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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF PDZ DOMAIN B
 
Authors :  K. Inaba, M. Suzuki
Date :  17 Jul 08  (Deposition) - 21 Oct 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.98
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Keywords :  Metalloproteinase, Membrane Protein, Pdz Domain, Hydrolase, Inner Membrane, Membrane, Metal-Binding, Metalloprotease, Protease, Transmembrane, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Inaba, M. Suzuki, K. Maegawa, Y. Akiyama
Crystal Structure Analysis Of Pdz-Domain B
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REGULATOR OF SIGMA E PROTEASE
    ChainsA
    EC Number3.4.24.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPGEX-5X-1
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentPDZ-DOMAIN B
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK12

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (1x)A
Biological Unit 2 (2x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1MLY6Mod. Amino AcidN-DIMETHYL-LYSINE
2MSE1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1MLY6Mod. Amino AcidN-DIMETHYL-LYSINE
2MSE1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 14)
No.NameCountTypeFull Name
1MLY12Mod. Amino AcidN-DIMETHYL-LYSINE
2MSE2Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2ZPM)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZPM)

(-) 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:86
 aligned with RSEP_ECOLI | P0AEH1 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:86
                                   233       243       253       263       273       283       293       303      
           RSEP_ECOLI   224 PVLENVQPNSAASKAGLQAGDRIVKVDGQPLTQWVTFVMLVRDNPGKSLALEIERQGSPLSLTLIPESKPGNGKAIGFVGIEPKVI 309
               SCOP domains -------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) PDZ-2zpmA01 A:224-277                                 -------------------------------- Pfam domains (1)
           Pfam domains (2) Peptidase_M50-2zpmA02 A:224-309                                                        Pfam domains (2)
         Sec.struct. author ....ee...hhhhhh......eeeee..ee..hhhhhhhhhhhh....eeeeeee..eeeeeee..eee......eee..ee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------- Transcript
                 2zpm A 224 PVLENVQPNSAASkAGLQAGDRIVkVDGQPLTQWVTFVmLVRDNPGkSLALEIERQGSPLSLTLIPESkPGNGkAIGFVGIEPkVI 309
                                   233   |   243    |  253       263      |273       283       293   |   303   |  
                                       237-MLY    248-MLY       262-MSE 270-MLY               292-MLY|       307-MLY
                                                                                                   297-MLY        

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  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 2ZPM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 2)

Asymmetric Unit
(-)
Clan: PDZ-like (184)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (RSEP_ECOLI | P0AEH1)
molecular function
    GO:0043856    anti-sigma factor antagonist activity    The function of binding to an anti-sigma factor and stopping, preventing or reducing the rate of its activity.
    GO:0045152    antisigma factor binding    Interacting selectively and non-covalently with an antisigma factor, a factor which inhibits the ability of the sigma factor to function as a transcriptional initiator.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RSEP_ECOLI | P0AEH12zpl 3id1 3id2 3id3 3id4

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