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PDBsum entry 1mbx

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protein ligands metals Protein-protein interface(s) links
Protein binding PDB id
1mbx
Jmol
Contents
Protein chains
142 a.a. *
87 a.a. *
Ligands
YBT ×5
GOL ×3
Metals
_ZN ×2
_CL
Waters ×184
* Residue conservation analysis
PDB id:
1mbx
Name: Protein binding
Title: Crystal structure analysis of clpsn with transition metal io
Structure: Atp-dependent clp protease atp-binding subunit cl chain: a, b. Engineered: yes. Protein ylja. Chain: c, d. Engineered: yes
Source: Escherichia coli. Organism_taxid: 562. Expressed in: escherichia coli. Expression_system_taxid: 562.
Biol. unit: Dimer (from PQS)
Resolution:
2.25Å     R-factor:   0.208     R-free:   0.231
Authors: F.Guo,L.Esser,S.K.Singh,M.R.Maurizi,D.Xia
Key ref:
F.Guo et al. (2002). Crystal structure of the heterodimeric complex of the adaptor, ClpS, with the N-domain of the AAA+ chaperone, ClpA. J Biol Chem, 277, 46753-46762. PubMed id: 12235156 DOI: 10.1074/jbc.M208104200
Date:
03-Aug-02     Release date:   11-Dec-02    
PROCHECK
Go to PROCHECK summary
 Headers
 References

Protein chains
Pfam   ArchSchema ?
P0ABH9  (CLPA_ECOLI) -  ATP-dependent Clp protease ATP-binding subunit ClpA
Seq:
Struc:
 
Seq:
Struc:
758 a.a.
142 a.a.
Protein chains
Pfam   ArchSchema ?
P0A8Q6  (CLPS_ECOLI) -  ATP-dependent Clp protease adapter protein ClpS
Seq:
Struc:
106 a.a.
87 a.a.
Key:    PfamA domain  Secondary structure  CATH domain

 Gene Ontology (GO) functional annotation 
  GO annot!
  Biological process     protein metabolic process   4 terms 
  Biochemical function     protein binding     3 terms  

 

 
DOI no: 10.1074/jbc.M208104200 J Biol Chem 277:46753-46762 (2002)
PubMed id: 12235156  
 
 
Crystal structure of the heterodimeric complex of the adaptor, ClpS, with the N-domain of the AAA+ chaperone, ClpA.
F.Guo, L.Esser, S.K.Singh, M.R.Maurizi, D.Xia.
 
  ABSTRACT  
 
Substrate selectivity and proteolytic activity for the E. coli ATP-dependent protease, ClpAP, is modulated by an adaptor protein, ClpS. ClpS binds to ClpA, the regulatory component of the ClpAP complex. We report the crystal structure of ClpS in complex with the isolated N-terminal domain of ClpA in two different crystal forms at 2.3- and 3.3-A resolution. The ClpS structure forms an alpha/beta-sandwich and is topologically analogous to the C-terminal domain of the ribosomal protein L7/L12. ClpS contacts two surfaces on the N-terminal domain in both crystal forms; the more extensive interface was shown to be favored in solution by protease protection experiments. The N-terminal 20 residues of ClpS are not visible in the crystal structures; the removal of the first 17 residues produces ClpSDeltaN, which binds to the ClpA N-domain but no longer inhibits ClpA activity. A zinc binding site involving two His and one Glu residue was identified crystallographically in the N-terminal domain of ClpA. In a model of ClpS bound to hexameric ClpA, ClpS is oriented with its N terminus directed toward the distal surface of ClpA, suggesting that the N-terminal region of ClpS may affect productive substrate interactions at the apical surface or substrate entry into the ClpA translocation channel.
 
  Selected figure(s)  
 
Figure 5.
Fig. 5. The Zn2+ binding site and its coordination in the N-domain of ClpA. A stereo pair shows the Zn2+ in tetrahedral coordination with four ligands in the ball-and-stick models and as labeled. The same four ligands in different conformation from the Zn2+-free N-domain are also shown as thin stick models. The helix H4 is shown as a ribbon in red, and the loop between helices H1 and H2 is shown as a blue coil.
Figure 7.
Fig. 7. A hexameric model of ClpA with ClpS bound. The hexameric model of ClpA is based on the crystal structure of the full-length ClpA (5). The two possible interfaces between ClpS and ClpA are shown. ClpS connected to ClpA through the interface C is shown in red; ClpS making the A interface is in yellow. The N-domain of each ClpA subunit is shown in green; the D1 ATPase domain is in gray; and the D2 ATPase domain is in blue.
 
  The above figures are reprinted by permission from the ASBMB: J Biol Chem (2002, 277, 46753-46762) copyright 2002.  
  Figures were selected by an automated process.  

Literature references that cite this PDB file's key reference

  PubMed id Reference
21368759 F.Wang, Z.Mei, Y.Qi, C.Yan, Q.Hu, J.Wang, and Y.Shi (2011).
Structure and mechanism of the hexameric MecA-ClpC molecular machine.
  Nature, 471, 331-335.
PDB codes: 2y1q 2y1r 3pxg 3pxi
22016057 S.M.Sriram, B.Y.Kim, and Y.T.Kwon (2011).
The N-end rule pathway: emerging functions and molecular principles of substrate recognition.
  Nat Rev Mol Cell Biol, 12, 735-747.  
19361434 D.J.Kojetin, P.D.McLaughlin, R.J.Thompson, D.Dubnau, P.Prepiak, M.Rance, and J.Cavanagh (2009).
Structural and motional contributions of the Bacillus subtilis ClpC N-domain to adaptor protein interactions.
  J Mol Biol, 387, 639-652.
PDB code: 2k77
19362814 F.Striebel, W.Kress, and E.Weber-Ban (2009).
Controlled destruction: AAA+ ATPases in protein degradation from bacteria to eukaryotes.
  Curr Opin Struct Biol, 19, 209-217.  
19609260 J.Kirstein, N.Molière, D.A.Dougan, and K.Turgay (2009).
Adapting the machine: adaptor proteins for Hsp100/Clp and AAA+ proteases.
  Nat Rev Microbiol, 7, 589-599.  
19317833 R.Schmidt, R.Zahn, B.Bukau, and A.Mogk (2009).
ClpS is the recognition component for Escherichia coli substrates of the N-end rule degradation pathway.
  Mol Microbiol, 72, 506-517.  
19373253 V.J.Schuenemann, S.M.Kralik, R.Albrecht, S.K.Spall, K.N.Truscott, D.A.Dougan, and K.Zeth (2009).
Structural basis of N-end rule substrate recognition in Escherichia coli by the ClpAP adaptor protein ClpS.
  EMBO Rep, 10, 508-514.
PDB codes: 2w9r 2wa8 2wa9
19726681 W.Kress, H.Mutschler, and E.Weber-Ban (2009).
Both ATPase domains of ClpA are critical for processing of stable protein structures.
  J Biol Chem, 284, 31441-31452.  
18279386 A.H.Erbse, J.N.Wagner, K.N.Truscott, S.K.Spall, J.Kirstein, K.Zeth, K.Turgay, A.Mogk, B.Bukau, and D.A.Dougan (2008).
Conserved residues in the N-domain of the AAA+ chaperone ClpA regulate substrate recognition and unfolding.
  FEBS J, 275, 1400-1410.  
19050717 A.Varshavsky (2008).
The N-end rule at atomic resolution.
  Nat Struct Mol Biol, 15, 1238-1240.  
18953640 D.Xia, L.Esser, M.Elberry, F.Zhou, L.Yu, and C.A.Yu (2008).
The road to the crystal structure of the cytochrome bc (1) complex from the anoxigenic, photosynthetic bacterium Rhodobacter sphaeroides.
  J Bioenerg Biomembr, 40, 485-492.  
18297088 J.Y.Hou, R.T.Sauer, and T.A.Baker (2008).
Distinct structural elements of the adaptor ClpS are required for regulating degradation by ClpAP.
  Nat Struct Mol Biol, 15, 288-294.  
17827297 Y.Zhang, and P.Zuber (2007).
Requirement of the zinc-binding domain of ClpX for Spx proteolysis in Bacillus subtilis and effects of disulfide stress on ClpXP activity.
  J Bacteriol, 189, 7669-7680.  
16810315 G.Thibault, Y.Tsitrin, T.Davidson, A.Gribun, and W.A.Houry (2006).
Large nucleotide-dependent movement of the N-terminal domain of the ClpX chaperone.
  EMBO J, 25, 3367-3376.  
16525504 J.Kirstein, T.Schlothauer, D.A.Dougan, H.Lilie, G.Tischendorf, A.Mogk, B.Bukau, and K.Turgay (2006).
Adaptor protein controlled oligomerization activates the AAA+ protein ClpC.
  EMBO J, 25, 1481-1491.  
16135238 C.M.Farrell, A.D.Grossman, and R.T.Sauer (2005).
Cytoplasmic degradation of ssrA-tagged proteins.
  Mol Microbiol, 57, 1750-1761.  
16262695 W.Majeran, G.Friso, K.J.van Wijk, and O.Vallon (2005).
The chloroplast ClpP complex in Chlamydomonas reinhardtii contains an unusual high molecular mass subunit with a large apical domain.
  FEBS J, 272, 5558-5571.  
14988733 I.Dreveny, H.Kondo, K.Uchiyama, A.Shaw, X.Zhang, and P.S.Freemont (2004).
Structural basis of the interaction between the AAA ATPase p97/VCP and its adaptor protein p47.
  EMBO J, 23, 1030-1039.
PDB code: 1s3s
14962378 M.R.Maurizi, and D.Xia (2004).
Protein binding and disruption by Clp/Hsp100 chaperones.
  Structure, 12, 175-183.  
12887894 H.K.Song, and M.J.Eck (2003).
Structural basis of degradation signal recognition by SspB, a specificity-enhancing factor for the ClpXP proteolytic machine.
  Mol Cell, 12, 75-86.
PDB codes: 1ox8 1ox9
14536076 I.Levchenko, R.A.Grant, D.A.Wah, R.T.Sauer, and T.A.Baker (2003).
Structure of a delivery protein for an AAA+ protease in complex with a peptide degradation tag.
  Mol Cell, 12, 365-372.
PDB codes: 1ou8 1ou9 1oul
12950913 R.Hengge, and B.Bukau (2003).
Proteolysis in prokaryotes: protein quality control and regulatory principles.
  Mol Microbiol, 49, 1451-1462.  
14570582 S.Gottesman (2003).
Proteolysis in bacterial regulatory circuits.
  Annu Rev Cell Dev Biol, 19, 565-587.  
12732307 U.Jenal, and R.Hengge-Aronis (2003).
Regulation by proteolysis in bacterial cells.
  Curr Opin Microbiol, 6, 163-172.  
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.