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(-) Description

Title :  CRYSTAL STRUCTURE OF THE PDZ DELETION MUTANT OF DEGS
 
Authors :  T. Clausen, R. Kurzbauer
Date :  30 Aug 07  (Deposition) - 27 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Serine Protease, Catalytic Triad, Hydrolase, Periplasm (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Hasselblatt, R. Kurzbauer, C. Wilken, T. Krojer, J. Sawa, J. Kurt, R. Kirk, S. Hasenbein, M. Ehrmann, T. Clausen
Regulation Of The Sigmae Stress Response By Degs: How The Pdz Domain Keeps The Protease Inactive In The Resting State And Allows Integration Of Different Omp-Derived Stress Signals Upon Folding Stress.
Genes Dev. V. 21 2659 2007
PubMed-ID: 17938245  |  Reference-DOI: 10.1101/GAD.445307
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEASE DEGS
    ChainsA, B, C
    EC Number3.4.21.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET21A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneDEGS, HHOB, HTRH
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2R3U)

(-) Sites  (0, 0)

(no "Site" information available for 2R3U)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R3U)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2R3U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R3U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R3U)

(-) Exons   (0, 0)

(no "Exon" information available for 2R3U)

(-) 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:202
 aligned with DEGS_ECOLI | P0AEE3 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:210
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
           DEGS_ECOLI    42 ETPASYNLAVRRAAPAVVNVYNRGLNTNSHNQLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPFQLATKIMDKLIRD 251
               SCOP domains d2r3ua_ A: Stress sensor p    rotease DegS, catalytic domain                                                                                                                                                       SCOP domains
               CATH domains 2r3uA01 A:42-141 Trypsin-l    ike serine proteases                                                  2r3uA02 A:142-251 Trypsin-like serine proteases                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhhhh..eeeeeeeee.----..eeeeeeeeeeeee...eeeee........eeeee.....eee.eeeeee....eeeee......................eeeeeehhhhh..eeeeeeeeeee...........eeee...........eeee....eeeeeeee...----......eeeeehhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2r3u A  42 MTPASYNLAVRRAAPAVVNVYNRGLN----NQLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDK----ETPEGIGFAIPFQLATKIMDKLIRD 251
                                    51        61     |   -|       81        91       101       111       121       131       141       151       161       171       181       191       201       211       221|    | 231       241       251
                                                    67   72                                                                                                                                                   222  227                        

Chain B from PDB  Type:PROTEIN  Length:195
 aligned with DEGS_ECOLI | P0AEE3 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:211
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251 
           DEGS_ECOLI    42 ETPASYNLAVRRAAPAVVNVYNRGLNTNSHNQLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPFQLATKIMDKLIRDG 252
               SCOP domains d2r3ub_ B: Stress senso              r protease DegS, catalytic domain                                                                                                                                              SCOP domains
               CATH domains 2r3uB01 B:42-141 Trypsi              n-like serine proteases                                        2r3uB02 B:142-252 Trypsin-like serine proteases                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh..eeeeee.--------------..eeeeee...eeeeehhhhh....eeee.....eeeeeeeeee....eeeee......................eeeeeehhhhh..eeeeeeeee..............eee...........eeee....eeeee......--........eeeeehhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r3u B  42 MTPASYNLAVRRAAPAVVNVYNR--------------LGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDK--DGETPEGIGFAIPFQLATKIMDKLIRDG 252
                                    51        61  |      -       |81        91       101       111       121       131       141       151       161       171       181       191       201       211       221|  |   231       241       251 
                                                 64             79                                                                                                                                            222  |                           
                                                                                                                                                                                                                 225                           

Chain C from PDB  Type:PROTEIN  Length:185
 aligned with DEGS_ECOLI | P0AEE3 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:210
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
           DEGS_ECOLI    42 ETPASYNLAVRRAAPAVVNVYNRGLNTNSHNQLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPFQLATKIMDKLIRD 251
               SCOP domains d2r3uc_ C: Stress senso         r protease DegS, catalytic domain                                                                                                                                                  SCOP domains
               CATH domains 2r3uC01 C:42-141 Trypsi         n-like serine proteases                                             2r3uC02 C:142-251 Trypsin-like serin          e proteases                                                      CATH domains
           Pfam domains (1) --------Trypsin-2r3uC04          C:50-245                                                                                                                                                                   --PDZ- Pfam domains (1)
           Pfam domains (2) --------Trypsin-2r3uC05          C:50-245                                                                                                                                                                   --PDZ- Pfam domains (2)
           Pfam domains (3) --------Trypsin-2r3uC06          C:50-245                                                                                                                                                                   --PDZ- Pfam domains (3)
         Sec.struct. author .....hhhhhhhhh..eeeeeee---------....eeeeeeeee...eeeeehhhhh...eeeee.....eeeeeeeeee....eeeee......................eeeeeehhhhh..eeeeeeeee..----------..eee...........eeee....eeeee.....------.....eeeeehhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2r3u C  42 MTPASYNLAVRRAAPAVVNVYNR---------LEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATG----------NFLQTDASINHGNSGGALVNSLGELMGINTLSFD------TPEGIGFAIPFQLATKIMDKLIRD 251
                                    51        61  |      -  |     81        91       101       111       121       131       141       151       161       171     |   -      |191       201       211       221      |231       241       251
                                                 64        74                                                                                                    177        188                              221    228                       

   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, 3)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 6)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Clan: PDZ-like (184)
(-)
Family: PDZ (172)
1aPDZ-2r3uC01C:248-251
1bPDZ-2r3uC02C:248-251
1cPDZ-2r3uC03C:248-251

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (DEGS_ECOLI | P0AEE3)
molecular function
    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: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.
    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).
    GO:0004252    serine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0071218    cellular response to misfolded protein    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a misfolded protein stimulus.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0071575    integral component of external side of plasma membrane    The component of the plasma membrane consisting of the gene products that penetrate only the external side of the membrane.
    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:0031226    intrinsic component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having either part of their peptide sequence embedded in the hydrophobic region of the membrane or some other covalently attached group such as a GPI anchor that is similarly embedded in the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    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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  3.4.21.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        DEGS_ECOLI | P0AEE31sot 1soz 1te0 1vcw 2qf0 2qf3 2qgr 2r3y 2rce 3b8j 3gcn 3gco 3gds 3gdu 3gdv 3lgi 3lgt 3lgu 3lgv 3lgw 3lgy 3lh1 3lh3 4rqy 4rqz 4rr0 4rr1

(-) Related Entries Specified in the PDB File

1sot 1soz 1vcw 2r3y