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(-) Description

Title :  STRUCTURAL BASIS OF N-END RULE SUBSTRATE RECOGNITION IN ESCHERICHIA COLI BY THE CLPAP ADAPTOR PROTEIN CLPS - THE PHE PEPTIDE STRUCTURE
 
Authors :  V. J. Schuenemann, S. M. Kralik, R. Albrecht, S. K. Spall, K. N. Truscott, D. A. Dougan, K. Zeth
Date :  03 Feb 09  (Deposition) - 28 Apr 09  (Release) - 02 Jun 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  N-End Rule, Phe Peptide, Clps, Clpa, Clpp, Peptide-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. J. Schuenemann, S. M. Kralik, R. Albrecht, S. K. Spall, K. N. Truscott, D. A. Dougan, K. Zeth
Structural Basis Of N-End Rule Substrate Recognition In Escherichia Coli By The Clpap Adaptor Protein Clps.
Embo Rep. V. 10 508 2009
PubMed-ID: 19373253  |  Reference-DOI: 10.1038/EMBOR.2009.62

(-) Compounds

Molecule 1 - ATP-DEPENDENT CLP PROTEASE ADAPTER PROTEIN CLPS
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET
    Expression System Strain: BL21(GOLD)
    Expression System Taxid: 511693
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Other Details: CLPS PROTEIN FROM E. COLI AND N-END RULE PEPTIDE
    Strain: K-12
    Synonym: CLPS - PHE-PEPTIDE COMPLEX
 
Molecule 2 - N-END RULE PEPTIDE
    Chains: B, D
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2WA8)

(-) Sites  (0, 0)

(no "Site" information available for 2WA8)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WA8)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Glu B:6 -Glu B:7
2Glu B:7 -Leu B:8
3Trp C:7 -Leu C:8
4Gln C:12 -Leu C:13
5Ala C:14 -Glu C:15
6Glu C:15 -Glu C:16
7Lys D:110 -Gly D:111
8Gly D:111 -Glu D:112

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WA8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2WA8)

(-) Exons   (0, 0)

(no "Exon" information available for 2WA8)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:88
 aligned with CLPS_ECOLI | P0A8Q6 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:88
                                    28        38        48        58        68        78        88        98        
           CLPS_ECOLI    19 RDALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA 106
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2wa8A00 A:19-106  [code=3.30.1390.10, no name defined]                                   CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeee.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 2wa8 A  19 RDALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA 106
                                    28        38        48        58        68        78        88        98        


Chain B from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 2wa8 B   1 FRSKGEELFT  10
                                    10


Chain C from PDB  Type:PROTEIN  Length:103
 aligned with CLPS_ECOLI | P0A8Q6 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:103
                                    13        23        33        43        53        63        73        83        93       103   
           CLPS_ECOLI     4 TNDWLDFDQLAEEKVRDALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA 106
               SCOP domains ------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------2wa8C01 C:26-106  [code=3.30.1390.10, no name defined]                            CATH domains
           Pfam domains (1) ------------------ClpS-2wa8C01 C:22-103                                                             --- Pfam domains (1)
           Pfam domains (2) ------------------ClpS-2wa8C02 C:22-103                                                             --- Pfam domains (2)
         Sec.struct. author ............hhhhhhh....eeeeeee.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 2wa8 C   4 TNDWLDFDQLAEEKVRDALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA 106
                                    13        23        33        43        53        63        73        83        93       103   


Chain D from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 2wa8 D 107 FRSKGE 112
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2WA8)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: ClpS] (10)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (CLPS_ECOLI | P0A8Q6)
molecular function
    GO:0051087    chaperone binding    Interacting selectively and non-covalently with a chaperone protein, a class of proteins that bind to nascent or unfolded polypeptides and ensure correct folding or transport.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0030163    protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0009408    response to heat    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.

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  Cis Peptide Bonds
    Ala C:14 - Glu C:15   [ RasMol ]  
    Gln C:12 - Leu C:13   [ RasMol ]  
    Glu B:6 - Glu B:7   [ RasMol ]  
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    Gly D:111 - Glu D:112   [ RasMol ]  
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CLPS_ECOLI | P0A8Q6: 1lzw 1mbu 1mbv 1mbx 1mg9 1r6o 1r6q 2w9r 2wa9 3o1f 3o2b 3o2h 3o2o

(-) Related Entries Specified in the PDB File

1lzw STRUCTURAL BASIS OF CLPS-MEDIATED SWITCH IN CLPA SUBSTRATERECOGNITION
1mbu CRYSTAL STRUCTURE ANALYSIS OF CLPSN HETERODIMER
1mbv CRYSTAL STRUCTURE ANALYSIS OF CLPSN HETERODIMER TETRAGONALFORM
1mbx CRYSTAL STRUCTURE ANALYSIS OF CLPSN WITH TRANSITION METALION BOUND
1mg9 THE STRUCTURAL BASIS OF CLPS-MEDIATED SWITCH IN CLPASUBSTRATE RECOGNITION
1r6o ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPA/ATP-DEPENDENT CLP PROTEASE ADAPTOR PROTEIN CLPS
1r6q CLPNS WITH FRAGMENTS
2w9r STRUCTURAL BASIS OF N-END RULE SUBSTRATE RECOGNITION IN ESCHERICHIA COLI BY THE CLPAP ADAPTOR PROTEIN CLPS
2wa9 STRUCTURAL BASIS OF N-END RULE SUBSTRATE RECOGNITION IN ESCHERICHIA COLI BY THE CLPAP ADAPTOR PROTEIN CLPS - TRP PEPTIDE STRUCTURE