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PDBsum entry 1hj8

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protein ligands metals links
Hydrolase PDB id
1hj8
Jmol
Contents
Protein chain
222 a.a. *
Ligands
BAM ×2
SO4
Metals
_CA
Waters ×228
* Residue conservation analysis
PDB id:
1hj8
Name: Hydrolase
Title: 1.00 aa trypsin from atlantic salmon
Structure: Trypsin i. Chain: a. Fragment: residues 21-242. Ec: 3.4.21.4
Source: Salmo salar. Atlantic salmon. Organism_taxid: 8030
Biol. unit: Monomer (from PDB file)
Resolution:
1.00Å     R-factor:   0.118     R-free:   0.149
Authors: H.-K.S.Leiros,S.M.Mcsweeney,A.O.Smalas
Key ref:
H.K.Leiros et al. (2001). Atomic resolution structures of trypsin provide insight into structural radiation damage. Acta Crystallogr D Biol Crystallogr, 57, 488-497. PubMed id: 11264577 DOI: 10.1107/S0907444901000646
Date:
09-Jan-01     Release date:   04-Jan-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
Pfam   ArchSchema ?
P35031  (TRY1_SALSA) -  Trypsin-1
Seq:
Struc:
242 a.a.
222 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.3.4.21.4  - Trypsin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Preferential cleavage: Arg-|-Xaa, Lys-|-Xaa.
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     extracellular region   2 terms 
  Biological process     digestion   2 terms 
  Biochemical function     catalytic activity     6 terms  

 

 
DOI no: 10.1107/S0907444901000646 Acta Crystallogr D Biol Crystallogr 57:488-497 (2001)
PubMed id: 11264577  
 
 
Atomic resolution structures of trypsin provide insight into structural radiation damage.
H.K.Leiros, S.M.McSweeney, A.O.Smalås.
 
  ABSTRACT  
 
Radiation damage is an inherent problem in protein X-ray crystallography and the process has recently been shown to be highly specific, exhibiting features such as cleavage of disulfide bonds, decarboxylation of acidic residues, increase in atomic B factors and increase in unit-cell volume. Reported here are two trypsin structures at atomic resolution (1.00 and 0.95 A), the data for which were collected at a third-generation synchrotron (ESRF) at two different beamlines. Both trypsin structures exhibit broken disulfide bonds; in particular, the bond from Cys191 to Cys220 is very sensitive to synchrotron radiation. The data set collected at the most intense beamline (ID14-EH4) shows increased structural radiation damage in terms of lower occupancies for cysteine residues, more breakage in the six disulfide bonds and more alternate conformations. It appears that high intensity and not only the total X-ray dose is most harmful to protein crystals.
 
  Selected figure(s)  
 
Figure 2.
Figure 2 The catalytic hydrogen bond from His57 N 1 to Asp102 O 2 in anionic salmon trypsin (AST). The 2mF[o] - DF[c] map is contoured at 2.0 (blue) and 4.0 (red), while the mF[o] - DF[c] map around the His57 side chain is contoured at +2.5 (green). Ser195 and Ser214 are also included in the figure, which was created with Bobscript (Esnouf, 1997[Esnouf, R. M. (1997). J. Mol. Graph. 15, 132-134.]).
Figure 3.
Figure 3 (a) Stereoview of the salt-bridge interactions that involve residues uniquely conserved in all cold-adapted trypsins (Leiros et al., 1999[Leiros, H.-K. S., Willassen, N. P. & Smalås, A. O. (1999). Extremophiles, 3, 205-219.], 2000[Leiros, H.-K. S., Willassen, N. P. & Smalås, A. O. (2000). Eur. J. Biochem. 267, 1039-1049.]). The 2mF[o] - DF[c] map of the side chains only is contoured at 1.8 . (b) Location of the ion-pair network relative to the N-terminal (red), the calcium-binding loop (blue) and the autolysis loop (yellow).
 
  The above figures are reprinted by permission from the IUCr: Acta Crystallogr D Biol Crystallogr (2001, 57, 488-497) copyright 2001.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21460448 G.Bunkóczi, and R.J.Read (2011).
Improvement of molecular-replacement models with Sculptor.
  Acta Crystallogr D Biol Crystallogr, 67, 303-312.  
21525648 M.Karuppasamy, F.Karimi Nejadasl, M.Vulovic, A.J.Koster, and R.B.Ravelli (2011).
Radiation damage in single-particle cryo-electron microscopy: effects of dose and dose rate.
  J Synchrotron Radiat, 18, 398-412.  
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.  
19793049 H.Y.Kaan, V.Ulaganathan, D.D.Hackney, and F.Kozielski (2010).
An allosteric transition trapped in an intermediate state of a new kinesin-inhibitor complex.
  Biochem J, 425, 55-60.
PDB code: 2wog
20944242 M.Warkentin, and R.E.Thorne (2010).
Glass transition in thaumatin crystals revealed through temperature-dependent radiation-sensitivity measurements.
  Acta Crystallogr D Biol Crystallogr, 66, 1092-1100.  
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
18073104 R.J.Southworth-Davies, M.A.Medina, I.Carmichael, and E.F.Garman (2007).
Observation of decreased radiation damage at higher dose rates in room temperature protein crystallography.
  Structure, 15, 1531-1541.  
17612488 S.Watanabe, R.Matsumi, T.Arai, H.Atomi, T.Imanaka, and K.Miki (2007).
Crystal structures of [NiFe] hydrogenase maturation proteins HypC, HypD, and HypE: insights into cyanation reaction by thiol redox signaling.
  Mol Cell, 27, 29-40.
PDB codes: 2z1c 2z1d 2z1e 2z1f
16549763 R.L.Owen, E.Rudiño-Piñera, and E.F.Garman (2006).
Experimental determination of the radiation dose limit for cryocooled protein crystals.
  Proc Natl Acad Sci U S A, 103, 4912-4917.  
15184683 B.Heras, M.A.Edeling, H.J.Schirra, S.Raina, and J.L.Martin (2004).
Crystal structures of the DsbG disulfide isomerase reveal an unstable disulfide.
  Proc Natl Acad Sci U S A, 101, 8876-8881.
PDB codes: 1v57 1v58
15054099 C.Meunier-Jamin, U.Kapp, G.A.Leonard, and S.McSweeney (2004).
The structure of the organic hydroperoxide resistance protein from Deinococcus radiodurans. Do conformational changes facilitate recycling of the redox disulfide?
  J Biol Chem, 279, 25830-25837.
PDB code: 1usp
15044735 H.K.Leiros, B.O.Brandsdal, O.A.Andersen, V.Os, I.Leiros, R.Helland, J.Otlewski, N.P.Willassen, and A.O.Smalås (2004).
Trypsin specificity as elucidated by LIE calculations, X-ray structures, and association constant measurements.
  Protein Sci, 13, 1056-1070.
PDB codes: 1utj 1utk 1utl 1utm 1utn 1uto 1utp 1utq
12876323 P.T.Erskine, L.Coates, S.Mall, R.S.Gill, S.P.Wood, D.A.Myles, and J.B.Cooper (2003).
Atomic resolution analysis of the catalytic site of an aspartic proteinase and an unexpected mode of binding by short peptides.
  Protein Sci, 12, 1741-1749.
PDB codes: 1oew 1oex
14563846 S.Parthasarathy, K.Eaazhisai, H.Balaram, P.Balaram, and M.R.Murthy (2003).
Structure of Plasmodium falciparum triose-phosphate isomerase-2-phosphoglycerate complex at 1.1-A resolution.
  J Biol Chem, 278, 52461-52470.
PDB code: 1o5x
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.