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(-) Description

Title :  STRUCTURE OF THE DELTA PDZ TRUNCATION OF THE DEGS PROTEASE
 
Authors :  J. Sohn, R. A. Grant, R. T. Sauer
Date :  26 Jun 07  (Deposition) - 11 Dec 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Degs, Protease, Periplasmic Stress Sensor, Htra, Allosteric Activation, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Sohn, R. A. Grant, R. T. Sauer
Allosteric Activation Of Degs, A Stress Sensor Pdz Protease
Cell(Cambridge, Mass. ) V. 131 572 2007
PubMed-ID: 17981123  |  Reference-DOI: 10.1016/J.CELL.2007.08.044

(-) Compounds

Molecule 1 - PROTEASE DEGS
    ChainsA, B, C
    EC Number3.4.21.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET21B
    Expression System StrainX90(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 27-256
    GeneDEGS, HHOB, HTRH
    Organism ScientificESCHERICHIA COLI
    Organism Taxid83333
    StrainK12

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:79 , HIS A:96 , VAL A:97 , HIS A:198 , GLY A:199 , ASN A:200 , SER A:201 , HOH A:351 , HOH A:377BINDING SITE FOR RESIDUE PO4 A 306
2AC2SOFTWARELEU B:79 , HIS B:96 , VAL B:97 , HIS B:198 , GLY B:199 , ASN B:200 , SER B:201 , LEU B:218BINDING SITE FOR RESIDUE PO4 B 307
3AC3SOFTWAREHIS C:96 , HIS C:198 , GLY C:199 , SER C:201 , LEU C:218BINDING SITE FOR RESIDUE PO4 C 308

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QF3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QF3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2QF3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2QF3)

(-) Exons   (0, 0)

(no "Exon" information available for 2QF3)

(-) 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:200
 aligned with DEGS_ECOLI | P0AEE3 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:221
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255 
           DEGS_ECOLI    36 QFDSTDETPASYNLAVRRAAPAVVNVYNRGLNTNSHNQLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPFQLATKIMDKLIRDGRVIR 256
               SCOP domains d2qf3a_ A: Stress sensor protea    se DegS, catalytic domain                                                                                                                                                                  SCOP domains
               CATH domains 2qf3A01 A:36-141 Trypsin-like s    erine proteases                                                        2qf3A02 A:142-256 Trypsin-like serine          proteases                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........hhhhhhhhh..eeeeeeee.----....eeeeeeeeee.....eeeeehhhhh...eeeee.....eee.eeeeee....eeeee......................eeeeeehhhhh..eeeeeeeee...---------..eee...........eeee....eeeeeeee.--------....eeeeehhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qf3 A  36 QFDSTDETPASYNLAVRRAAPAVVNVYNRGL----HNQLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGR---------NFLQTDASINHGNSGGALVNSLGELMGINTLSF--------PEGIGFAIPFQLATKIMDKLIRDGRVIR 256
                                    45        55        65|    |  75        85        95       105       115       125       135       145       155       165       175  |      -  |    195       205       215    |    -   |   235       245       255 
                                                         66   71                                                                                                        178       188                             220      229                           

Chain B from PDB  Type:PROTEIN  Length:200
 aligned with DEGS_ECOLI | P0AEE3 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:214
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247    
           DEGS_ECOLI    38 DSTDETPASYNLAVRRAAPAVVNVYNRGLNTNSHNQLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPFQLATKIMDKLIRD 251
               SCOP domains d2qf3b_ B: Stress sensor prote       ase DegS, catalytic domain                                                                                                                                                        SCOP domains
               CATH domains 2qf3B01 B:38-141 Trypsin-like        serine proteases                                                   2qf3B02 B:142-251 Trypsin-like serine proteases                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhhhh..eeeeeee...-------.eeeeeeeee.....eeeeehhhhh...eeeee.....eeeeeeeeee....eeeee......................eeeeeehhhhh..eeeeeeeeee.............eee...........eeee....eeeee....-------.....eeeeehhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qf3 B  38 DSTDETPASYNLAVRRAAPAVVNVYNRGLN-------EIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSF-------TPEGIGFAIPFQLATKIMDKLIRD 251
                                    47        57        67       |77        87        97       107       117       127       137       147       157       167       177       187       197       207       217  |      -|      237       247    
                                                        67      75                                                                                                                                              220     228                       

Chain C from PDB  Type:PROTEIN  Length:195
 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 d2qf3c_ C: Stress sensor protease DegS, catalytic domain                                                                                                                                                           SCOP domains
               CATH domains 2qf3C01 C:42-141 Trypsin-like serine proteases                                                      2qf3C02 C:142-251 Trypsin-like serine         proteases                                                        CATH domains
           Pfam domains (1) --------Trypsin-2qf3C04 C:50-245                                                                                                                                                                            --PDZ- Pfam domains (1)
           Pfam domains (2) --------Trypsin-2qf3C05 C:50-245                                                                                                                                                                            --PDZ- Pfam domains (2)
           Pfam domains (3) --------Trypsin-2qf3C06 C:50-245                                                                                                                                                                            --PDZ- Pfam domains (3)
         Sec.struct. author .....hhhhhhhhh..eeeeeeeee.......eeeeeeeeeee.....eeeeehhhhh...eeeee.....eeeeeeeeee....eeeee......................eeeeeehhhhh..eeeeeeeee...--------...eee...........eeee....eeeeeeee.-------.....eeeeehhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qf3 C  42 ETPASYNLAVRRAAPAVVNVYNRGLNTNSHNQLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGR--------QNFLQTDASINHGNSGGALVNSLGELMGINTLSF-------TPEGIGFAIPFQLATKIMDKLIRD 251
                                    51        61        71        81        91       101       111       121       131       141       151       161       171      |  -     | 191       201       211        |-      |231       241       251
                                                                                                                                                                  178      187                              220     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-2qf3C01C:248-251
1bPDZ-2qf3C02C:248-251
1cPDZ-2qf3C03C: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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 Related Entries

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

UniProtKB/Swiss-Prot
        DEGS_ECOLI | P0AEE31sot 1soz 1te0 1vcw 2qf0 2qgr 2r3u 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

2qf0 SAME MOLECULE, DIFFERENT CRYSTAL FORM
2qgr