spacer
spacer

PDBsum entry 2bi3

Go to PDB code: 
protein ligands metals Protein-protein interface(s) links
Transferase PDB id
2bi3
Jmol
Contents
Protein chains
360 a.a. *
Ligands
PLP ×2
1PE
PEG ×3
Metals
_MG ×4
_CL ×4
Waters ×604
* Residue conservation analysis
PDB id:
2bi3
Name: Transferase
Title: Radiation damage of the schiff base in phosphoserine aminotransferase (structure d)
Structure: Phosphoserine aminotransferase. Chain: a, b. Engineered: yes. Other_details: pyridoxal-5'-phosphate linked to 196
Source: Bacillus alcalophilus. Organism_taxid: 1445. Expressed in: escherichia coli. Expression_system_taxid: 469008.
Biol. unit: Dimer (from PDB file)
Resolution:
1.69Å     R-factor:   0.180     R-free:   0.229
Authors: A.P.Dubnovitsky,R.B.G.Ravelli,A.N.Popov,A.C.Papageorgiou
Key ref:
A.P.Dubnovitsky et al. (2005). Strain relief at the active site of phosphoserine aminotransferase induced by radiation damage. Protein Sci, 14, 1498-1507. PubMed id: 15883191 DOI: 10.1110/ps.051397905
Date:
20-Jan-05     Release date:   19-May-05    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
Q9RME2  (SERC_BACAO) -  Phosphoserine aminotransferase
Seq:
Struc:
361 a.a.
360 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.2.6.1.52  - Phosphoserine transaminase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction:
1. O-phospho-L-serine + 2-oxoglutarate = 3-phosphonooxypyruvate + L-glutamate
2. 4-phosphonooxy-L-threonine + 2-oxoglutarate = (3R)-3-hydroxy-2-oxo-4- phosphonooxybutanoate + L-glutamate
O-phospho-L-serine
+ 2-oxoglutarate
= 3-phosphonooxypyruvate
+ L-glutamate
4-phosphonooxy-L-threonine
+ 2-oxoglutarate
= (3R)-3-hydroxy-2-oxo-4- phosphonooxybutanoate
+ L-glutamate
      Cofactor: Pyridoxal 5'-phosphate
Pyridoxal 5'-phosphate
Bound ligand (Het Group name = PLP) matches with 93.00% similarity
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     metabolic process   3 terms 
  Biochemical function     catalytic activity     5 terms  

 

 
    reference    
 
 
DOI no: 10.1110/ps.051397905 Protein Sci 14:1498-1507 (2005)
PubMed id: 15883191  
 
 
Strain relief at the active site of phosphoserine aminotransferase induced by radiation damage.
A.P.Dubnovitsky, R.B.Ravelli, A.N.Popov, A.C.Papageorgiou.
 
  ABSTRACT  
 
The X-ray susceptibility of the lysine-pyridoxal-5'-phosphate Schiff base in Bacillus alcalophilus phosphoserine aminotransferase has been investigated using crystallographic data collected at 100 K to 1.3 A resolution, complemented by on-line spectroscopic studies. X-rays induce deprotonation of the internal aldimine, changes in the Schiff base conformation, displacement of the cofactor molecule, and disruption of the Schiff base linkage between pyridoxal-5'-phosphate and the Lys residue. Analysis of the "undamaged" structure reveals a significant chemical strain on the internal aldimine bond that leads to a pronounced geometrical distortion of the cofactor. However, upon crystal exposure to the X-rays, the strain and distortion are relaxed and eventually diminished when the total absorbed dose has exceeded 4.7 x 10(6) Ggamma. Our data provide new insights into the enzymatic activation of pyridoxal-5'-phosphate and suggest that special care should be taken while using macromolecular crystallography to study details in strained active sites.
 
  Selected figure(s)  
 
Figure 3.
Figure 3. X-ray-induced structural changes in the active site of BALC PSAT. Sigma A-weighted difference Fourier maps (wF[A]-wF[n]) between the first data set, A, and the successive data sets, B-G, respectively, are shown. Superimposed atomic coordinates from the model A are presented. The green density represents maps contoured at 6.5 , and the blue density represents maps contoured at -6.0 . The figure was produced using BOBSCRIPT (Esnouf 1997) and Raster 3D (Merritt and Murphy 1994). (A) wF[A]-wF[B] map. (B) wF[A]-wF[C] map. (C) wF[A]-wF[D] map. (D) wF[A]-wF[E] map. (E) wF[A]-wF[F] map. (F) wF[A]-wF[G] map.
Figure 6.
Figure 6. Distortion of pyridoxal-5'-phosphate in the active site of BALC PSAT. Atomic coordinates of PLP and Lys196 side chain from the model H are presented in black. In gray, the superimposed planar conformation of the PLP molecule from the atomic resolution structure of BALC PSAT is shown (PDB accession code 1W23). The figure was produced using MOLSCRIPT (Kraulis 1991) and Raster 3D (Merritt and Murphy 1994).
 
  The above figures are reprinted by permission from the Protein Society: Protein Sci (2005, 14, 1498-1507) copyright 2005.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
22338689 M.Schmidt, V.Šrajer, N.Purwar, and S.Tripathi (2012).
The kinetic dose limit in room-temperature time-resolved macromolecular crystallography.
  J Synchrotron Radiat, 19, 264-273.  
21525640 D.H.Juers, and M.Weik (2011).
Similarities and differences in radiation damage at 100 K versus 160 K in a crystal of thermolysin.
  J Synchrotron Radiat, 18, 329-337.  
20382986 E.F.Garman (2010).
Radiation damage in macromolecular crystallography: what is it and why should we care?
  Acta Crystallogr D Biol Crystallogr, 66, 339-351.  
20382994 G.P.Bourenkov, and A.N.Popov (2010).
Optimization of data collection taking radiation damage into account.
  Acta Crystallogr D Biol Crystallogr, 66, 409-419.  
20382997 M.Weik, and J.P.Colletier (2010).
Temperature-dependent macromolecular X-ray crystallography.
  Acta Crystallogr D Biol Crystallogr, 66, 437-446.  
21070940 P.Carpentier, A.Royant, M.Weik, and D.Bourgeois (2010).
Raman-assisted crystallography suggests a mechanism of X-ray-induced disulfide radical formation and reparation.
  Structure, 18, 1410-1419.
PDB codes: 2xbr 2xbs
20944241 T.Petrova, S.Ginell, A.Mitschler, Y.Kim, V.Y.Lunin, G.Joachimiak, A.Cousido-Siah, I.Hazemann, A.Podjarny, K.Lazarski, and A.Joachimiak (2010).
X-ray-induced deterioration of disulfide bridges at atomic resolution.
  Acta Crystallogr D Biol Crystallogr, 66, 1075-1091.
PDB codes: 3mnb 3mnc 3mns 3mnx 3mo3 3mo6 3mo9 3moc 3mty 3mu0 3mu1 3mu4 3mu5 3mu8 3odd 3odf
20199659 V.Mishra, V.Ali, T.Nozaki, and V.Bhakuni (2010).
Entamoeba histolytica Phosphoserine aminotransferase (EhPSAT): insights into the structure-function relationship.
  BMC Res Notes, 3, 52.  
19520834 B.Sjöblom, M.Polentarutti, and K.Djinovic-Carugo (2009).
Structural study of X-ray induced activation of carbonic anhydrase.
  Proc Natl Acad Sci U S A, 106, 10609-10613.
PDB codes: 2vva 2vvb
19240325 J.M.Holton (2009).
A beginner's guide to radiation damage.
  J Synchrotron Radiat, 16, 133-142.  
19240328 J.McGeehan, R.B.Ravelli, J.W.Murray, R.L.Owen, F.Cipriani, S.McSweeney, M.Weik, and E.F.Garman (2009).
Colouring cryo-cooled crystals: online microspectrophotometry.
  J Synchrotron Radiat, 16, 163-172.  
19240329 R.L.Owen, A.R.Pearson, A.Meents, P.Boehler, V.Thominet, and C.Schulze-Briese (2009).
A new on-axis multimode spectrometer for the macromolecular crystallography beamlines of the Swiss Light Source.
  J Synchrotron Radiat, 16, 173-182.  
18701720 J.P.Colletier, D.Bourgeois, B.Sanson, D.Fournier, J.L.Sussman, I.Silman, and M.Weik (2008).
Shoot-and-Trap: use of specific x-ray damage to study structural protein dynamics by temperature-controlled cryo-crystallography.
  Proc Natl Acad Sci U S A, 105, 11742-11747.
PDB codes: 2vja 2vjb 2vjc 2vjd 2vt6 2vt7
17211072 J.M.Holton (2007).
XANES measurements of the rate of radiation damage to selenomethionine side chains.
  J Synchrotron Radiat, 14, 51-72.  
17959373 T.De la Mora-Rey, and C.M.Wilmot (2007).
Synergy within structural biology of single crystal optical spectroscopy and X-ray crystallography.
  Curr Opin Struct Biol, 17, 580-586.  
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.