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PDBsum entry 1ixi

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Phosphate transport PDB id
1ixi
Jmol
Contents
Protein chain
321 a.a. *
Ligands
2HP
Waters ×212
* Residue conservation analysis
PDB id:
1ixi
Name: Phosphate transport
Title: Phosphate-binding protein mutant with asp 56 replaced by asn complex with monobasic phosphate ion
Structure: Phosphate-binding protein. Chain: a. Engineered: yes. Mutation: yes
Source: Escherichia coli. Organism_taxid: 562. Strain: pan92. Gene: potential. Expressed in: escherichia coli. Expression_system_taxid: 562. Other_details: pibi24, international biotechnologies
Resolution:
1.89Å     R-factor:   0.200     R-free:   0.294
Authors: Z.Wang,F.A.Quiocho
Key ref: Z.Wang et al. (1997). A low energy short hydrogen bond in very high resolution structures of protein receptor--phosphate complexes. Nat Struct Biol, 4, 519-522. PubMed id: 9228942
Date:
17-Oct-96     Release date:   22-Oct-97    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P0AG82  (PSTS_ECOLI) -  Phosphate-binding protein PstS
Seq:
Struc:
346 a.a.
321 a.a.*
Key:    PfamA domain  Secondary structure  CATH domain
* PDB and UniProt seqs differ at 1 residue position (black cross)

 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     periplasmic space   2 terms 
  Biological process     phosphate ion transmembrane transport   5 terms 
  Biochemical function     transporter activity     3 terms  

 

 
Nat Struct Biol 4:519-522 (1997)
PubMed id: 9228942  
 
 
A low energy short hydrogen bond in very high resolution structures of protein receptor--phosphate complexes.
Z.Wang, H.Luecke, N.Yao, F.A.Quiocho.
 
  ABSTRACT  
 
A very short hydrogen bond between an Asp and a phosphate is established in two high resolution structures (0.98 and 1.05 A). A mutant complex that changes the Asp to an Asn, which forms a normal hydrogen bond, has a similar free energy of binding to the wild type complex, suggesting that the contribution of the short hydrogen bond is not extraordinarily strong.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
20820461 C.Bazzicalupi, A.Bencini, and V.Lippolis (2010).
Tailoring cyclic polyamines for inorganic/organic phosphate binding.
  Chem Soc Rev, 39, 3709-3728.  
19290474 A.Berna, F.Bernier, E.Chabrière, M.Elias, K.Scott, and A.Suh (2009).
For whom the bell tolls? DING proteins in health and disease.
  Cell Mol Life Sci, 66, 2205-2218.  
18700034 D.R.Livesay, D.H.Huynh, S.Dallakyan, and D.J.Jacobs (2008).
Hydrogen bond networks determine emergent mechanical and thermodynamic properties across a protein family.
  Chem Cent J, 2, 17.  
17473016 M.J.Borrok, L.L.Kiessling, and K.T.Forest (2007).
Conformational changes of glucose/galactose-binding protein illuminated by open, unliganded, and ultra-high-resolution ligand-bound structures.
  Protein Sci, 16, 1032-1041.
PDB codes: 2fvy 2fw0
17154531 K.S.Champagne, E.Piscitelli, and C.S.Francklyn (2006).
Substrate recognition by the hetero-octameric ATP phosphoribosyltransferase from Lactococcus lactis.
  Biochemistry, 45, 14933-14943.  
16531243 R.Morales, A.Berna, P.Carpentier, C.Contreras-Martel, F.Renault, M.Nicodeme, M.L.Chesne-Seck, F.Bernier, J.Dupuy, C.Schaeffer, H.Diemer, A.Van-Dorsselaer, J.C.Fontecilla-Camps, P.Masson, D.Rochu, and E.Chabriere (2006).
Serendipitous discovery and X-ray structure of a human phosphate binding apolipoprotein.
  Structure, 14, 601-609.
PDB codes: 2cap 2v3q
16096056 I.Artsimovitch, M.N.Vassylyeva, D.Svetlov, V.Svetlov, A.Perederina, N.Igarashi, N.Matsugaki, S.Wakatsuki, T.H.Tahirov, and D.G.Vassylyev (2005).
Allosteric modulation of the RNA polymerase catalytic reaction is an essential component of transcription control by rifamycins.
  Cell, 122, 351-363.
PDB codes: 2a68 2a69 2a6e
16051603 K.S.Champagne, M.Sissler, Y.Larrabee, S.Doublié, and C.S.Francklyn (2005).
Activation of the hetero-octameric ATP phosphoribosyl transferase through subunit interface rearrangement by a tRNA synthetase paralog.
  J Biol Chem, 280, 34096-34104.
PDB codes: 1z7m 1z7n
15281134 D.B.Sherman, S.Zhang, J.B.Pitner, and A.Tropsha (2004).
Evaluation of the relative stability of liganded versus ligand-free protein conformations using Simplicial Neighborhood Analysis of Protein Packing (SNAPP) method.
  Proteins, 56, 828-838.  
15281126 J.Khandogin, and D.M.York (2004).
Quantum descriptors for biological macromolecules from linear-scaling electronic structure methods.
  Proteins, 56, 724-737.  
12842040 N.K.Vyas, M.N.Vyas, and F.A.Quiocho (2003).
Crystal structure of M tuberculosis ABC phosphate transport receptor: specificity and charge compensation dominated by ion-dipole interactions.
  Structure, 11, 765-774.
PDB code: 1pc3
11863460 P.J.O'Brien, and D.Herschlag (2002).
Alkaline phosphatase revisited: hydrolysis of alkyl phosphates.
  Biochemistry, 41, 3207-3225.  
11468363 D.D.Leonidas, G.B.Chavali, A.M.Jardine, S.Li, R.Shapiro, and K.R.Acharya (2001).
Binding of phosphate and pyrophosphate ions at the active site of human angiogenin as revealed by X-ray crystallography.
  Protein Sci, 10, 1669-1676.
PDB codes: 1h52 1h53 1hby
10737762 J.M.Johnson, and G.M.Church (2000).
Predicting ligand-binding function in families of bacterial receptors.
  Proc Natl Acad Sci U S A, 97, 3965-3970.  
10713988 M.Glick, and A.Goldblum (2000).
A novel energy-based stochastic method for positioning polar protons in protein structures from X-rays.
  Proteins, 38, 273-287.  
  9865949 P.S.Ledvina, A.L.Tsai, Z.Wang, E.Koehl, and F.A.Quiocho (1998).
Dominant role of local dipolar interactions in phosphate binding to a receptor cleft with an electronegative charge surface: equilibrium, kinetic, and crystallographic studies.
  Protein Sci, 7, 2550-2559.
PDB code: 1a40
9914254 S.Longhi, M.Czjzek, and C.Cambillau (1998).
Messages from ultrahigh resolution crystal structures.
  Curr Opin Struct Biol, 8, 730-737.  
9345627 Z.Dauter, V.S.Lamzin, and K.S.Wilson (1997).
The benefits of atomic resolution.
  Curr Opin Struct Biol, 7, 681-688.  
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.