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(-) Description

Title :  E. COLI CLPS IN COMPLEX WITH A LEU 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 :  1.70
Chains :  Asym./Biol. Unit :  A,B
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
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CLPS
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: YLJA
 
Molecule 2 - DNA PROTECTION DURING STARVATION PROTEIN
    Chains: B
    EC Number: 1.16.-.-
    Engineered: YES
    Fragment: UNP RESIDUES 6-16
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Synonym: PEXB, VTM
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3O2H)

(-) Sites  (0, 0)

(no "Site" information available for 3O2H)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O2H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3O2H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O2H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3O2H)

(-) Exons   (0, 0)

(no "Exon" information available for 3O2H)

(-) Sequences/Alignments

Asymmetric/Biological 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:95
 aligned with CLPS_ECOLI | P0A8Q6 from UniProtKB/Swiss-Prot  Length:106

    Alignment length:95
                                    21        31        41        51        61        71        81        91       101     
           CLPS_ECOLI    12 QLAEEKVRDALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA 106
               SCOP domains d3o2ha_ A: Adaptor protein ClpS (YljA)                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh......eeeeeee.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhheeeeeeeehhhhhhhhhhhhhhhhhh....eeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 3o2h A  12 QLAEEKVRDALKPPSMYKVILVNDDYTPMEFVIDVLQKFFSYDVERATQLMLAVHYQGKAICGVFTAEVAETKVAMVNKYARENEHPLLCTLEKA 106
                                    21        31        41        51        61        71        81        91       101     


Chain B from PDB  Type:PROTEIN  Length:11
 aligned with DPS_ECOLI | P0ABT2 from UniProtKB/Swiss-Prot  Length:167

    Alignment length:11
                                    15 
            DPS_ECOLI     6 LVKSKATNLLY  16
               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
                 3o2h B   1 LVKSKATNLLY  11
                                    10
   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, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O2H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3O2H)

(-) Gene Ontology  (18, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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.

Chain B   (DPS_ECOLI | P0ABT2)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008199    ferric iron binding    Interacting selectively and non-covalently with ferric iron, Fe(III).
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016722    oxidoreductase activity, oxidizing metal ions    Catalysis of an oxidation-reduction in which the oxidation state of metal ion is altered.
    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:0006879    cellular iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions at the level of a cell.
    GO:0030261    chromosome condensation    The progressive compaction of dispersed interphase chromatin into threadlike chromosomes prior to mitotic or meiotic nuclear division, or during apoptosis, in eukaryotic cells.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0042594    response to starvation    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 starvation stimulus, deprivation of nourishment.
    GO:0006950    response to stress    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 disturbance in organismal or cellular homeostasis, usually, but not necessarily, exogenous (e.g. temperature, humidity, ionizing radiation).
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0009295    nucleoid    The region of a virus, bacterial cell, mitochondrion or chloroplast to which the nucleic acid is confined.

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  3o2h
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  1.16.-.-
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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 3o2b 3o2o
        DPS_ECOLI | P0ABT2: 1dps 1f30 1f33 1jre 1jts 1l8h 1l8i 2w9r

(-) Related Entries Specified in the PDB File

2w9r ORIGINAL ENTRY THAT WAS SOURCE OF STRUCTURE FACTORS FOR REFINEMENT
3o1f
3o2h
3o2o