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(-) Description

Title :  CRYSTAL STRUCTURE OF RSEP PDZ2 DOMAIN
 
Authors :  X. Li, B. Wang, L. Feng, J. Wang, Y. Shi
Date :  20 Jul 09  (Deposition) - 11 Aug 09  (Release) - 08 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.09
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Cell Inner Membrane, Cell Membrane, Membrane, Metal-Binding, Metalloprotease, Protease, Transmembrane, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Li, B. Wang, L. Feng, H. Kang, Y. Qi, J. Wang, Y. Shi
Cleavage Of Rsea By Rsep Requires A Carboxyl-Terminal Hydrophobic Amino Acid Following Degs Cleavage
Proc. Natl. Acad. Sci. Usa V. 106 14837 2009
PubMed-ID: 19706448  |  Reference-DOI: 10.1073/PNAS.0903289106
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - REGULATOR OF SIGMA E PROTEASE
    Chains: A, B
    EC Number: 3.4.24.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: PDZ2 DOMAIN, RESIDUES 222-309
    Gene: RSEP
    Organism Scientific: ESCHERICHIA COLI K-12
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric/Biological Unit (1, 10)
No.NameCountTypeFull Name
1IOD10Ligand/IonIODIDE ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:220 , GLU A:223BINDING SITE FOR RESIDUE IOD A 101
2AC2SOFTWAREGLY A:280BINDING SITE FOR RESIDUE IOD A 102
3AC3SOFTWAREGLN B:252BINDING SITE FOR RESIDUE IOD A 103
4AC4SOFTWAREILE B:222 , VAL B:258BINDING SITE FOR RESIDUE IOD B 105
5AC5SOFTWAREHIS B:220 , LYS B:307BINDING SITE FOR RESIDUE IOD B 101
6AC6SOFTWAREGLY B:280 , PRO B:282BINDING SITE FOR RESIDUE IOD B 102
7AC7SOFTWAREPRO B:293BINDING SITE FOR RESIDUE IOD B 103
8AC8SOFTWAREHIS B:220BINDING SITE FOR RESIDUE IOD B 310
9AC9SOFTWAREMET A:221 , ILE A:222BINDING SITE FOR RESIDUE IOD A 105

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ID2)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Asn A:232 -Ser A:233
2Gly A:296 -Lys A:297
3Asn B:232 -Ser B:233
4Gly B:296 -Lys B:297

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ID2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ID2)

(-) Exons   (0, 0)

(no "Exon" information available for 3ID2)

(-) 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:90
 aligned with RSEP_ECOLI | P0AEH1 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:90
                                   229       239       249       259       269       279       289       299       309
           RSEP_ECOLI   220 PQIEPVLENVQPNSAASKAGLQAGDRIVKVDGQPLTQWVTFVMLVRDNPGKSLALEIERQGSPLSLTLIPESKPGNGKAIGFVGIEPKVI 309
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........ee...hhhhhhh.....eeeee..ee..hhhhhhhhhhhh....eeeeeee..eeeeeee..eee......eee..ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 3id2 A 220 HMIEPVLENVQPNSAASKAGLQAGDRIVKVDGQPLTQWVTFVMLVRDNPGKSLALEIERQGSPLSLTLIPESKPGNGKAIGFVGIEPKVI 309
                                   229       239       249       259       269       279       289       299       309


Chain B from PDB  Type:PROTEIN  Length:90
 aligned with RSEP_ECOLI | P0AEH1 from UniProtKB/Swiss-Prot  Length:450

    Alignment length:90
                                   229       239       249       259       269       279       289       299       309
           RSEP_ECOLI   220 PQIEPVLENVQPNSAASKAGLQAGDRIVKVDGQPLTQWVTFVMLVRDNPGKSLALEIERQGSPLSLTLIPESKPGNGKAIGFVGIEPKVI 309
               SCOP domains ------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........ee...hhhhhh......eeeee..ee..hhhhhhhhhhh.....eeeeeee..eeeeeee..eee......eee..ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------ Transcript
                 3id2 B 220 HMIEPVLENVQPNSAASKAGLQAGDRIVKVDGQPLTQWVTFVMLVRDNPGKSLALEIERQGSPLSLTLIPESKPGNGKAIGFVGIEPKVI 309
                                   229       239       249       259       269       279       289       299       309
   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 3ID2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ID2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ID2)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (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 | P0AEH1: 2zpl 2zpm 3id1 3id3 3id4

(-) Related Entries Specified in the PDB File

3id1 RSEP PDZ1 DOMAIN
3id3 RSEP PDZ2 I304A DOMAIN
3id4 RSEP PDZ2 FUSED GKASPV PEPTIDE DOMAIN