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PDBsum entry 1kyi

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protein ligands Protein-protein interface(s) links
Chaperone/hydrolase PDB id
1kyi
Jmol
Contents
Protein chains
(+ 6 more) 321 a.a. *
(+ 6 more) 173 a.a. *
Ligands
ATP ×12
LVS ×12
* Residue conservation analysis
PDB id:
1kyi
Name: Chaperone/hydrolase
Title: Hsluv (h. Influenzae)-nlvs vinyl sulfone inhibitor complex
Structure: Atp-dependent hsl protease atp-binding subunit hs chain: a, b, c, d, e, f, s, t, u, v, w, x. Synonym: hslu. Engineered: yes. Atp-dependent protease hslv. Chain: g, h, i, j, k, l, m, n, o, p, q, r. Synonym: hslv. Engineered: yes
Source: Haemophilus influenzae. Organism_taxid: 71421. Strain: rd kw20. Gene: hslu. Expressed in: escherichia coli bl21(de3). Expression_system_taxid: 469008. Gene: hslv.
Biol. unit: 24mer (from PQS)
Resolution:
3.10Å     R-factor:   0.266     R-free:   0.288
Authors: M.C.Sousa,B.M.Kessler,H.S.Overkleeft,D.B.Mckay
Key ref:
M.C.Sousa et al. (2002). Crystal structure of HslUV complexed with a vinyl sulfone inhibitor: corroboration of a proposed mechanism of allosteric activation of HslV by HslU. J Mol Biol, 318, 779-785. PubMed id: 12054822 DOI: 10.1016/S0022-2836(02)00145-6
Date:
04-Feb-02     Release date:   15-May-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P43773  (HSLU_HAEIN) -  ATP-dependent protease ATPase subunit HslU
Seq:
Struc:
444 a.a.
321 a.a.
Protein chains
Pfam   ArchSchema ?
P43772  (HSLV_HAEIN) -  ATP-dependent protease subunit HslV
Seq:
Struc:
175 a.a.
173 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Enzyme reactions 
   Enzyme class: Chains G, H, I, J, K, L, M, N, O, P, Q, R: E.C.3.4.25.2  - HslU--HslV peptidase.
[IntEnz]   [ExPASy]   [KEGG]   [BRENDA]
 Gene Ontology (GO) functional annotation 
  GO annot!
  Cellular component     cytoplasm   3 terms 
  Biological process     metabolic process   6 terms 
  Biochemical function     catalytic activity     11 terms  

 

 
DOI no: 10.1016/S0022-2836(02)00145-6 J Mol Biol 318:779-785 (2002)
PubMed id: 12054822  
 
 
Crystal structure of HslUV complexed with a vinyl sulfone inhibitor: corroboration of a proposed mechanism of allosteric activation of HslV by HslU.
M.C.Sousa, B.M.Kessler, H.S.Overkleeft, D.B.McKay.
 
  ABSTRACT  
 
On the basis of the structure of a HslUV complex, a mechanism of allosteric activation of the HslV protease, wherein binding of the HslU chaperone propagates a conformational change to the active site cleft of the protease, has been proposed. Here, the 3.1 A X-ray crystallographic structure of Haemophilus influenzae HslUV complexed with a vinyl sulfone inhibitor is described. The inhibitor, which reacts to form a covalent linkage to Thr1 of HslV, binds in an "antiparallel beta" manner, with hydrogen-bond interactions between the peptide backbone of the protease and that of the inhibitor, and with two leucinyl side chains of the inhibitor binding in the S1 and S3 specificity pockets of the protease. Comparison of the structure of the HslUV-inhibitor complex with that of HslV without inhibitor and in the absence of HslU reveals that backbone interactions would correctly position a substrate for cleavage in the HslUV complex, but not in the HslV protease alone, corroborating the proposed mechanism of allosteric activation. This activation mechanism differs from that of the eukaryotic proteasome, for which binding of activators opens a gated channel that controls access of substrates to the protease, but does not perturb the active site environment.
 
  Selected figure(s)  
 
Figure 1.
Figure 1. (a) Stereo view of F[o] -F[c] electron density map showing inhibitor bound to one subunit of HslV. Phases were computed from HslUV model that resulted from one cycle of simulated annealing after all inhibitor atoms were omitted from the model. Contour levels, 5s (magenta), 12.5s (cyan). The Figure was prepared with BOBSCRIPT[25.] and RASTER3D. [26.] (b) Proposed structure of NLVS-HslV covalent complex with Thr1 of HslV. [14.] Inhibitor atoms and bonds are drawn bold; HslV atoms/bonds are drawn fine. The S1 and S3 HslV binding pockets are shown schematically above the moieties they bind. Orientation of inhibitor is similar to orientation in part (a).
Figure 2.
Figure 2. Stereo views of the HslUV-NLVS inhibitor complex. (a) View showing the hydrogen bonding interactions of the inhibitor with HslV polypeptide backbone in the HslUV-NLVS complex. Carbon atoms of HslV are green; carbon atoms of inhibitor are gray; nitrogen atoms, blue; oxygen atoms, red; sulfur atom, yellow. (b) Superposition of the substrate binding clefts of HslUV-NLVS and the yeast proteasome with epoxomycin (subunit K of PDB 1G65).[15.] Hydrogen bonds between protein and inhibitor are the same as shown in part (a). Selected residues are labeled with format "HslV#/proteasome#". Color scheme: HslV of HslUV-NLVS complex, green; NLVS inhibitor atoms, cyan; proteasome, red; epoxomycin inhibitor atoms, gold. (c) View showing the inhibitor (semi-transparent CPK model) and the binding pockets of HslUV. HslV protomer to which NLVS is covalently attached is green; adjacent HslV protomer, yellow; HslU, magenta; inhibitor, gray. Selected side chains are included. Carbon atoms are the same color as corresponding protomer; oxygen atoms, red; nitrogen atoms, blue; sulfur atoms, cyan. (d) View showing the displacement of upper strand of substrate binding cleft of uncomplexed HslV [9.] relative to HslUV-NLVS; when lower segments of polypeptides are superimposed, upper segment of uncomplexed HslV is displaced vert, similar 3-4 Å from its position in the HslUV-NLVS complex. For clarity, only selected peptide backbone and C^a atoms of the proteins and "backbone" atoms of the inhibitor are included. Color scheme: HslV of HslUV-NLVS complex, green; NLVS inhibitor atoms, cyan; uncomplexed HslV, magenta. Superpositions were computed with the program LSQMAN.[27.] The Figure was prepared with MOLSCRIPT [28.] and RASTER3D. [26.]
 
  The above figures are reprinted by permission from Elsevier: J Mol Biol (2002, 318, 779-785) copyright 2002.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
20305655 B.G.Lee, E.Y.Park, K.E.Lee, H.Jeon, K.H.Sung, H.Paulsen, H.Rübsamen-Schaeff, H.Brötz-Oesterhelt, and H.K.Song (2010).
Structures of ClpP in complex with acyldepsipeptide antibiotics reveal its activation mechanism.
  Nat Struct Mol Biol, 17, 471-478.
PDB codes: 3ktg 3kth 3kti 3ktj 3ktk
20541423 N.Gallastegui, and M.Groll (2010).
The 26S proteasome: assembly and function of a destructive machine.
  Trends Biochem Sci, 35, 634-642.  
19801685 J.W.Lee, E.Park, M.S.Jeong, Y.J.Jeon, S.H.Eom, J.H.Seol, and C.H.Chung (2009).
HslVU ATP-dependent protease utilizes maximally six among twelve threonine active sites during proteolysis.
  J Biol Chem, 284, 33475-33484.  
19828442 N.Koga, T.Kameda, K.Okazaki, and S.Takada (2009).
Paddling mechanism for the substrate translocation by AAA+ motor revealed by multiscale molecular simulations.
  Proc Natl Acad Sci U S A, 106, 18237-18242.  
19914167 S.E.Glynn, A.Martin, A.R.Nager, T.A.Baker, and R.T.Sauer (2009).
Structures of asymmetric ClpX hexamers reveal nucleotide-dependent motions in a AAA+ protein-unfolding machine.
  Cell, 139, 744-756.
PDB codes: 3hte 3hws
18838376 E.Park, J.W.Lee, S.H.Eom, J.H.Seol, and C.H.Chung (2008).
Binding of MG132 or Deletion of the Thr Active Sites in HslV Subunits Increases the Affinity of HslV Protease for HslU ATPase and Makes This Interaction Nucleotide-independent.
  J Biol Chem, 283, 33258-33266.  
18582897 J.A.Yakamavich, T.A.Baker, and R.T.Sauer (2008).
Asymmetric nucleotide transactions of the HslUV protease.
  J Mol Biol, 380, 946-957.  
18466635 J.Snider, G.Thibault, and W.A.Houry (2008).
The AAA+ superfamily of functionally diverse proteins.
  Genome Biol, 9, 216.  
17979190 S.H.Rho, H.H.Park, G.B.Kang, Y.J.Im, M.S.Kang, B.K.Lim, I.S.Seong, J.Seol, C.H.Chung, J.Wang, and S.H.Eom (2008).
Crystal structure of Bacillus subtilis CodW, a noncanonical HslV-like peptidase with an impaired catalytic apparatus.
  Proteins, 71, 1020-1026.
PDB codes: 2z3a 2z3b
17612489 A.Martin, T.A.Baker, and R.T.Sauer (2007).
Distinct static and dynamic interactions control ATPase-peptidase communication in a AAA+ protease.
  Mol Cell, 27, 41-52.  
16819825 H.Frase, J.Hudak, and I.Lee (2006).
Identification of the proteasome inhibitor MG262 as a potent ATP-dependent inhibitor of the Salmonella enterica serovar Typhimurium Lon protease.
  Biochemistry, 45, 8264-8274.  
16762831 R.Suno, H.Niwa, D.Tsuchiya, X.Zhang, M.Yoshida, and K.Morikawa (2006).
Structure of the whole cytosolic region of ATP-dependent protease FtsH.
  Mol Cell, 22, 575-585.
PDB codes: 2dhr 2di4 4eiw
16149114 C.Drahl, B.F.Cravatt, and E.J.Sorensen (2005).
Protein-reactive natural products.
  Angew Chem Int Ed Engl, 44, 5788-5809.  
15843987 D.Frees, L.E.Thomsen, and H.Ingmer (2005).
Staphylococcus aureus ClpYQ plays a minor role in stress survival.
  Arch Microbiol, 183, 286-291.  
15678420 M.Groll, M.Bochtler, H.Brandstetter, T.Clausen, and R.Huber (2005).
Molecular machines for protein degradation.
  Chembiochem, 6, 222-256.  
15696175 R.E.Burton, T.A.Baker, and R.T.Sauer (2005).
Nucleotide-dependent substrate recognition by the AAA+ HslUV protease.
  Nat Struct Mol Biol, 12, 245-251.  
15454077 R.T.Sauer, D.N.Bolon, B.M.Burton, R.E.Burton, J.M.Flynn, R.A.Grant, G.L.Hersch, S.A.Joshi, J.A.Kenniston, I.Levchenko, S.B.Neher, E.S.Oakes, S.M.Siddiqui, D.A.Wah, and T.A.Baker (2004).
Sculpting the proteome with AAA(+) proteases and disassembly machines.
  Cell, 119, 9.  
15064753 S.A.Joshi, G.L.Hersch, T.A.Baker, and R.T.Sauer (2004).
Communication between ClpX and ClpP during substrate processing and degradation.
  Nat Struct Mol Biol, 11, 404-411.  
14675543 M.Groll, and T.Clausen (2003).
Molecular shredders: how proteasomes fulfill their role.
  Curr Opin Struct Biol, 13, 665-673.  
14570582 S.Gottesman (2003).
Proteolysis in bacterial regulatory circuits.
  Annu Rev Cell Dev Biol, 19, 565-587.  
12445774 D.A.Wah, I.Levchenko, T.A.Baker, and R.T.Sauer (2002).
Characterization of a specificity factor for an AAA+ ATPase: assembly of SspB dimers with ssrA-tagged proteins and the ClpX hexamer.
  Chem Biol, 9, 1237-1245.  
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.