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PDBsum entry 1gci
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Serine protease PDB id
1gci

 

 

 

 

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Contents
Protein chain
269 a.a. *
Ligands
SO4
GOL
Metals
_CA ×2
Waters ×384
* Residue conservation analysis
PDB id:
1gci
Name: Serine protease
Title: The 0.78 angstroms structure of a serine protease-bacillus lentus subtilisin
Structure: Subtilisin. Chain: a. Engineered: yes
Source: Bacillus lentus. Organism_taxid: 1467. Expressed in: bacillus subtilis. Expression_system_taxid: 1423
Resolution:
0.78Å     R-factor:   0.099     R-free:   0.103
Authors: R.Bott,P.Kuhn
Key ref:
P.Kuhn et al. (1998). The 0.78 A structure of a serine protease: Bacillus lentus subtilisin. Biochemistry, 37, 13446-13452. PubMed id: 9753430 DOI: 10.1021/bi9813983
Date:
02-Sep-98     Release date:   21-Oct-98    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chain
P29600  (SUBS_LEDLE) -  Subtilisin Savinase from Lederbergia lenta
Seq:
Struc: 		269 a.a.
269 a.a.
Key:    Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: E.C.3.4.21.62  - subtilisin.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
      Reaction: Hydrolysis of proteins with broad specificity for peptide bonds, and a preference for a large uncharged residue in P1. Hydrolyzes peptide amides.

 

 
DOI no: 10.1021/bi9813983 Biochemistry 37:13446-13452 (1998)
PubMed id: 9753430  
 
 
The 0.78 A structure of a serine protease: Bacillus lentus subtilisin.
P.Kuhn, M.Knapp, S.M.Soltis, G.Ganshaw, M.Thoene, R.Bott.
 
  ABSTRACT  
 
Ultrahigh-resolution X-ray diffraction data from cryo-cooled, B. lentus subtilisin crystals has been collected to a resolution of 0.78 A. The refined model coordinates have a rms deviation of 0.22 A relative to the same structure determined at room temperature and 2.0 A resolution. Several regions of main-chain and side-chain disorder have been identified for 21 out of 269 residues in one polypeptide chain. Hydrogen atoms appear as significant peaks in the Fo - Fc difference electron density map, and carbon, nitrogen, and oxygen atoms can be differentiated. The estimated standard deviation (ESD) for all main-chain non-hydrogen bond lengths is 0.009 A and 0.5 degrees for bond angles based on an unrestrained full-matrix least-squares refinement. Hydrogen bonds are resolved in the serine protease catalytic triad (Ser-His-Asp). Electron density is observed for an unusual, short hydrogen bond between aspartic acid and histidine in the catalytic triad. The hydrogen atom, identified by NMR in numerous serine proteases, appears to be shared by the heteroatoms in the bond. This represents the first reported correlation between detailed chemical features identified by NMR and those in a cryo-cooled crystallographic structure determination at ultrahigh resolution. The short hydrogen bond, designated "catalytic hydrogen bond", occurs as part of an elaborate hydrogen bond network, involving Asp of the catalytic triad. While unusual, these features appear to have conserved analogues in other serine protease families although specific details differ from family to family.
 

Literature references that cite this PDB file's key reference

  PubMed id Reference
19690373 M.J.Schnieders, T.D.Fenn, V.S.Pande, and A.T.Brunger (2009).
Polarizable atomic multipole X-ray refinement: application to peptide crystals.
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19688822 M.Shokhen, N.Khazanov, and A.Albeck (2009).
Challenging a paradigm: theoretical calculations of the protonation state of the Cys25-His159 catalytic diad in free papain.
  Proteins, 77, 916-926.  
18655058 O.Almog, A.González, N.Godin, M.de Leeuw, M.J.Mekel, D.Klein, S.Braun, G.Shoham, and R.L.Walter (2009).
The crystal structures of the psychrophilic subtilisin S41 and the mesophilic subtilisin Sph reveal the same calcium-loaded state.
  Proteins, 74, 489-496.
PDB codes: 2gko 2ixt 3d43
18814299 P.Labute (2009).
Protonate3D: assignment of ionization states and hydrogen coordinates to macromolecular structures.
  Proteins, 75, 187-205.  
18637174 A.Golovin, and K.Henrick (2008).
MSDmotif: exploring protein sites and motifs.
  BMC Bioinformatics, 9, 312.  
18247345 D.Bandyopadhyay, and E.L.Mehler (2008).
Quantitative expression of protein heterogeneity: Response of amino acid side chains to their local environment.
  Proteins, 72, 646-659.  
18323618 E.Nishibori, T.Nakamura, M.Arimoto, S.Aoyagi, H.Ago, M.Miyano, T.Ebisuzaki, and M.Sakata (2008).
Application of maximum-entropy maps in the accurate refinement of a putative acylphosphatase using 1.3 A X-ray diffraction data.
  Acta Crystallogr D Biol Crystallogr, 64, 237-247.  
  17401191 A.Shaw, M.L.Saldajeno, M.A.Kolkman, B.E.Jones, and R.Bott (2007).
Structure determination and analysis of a bacterial chymotrypsin from Cellulomonas bogoriensis.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 63, 266-269.
PDB code: 2ea3
17642517 H.U.Ahmed, M.P.Blakeley, M.Cianci, D.W.Cruickshank, J.A.Hubbard, and J.R.Helliwell (2007).
The determination of protonation states in proteins.
  Acta Crystallogr D Biol Crystallogr, 63, 906-922.
PDB codes: 2uu8 2uuf 2uuj 2uuk 2yz4
18084073 J.Wang, M.Dauter, R.Alkire, A.Joachimiak, and Z.Dauter (2007).
Triclinic lysozyme at 0.65 A resolution.
  Acta Crystallogr D Biol Crystallogr, 63, 1254-1268.
PDB code: 2vb1
17452786 M.Jaskolski, M.Gilski, Z.Dauter, and A.Wlodawer (2007).
Stereochemical restraints revisited: how accurate are refinement targets and how much should protein structures be allowed to deviate from them?
  Acta Crystallogr D Biol Crystallogr, 63, 611-620.  
17372355 M.Sherawat, P.Kaur, M.Perbandt, C.Betzel, W.A.Slusarchyk, G.S.Bisacchi, C.Chang, B.L.Jacobson, H.M.Einspahr, and T.P.Singh (2007).
Structure of the complex of trypsin with a highly potent synthetic inhibitor at 0.97 A resolution.
  Acta Crystallogr D Biol Crystallogr, 63, 500-507.
PDB code: 2ayw
17428317 W.A.Stanley, N.V.Pursiainen, E.F.Garman, A.H.Juffer, M.Wilmanns, and P.Kursula (2007).
A previously unobserved conformation for the human Pex5p receptor suggests roles for intrinsic flexibility and rigid domain motions in ligand binding.
  BMC Struct Biol, 7, 24.
PDB code: 2j9q
16604066 A.Y.Lyubimov, P.I.Lario, I.Moustafa, and A.Vrielink (2006).
Atomic resolution crystallography reveals how changes in pH shape the protein microenvironment.
  Nat Chem Biol, 2, 259-264.
PDB codes: 1n4u 1n4v 1n4w 2gew
16552136 J.Hakanpää, M.Linder, A.Popov, A.Schmidt, and J.Rouvinen (2006).
Hydrophobin HFBII in detail: ultrahigh-resolution structure at 0.75 A.
  Acta Crystallogr D Biol Crystallogr, 62, 356-367.
PDB code: 2b97
  16511027 D.Dong, T.Ihara, H.Motoshima, and K.Watanabe (2005).
Crystallization and preliminary X-ray crystallographic studies of a psychrophilic subtilisin-like protease Apa1 from Antarctic Pseudoalteromonas sp. strain AS-11.
  Acta Crystallogr Sect F Struct Biol Cryst Commun, 61, 308-311.  
15983423 H.Bönisch, C.L.Schmidt, P.Bianco, and R.Ladenstein (2005).
Ultrahigh-resolution study on Pyrococcus abyssi rubredoxin. I. 0.69 A X-ray structure of mutant W4L/R5S.
  Acta Crystallogr D Biol Crystallogr, 61, 990.
PDB codes: 1yk4 1yk5
15608379 K.V.Dunlop, R.T.Irvin, and B.Hazes (2005).
Pros and cons of cryocrystallography: should we also collect a room-temperature data set?
  Acta Crystallogr D Biol Crystallogr, 61, 80-87.
PDB codes: 1x6p 1x6q 1x6r 1x6x 1x6y 1x6z
15782396 R.E.Cachau, and A.D.Podjarny (2005).
High-resolution crystallography and drug design.
  J Mol Recognit, 18, 196-202.  
15103633 C.N.Schutz, and A.Warshel (2004).
The low barrier hydrogen bond (LBHB) proposal revisited: the case of the Asp... His pair in serine proteases.
  Proteins, 55, 711-723.  
15146478 E.I.Howard, R.Sanishvili, R.E.Cachau, A.Mitschler, B.Chevrier, P.Barth, V.Lamour, M.Van Zandt, E.Sibley, C.Bon, D.Moras, T.R.Schneider, A.Joachimiak, and A.Podjarny (2004).
Ultrahigh resolution drug design I: details of interactions in human aldose reductase-inhibitor complex at 0.66 A.
  Proteins, 55, 792-804.
PDB code: 1us0
15272156 F.Ruiz, I.Hazemann, A.Mitschler, A.Joachimiak, T.Schneider, M.Karplus, and A.Podjarny (2004).
The crystallographic structure of the aldose reductase-IDD552 complex shows direct proton donation from tyrosine 48.
  Acta Crystallogr D Biol Crystallogr, 60, 1347-1354.
PDB codes: 1t40 1t41
14597632 G.R.Stranzl, K.Gruber, G.Steinkellner, K.Zangger, H.Schwab, and C.Kratky (2004).
Observation of a short, strong hydrogen bond in the active site of hydroxynitrile lyase from Hevea brasiliensis explains a large pKa shift of the catalytic base induced by the reaction intermediate.
  J Biol Chem, 279, 3699-3707.  
15103133 K.E.McAuley, A.Svendsen, S.A.Patkar, and K.S.Wilson (2004).
Structure of a feruloyl esterase from Aspergillus niger.
  Acta Crystallogr D Biol Crystallogr, 60, 878-887.
PDB codes: 1uwc 1uza
14747995 M.Shokhen, and A.Albeck (2004).
Is there a weak H-bond --> LBHB transition on tetrahedral complex formation in serine proteases?
  Proteins, 54, 468-477.  
14675549 A.Vrielink, and N.Sampson (2003).
Sub-Angstrom resolution enzyme X-ray structures: is seeing believing?
  Curr Opin Struct Biol, 13, 709-715.  
12794865 B.G.Davis, R.F.Sala, D.R.Hodgson, A.Ullman, K.Khumtaveeporn, D.A.Estell, K.Sanford, R.R.Bott, and J.B.Jones (2003).
Selective protein degradation by ligand-targeted enzymes: towards the creation of catalytic antagonists.
  Chembiochem, 4, 533-537.  
14675548 B.W.Dijkstra, and R.G.Matthews (2003).
Catalysis and regulation - from structure to function.
  Curr Opin Struct Biol, 13, 706-708.  
12704087 D.A.Kraut, K.S.Carroll, and D.Herschlag (2003).
Challenges in enzyme mechanism and energetics.
  Annu Rev Biochem, 72, 517-571.  
12937341 N.Engler, A.Ostermann, N.Niimura, and F.G.Parak (2003).
Hydrogen atoms in proteins: positions and dynamics.
  Proc Natl Acad Sci U S A, 100, 10243-10248.  
12871974 Q.Liu, Q.Huang, M.Teng, C.M.Weeks, C.Jelsch, R.Zhang, and L.Niu (2003).
The crystal structure of a novel, inactive, lysine 49 PLA2 from Agkistrodon acutus venom: an ultrahigh resolution, AB initio structure determination.
  J Biol Chem, 278, 41400-41408.
PDB code: 1mc2
11910039 A.Kahyaoglu, and F.Jordan (2002).
Direct proton magnetic resonance determination of the pKa of the active center histidine in thiolsubtilisin.
  Protein Sci, 11, 965-973.  
11896054 G.Katona, R.C.Wilmouth, P.A.Wright, G.I.Berglund, J.Hajdu, R.Neutze, and C.J.Schofield (2002).
X-ray structure of a serine protease acyl-enzyme complex at 0.95-A resolution.
  J Biol Chem, 277, 21962-21970.
PDB code: 1gvk
11258922 C.Betzel, S.Gourinath, P.Kumar, P.Kaur, M.Perbandt, S.Eschenburg, and T.P.Singh (2001).
Structure of a serine protease proteinase K from Tritirachium album limber at 0.98 A resolution.
  Biochemistry, 40, 3080-3088.
PDB code: 1ic6
11389594 G.T.Marks, T.K.Harris, M.A.Massiah, A.S.Mildvan, and D.H.Harrison (2001).
Mechanistic implications of methylglyoxal synthase complexed with phosphoglycolohydroxamic acid as observed by X-ray crystallography and NMR spectroscopy.
  Biochemistry, 40, 6805-6818.
PDB code: 1ik4
11264577 H.K.Leiros, S.M.McSweeney, and A.O.Smalås (2001).
Atomic resolution structures of trypsin provide insight into structural radiation damage.
  Acta Crystallogr D Biol Crystallogr, 57, 488-497.
PDB codes: 1hj8 1hj9
11575777 J.Overgaard, B.Schiøtt, F.K.Larsen, and B.B.Iversen (2001).
The charge density distribution in a model compound of the catalytic triad in serine proteases.
  Chemistry, 7, 3756-3767.  
11264580 R.A.Steiner, H.J.Rozeboom, A.de Vries, K.H.Kalk, G.N.Murshudov, K.S.Wilson, and B.W.Dijkstra (2001).
X-ray structure of bovine pancreatic phospholipase A2 at atomic resolution.
  Acta Crystallogr D Biol Crystallogr, 57, 516-526.
PDB code: 1g4i
11223515 S.Teixeira, L.Lo Leggio, R.Pickersgill, and C.Cardin (2001).
Anisotropic refinement of the structure of Thermoascus aurantiacus xylanase I.
  Acta Crystallogr D Biol Crystallogr, 57, 385-392.
PDB code: 1fxm
11173501 T.Gutberlet, U.Heinemann, and M.Steiner (2001).
Protein crystallography with neutrons--status and perspectives.
  Acta Crystallogr D Biol Crystallogr, 57, 349-354.  
11468409 T.Shimizu, T.Nakatsu, K.Miyairi, T.Okuno, and H.Kato (2001).
Crystallization and preliminary X-ray study of endopolygalacturonase from the pathogenic fungus Stereum purpureum.
  Acta Crystallogr D Biol Crystallogr, 57, 1171-1173.  
11134922 W.R.Rypniewski, P.R.Ostergaard, M.Nørregaard-Madsen, M.Dauter, and K.S.Wilson (2001).
Fusarium oxysporum trypsin at atomic resolution at 100 and 283 K: a study of ligand binding.
  Acta Crystallogr D Biol Crystallogr, 57, 8.
PDB codes: 1fn8 1fy4 1fy5 1gdn 1gdq 1gdu
10801485 A.Mølgaard, S.Kauppinen, and S.Larsen (2000).
Rhamnogalacturonan acetylesterase elucidates the structure and function of a new family of hydrolases.
  Structure, 8, 373-383.
PDB codes: 1deo 1dex
10666594 D.Housset, F.Benabicha, V.Pichon-Pesme, C.Jelsch, A.Maierhofer, S.David, J.C.Fontecilla-Camps, and C.Lecomte (2000).
Towards the charge-density study of proteins: a room-temperature scorpion-toxin structure at 0.96 A resolution as a first test case.
  Acta Crystallogr D Biol Crystallogr, 56, 151-160.  
10739939 M.Würtele, M.Hahn, K.Hilpert, and W.Höhne (2000).
Atomic resolution structure of native porcine pancreatic elastase at 1.1 A.
  Acta Crystallogr D Biol Crystallogr, 56, 520-523.
PDB code: 1qnj
10702283 S.Di Marco, M.Rizzi, C.Volpari, M.A.Walsh, F.Narjes, S.Colarusso, R.De Francesco, V.G.Matassa, and M.Sollazzo (2000).
Inhibition of the hepatitis C virus NS3/4A protease. The crystal structures of two protease-inhibitor complexes.
  J Biol Chem, 275, 7152-7157.
PDB codes: 1dxp 1dy8 1dy9
10508669 J.C.Beauchamp, and N.W.Isaacs (1999).
Methods for X-ray diffraction analysis of macromolecular structures.
  Curr Opin Chem Biol, 3, 525-529.  
10494852 K.Gruber, M.Gugganig, U.G.Wagner, and C.Kratky (1999).
Atomic resolution crystal structure of hydroxynitrile lyase from Hevea brasiliensis.
  Biol Chem, 380, 993.
PDB code: 1qj4
  10595562 K.S.Makarova, and N.V.Grishin (1999).
Thermolysin and mitochondrial processing peptidase: how far structure-functional convergence goes.
  Protein Sci, 8, 2537-2540.  
10449323 R.Bott, and R.Boelens (1999).
The role of high-resolution structural studies in the development of commercial enzymes.
  Curr Opin Biotechnol, 10, 391-397.  
10328262 T.K.Harris, and A.S.Mildvan (1999).
High-precision measurement of hydrogen bond lengths in proteins by nuclear magnetic resonance methods.
  Proteins, 35, 275-282.  
9914254 S.Longhi, M.Czjzek, and C.Cambillau (1998).
Messages from ultrahigh resolution crystal structures.
  Curr Opin Struct Biol, 8, 730-737.  
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.

 

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