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(-) Description

Title :  STRUCTURE OF THE ZBD-XB COMPLEX
 
Authors :  E. Y. Park, B. G. Lee, S. B. Hong, H. W. Kim, H. K. Song
Date :  22 Jun 06  (Deposition) - 13 Feb 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B,P,Q
Keywords :  Protein-Peptide Complex, Metal Binding Protein, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Y. Park, B. G. Lee, S. B. Hong, H. W. Kim, H. Jeon, H. K. Song
Structural Basis Of Sspb-Tail Recognition By The Zinc Binding Domain Of Clpx.
J. Mol. Biol. V. 367 514 2007
PubMed-ID: 17258768  |  Reference-DOI: 10.1016/J.JMB.2007.01.003
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: ZINC BINDING DOMAIN(ZBD)
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: CLPX
 
Molecule 2 - SSPB-TAIL PEPTIDE
    Chains: P, Q
    Engineered: YES
    Other Details: XB PEPTIDE (APALRVVK) IS SYNTHESIZED. EXCEPT THE FIRST ALANINE, THE SEQUENCE OCCURS NATURALLY IN E. COLI SSPB
    Synonym: XB
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABPQ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:14 , CYS A:17 , CYS A:36 , CYS A:39BINDING SITE FOR RESIDUE ZN A 100
2AC2SOFTWARECYS B:14 , CYS B:17 , CYS B:36 , CYS B:39BINDING SITE FOR RESIDUE ZN B 100

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2DS8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2DS8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2DS8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2DS8)

(-) Exons   (0, 0)

(no "Exon" information available for 2DS8)

(-) 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:43
 aligned with CLPX_ECOLI | P0A6H1 from UniProtKB/Swiss-Prot  Length:424

    Alignment length:43
                                    19        29        39        49   
           CLPX_ECOLI    10 GKLLYCSFCGKSQHEVRKLIAGPSVYICDECVDLCNDIIREEI  52
               SCOP domains d2ds8a_ A: automated matches                SCOP domains
               CATH domains ------------------------------------------- CATH domains
               Pfam domains ------------------------------------------- Pfam domains
         Sec.struct. author ..................eee....eeehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------- PROSITE
                 Transcript ------------------------------------------- Transcript
                 2ds8 A   9 GKLLYCSFCGKSQHEVRKLIAGPSVYICDECVDLCNDIIREEI  51
                                    18        28        38        48   


Chain B from PDB  Type:PROTEIN  Length:41
 aligned with CLPX_ECOLI | P0A6H1 from UniProtKB/Swiss-Prot  Length:424

    Alignment length:41
                                    20        30        40        50 
           CLPX_ECOLI    11 KLLYCSFCGKSQHEVRKLIAGPSVYICDECVDLCNDIIREE  51
               SCOP domains d2ds8b_ B: automated matches              SCOP domains
               CATH domains ----------------------------------------- CATH domains
               Pfam domains ----------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh..eeee..eeeehhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------- PROSITE
                 Transcript ----------------------------------------- Transcript
                 2ds8 B  10 KLLYCSFCGKSQHEVRKLIAGPSVYICDECVDLCNDIIREE  50
                                    19        29        39        49 


Chain P from PDB  Type:PROTEIN  Length:6
 aligned with SSPB_ECOLI | P0AFZ3 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:6
           SSPB_ECOLI   160 ALRVVK 165
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ..ee.. Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 2ds8 P 160 ALRVVK 165


Chain Q from PDB  Type:PROTEIN  Length:6
 aligned with SSPB_ECOLI | P0AFZ3 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:6
           SSPB_ECOLI   160 ALRVVK 165
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ..eeee Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 2ds8 Q 160 ALRVVK 165
   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/Biological Unit
(-)
Class: Small proteins (3458)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2DS8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2DS8)

(-) Gene Ontology  (21, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (CLPX_ECOLI | P0A6H1)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004176    ATP-dependent peptidase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate, to drive the hydrolysis of peptide bonds.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
    GO:0051082    unfolded protein binding    Interacting selectively and non-covalently with an unfolded protein.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0051704    multi-organism process    A biological process which involves another organism of the same or different species.
    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:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0043335    protein unfolding    The process of assisting in the disassembly of non-covalent linkages in a protein or protein aggregate, often where the proteins are in a non-functional or denatured state.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.

Chain P,Q   (SSPB_ECOLI | P0AFZ3)
molecular function
    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:0045732    positive regulation of protein catabolic process    Any process that activates or increases the frequency, rate or extent of 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.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005840    ribosome    An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CLPX_ECOLI | P0A6H1: 1ovx 2ds5 2ds6 2ds7 3hte 3hws 4i34 4i4l 4i5o 4i63 4i81 4i9k
        SSPB_ECOLI | P0AFZ3: 1ox8 1ox9 1yfn

(-) Related Entries Specified in the PDB File

2ds5 ZBD ALONE IN ORTHORHOMBIC CRYSTAL FORM
2ds6 ZBD ALONE IN TETRAGOANL CRYSTAL FORM
2ds7 ZBD ALONE IN HEXAGONAL CRYSTAL FORM