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(-) Description

Title :  E. COLI CLPS IN COMPLEX WITH A PHE N-END RULE PEPTIDE
 
Authors :  G. Roman-Hernandez, R. A. Grant, R. T. Sauer, T. A. Baker, A. De Regt
Date :  22 Jul 10  (Deposition) - 14 Dec 11  (Release) - 25 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Adaptor, Protein-Peptide Complex, Peptide-Binding Protein, N-End Rule Peptide, Peptide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Roman-Hernandez, J. Y. Hou, R. A. Grant, R. T. Sauer, T. A. Baker
The Clps Adaptor Mediates Staged Delivery Of N-End Rule Substrates To The Aaa+ Clpap Protease.
Mol. Cell V. 43 217 2011
PubMed-ID: 21777811  |  Reference-DOI: 10.1016/J.MOLCEL.2011.06.009

(-) Compounds

Molecule 1 - ATP-DEPENDENT CLP PROTEASE ADAPTOR PROTEIN CLPS
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 2-106
    Gene: CLPS, YLJA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
 
Molecule 2 - PHE N-END RULE PEPTIDE
    Chains: B, D
    Engineered: YES
    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  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2SO41Ligand/IonSULFATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO41Ligand/IonSULFATE ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO4-1Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:66 , TYR A:67 , GLN A:68 , GLY A:69BINDING SITE FOR RESIDUE SO4 A 107
2AC2SOFTWARELYS A:23 , ARG A:93BINDING SITE FOR RESIDUE CL A 1

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O2B)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3O2B)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O2B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3O2B)

(-) Exons   (0, 0)

(no "Exon" information available for 3O2B)

(-) 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:84
 aligned with CLPS_ECOLI | P0A8Q6 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:84
                                    32        42        52        62        72        82        92       102    
           CLPS_ECOLI    23 KPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA 106
               SCOP domains d3o2ba_ A: automated matches                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeee.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------ Transcript
                 3o2b A  23 KPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA 106
                                    32        42        52        62        72        82        92       102    


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
                 3o2b B   1 FRSKGEELFT  10
                                    10


Chain C from PDB  Type:PROTEIN  Length:105
 aligned with CLPS_ECOLI | P0A8Q6 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:105
                                    11        21        31        41        51        61        71        81        91       101     
           CLPS_ECOLI     2 GKTNDWLDFDQLAEEKVRDALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA 106
               SCOP domains d3o2bc_ C: automated matches                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------- Transcript
                 3o2b C   2 GKTNDWLDFDQLAEEKVRDALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA 106
                                    11        21        31        41        51        61        71        81        91       101     


Chain D from PDB  Type:PROTEIN  Length:5
                                     
               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
                 3o2b D   1 FRSKG   5
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O2B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3O2B)

(-) 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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 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 2wa8 2wa9 3o1f 3o2h 3o2o

(-) Related Entries Specified in the PDB File

2wa8 ORIGINAL ENTRY THAT WAS THE SOURCE OF STRUCTURE FACTORS USED IN REFINEMENT
3o1f SAME PROTEIN WITH NO BOUND PEPTIDE
3o2b SAME PROTEIN WITH LEU N-END RULE PEPTIDE BOUND
3o2o