adenosyl) P5-(5'-uridyl) pentaphosphate (UP5A) and Mg2+ at 2.2 A: implications for water-mediated specificity.
  Biochemistry, 35, 9716-9727.
PDB codes: 1ukd 1uke
8639589 M.A.Sinev, E.V.Sineva, V.Ittah, and E.Haas (1996).
Domain closure in adenylate kinase.
  Biochemistry, 35, 6425-6437.  
8523045 M.T.Barakat, and P.M.Dean (1995).
The atom assignment problem in automated de novo drug design. 3. Algorithms for optimization of fragment placement onto 3D molecular graphs.
  J Comput Aided Mol Des, 9, 359-372.  
8594162 M.T.Barakat, and P.M.Dean (1995).
The atom assignment problem in automated de novo drug design. 4. Tests for site-directed fragment placement based on molecular complementarity.
  J Comput Aided Mol Des, 9, 448-456.  
7635152 P.Spuergin, U.Abele, and G.E.Schulz (1995).
Stability, activity and structure of adenylate kinase mutants.
  Eur J Biochem, 231, 405-413.
PDB code: 3aky
  7670369 U.Abele, and G.E.Schulz (1995).
High-resolution structures of adenylate kinase from yeast ligated with inhibitor Ap5A, showing the pathway of phosphoryl transfer.
  Protein Sci, 4, 1262-1271.
PDB codes: 1aky 2aky
7937733 M.B.Berry, B.Meador, T.Bilderback, P.Liang, M.Glaser, and G.N.Phillips (1994).
The closed conformation of a highly flexible protein: the structure of E. coli adenylate kinase with bound AMP and AMPPNP.
  Proteins, 19, 183-198.
PDB code: 1ank
7876898 P.L.Chau, and P.M.Dean (1994).
Electrostatic complementarity between proteins and ligands. 1. Charge disposition, dielectric and interface effects.
  J Comput Aided Mol Des, 8, 513-525.  
7876899 P.L.Chau, and P.M.Dean (1994).
Electrostatic complementarity between proteins and ligands. 2. Ligand moieties.
  J Comput Aided Mol Des, 8, 527-544.  
8081756 W.Huang, Y.Lindqvist, G.Schneider, K.J.Gibson, D.Flint, and G.Lorimer (1994).
Crystal structure of an ATP-dependent carboxylase, dethiobiotin synthetase, at 1.65 A resolution.
  Structure, 2, 407-414.
PDB code: 1dts
8451239 C.W.Müller, and G.E.Schulz (1993).
Crystal structures of two mutants of adenylate kinase from Escherichia coli that modify the Gly-loop.
  Proteins, 15, 42-49.
PDB codes: 1e4v 1e4y
1544504 V.Magdolen, R.Schricker, G.Strobel, H.Germaier, and W.Bandlow (1992).
In vivo import of yeast adenylate kinase into mitochondria affected by site-directed mutagenesis.
  FEBS Lett, 299, 267-272.  
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.

 

spacer
spacer