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(-) Description

Title :  STRUCTURE OF THE PROTEASE DOMAIN OF DEGS (DEGS-DELTAPDZ) AT 1.65 A
 
Authors :  J. Sohn, R. A. . Grant, R. T. Sauer
Date :  20 Jan 10  (Deposition) - 25 Aug 10  (Release) - 10 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Protease, Stress-Sensor, Htra, Pdz Omp, Hydrolase, Serine Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Sohn, R. A. Grant, R. T. Sauer
Allostery Is An Intrinsic Property Of The Protease Domain O Degs: Implications For Enzyme Function And Evolution.
J. Biol. Chem. V. 285 34039 2010
PubMed-ID: 20739286  |  Reference-DOI: 10.1074/JBC.M110.135541

(-) Compounds

Molecule 1 - PROTEASE DEGS
    Chains: A, B, C
    EC Number: 3.4.21.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: X90(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PROTEASE DOMAIN
    Gene: B3235, DEGS, HHOB, HTRH, JW3204
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1PO42Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:186 , PHE A:189 , ILE A:236 , HOH A:300 , HOH A:326 , HOH A:616 , LEU B:32BINDING SITE FOR RESIDUE PO4 A 2
2AC2SOFTWARETYR A:47 , GLN A:170 , HOH A:628 , TYR B:47 , GLN B:170 , TYR C:47 , GLN C:170BINDING SITE FOR RESIDUE PO4 B 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3LGI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LGI)

(-) 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:220
 aligned with DEGS_ECOLI | P0AEE3 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:220
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256
           DEGS_ECOLI    37 FDSTDETPASYNLAVRRAAPAVVNVYNRGLNTNSHNQLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPFQLATKIMDKLIRDGRVIR 256
               SCOP domains d3lgia_ A: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhhhhhh..eeeeeee...........eeeeeeeeeee...eeeeehhhhh...eeeee.....eeeeeeeeee....eeeee......................eeeeeehhhhh..eeeeeeeeee.............eee...........eee.....eeeee................eeeeehhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lgi A  37 FDSTDETPASYNLAVRRAAPAVVNVYNRGLNTNSHNQLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPFQLATKIMDKLIRDGRVIR 256
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256


Chain B from PDB  Type:PROTEIN  Length:228
 aligned with DEGS_ECOLI | P0AEE3 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:228
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248        
           DEGS_ECOLI    29 LNPLSTPQFDSTDETPASYNLAVRRAAPAVVNVYNRGLNTNSHNQLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPFQLATKIMDKLIRDGRVIR 256
               SCOP domains d3lgib_ B: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..................hhhhhhhhh..eeeeeeeee.......eeeeeeeeeeeee...eeeeehhhhh...eeeee.....eeeeeeeeee....eeeee......................eeeeeehhhhh..eeeeeeeee..............eee...........eeee....eeeee................eeeeehhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3lgi B  29 LNPLSTPQFDSTDETPASYNLAVRRAAPAVVNVYNRGLNTNSHNQLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPFQLATKIMDKLIRDGRVIR 256
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248        


Chain C from PDB  Type:PROTEIN  Length:215
 aligned with DEGS_ECOLI | P0AEE3 from UniProtKB/Swiss-Prot  Length:355

    Alignment length:219
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247         
           DEGS_ECOLI    38 DSTDETPASYNLAVRRAAPAVVNVYNRGLNTNSHNQLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPFQLATKIMDKLIRDGRVIR 256
               SCOP domains d3lgic_ C: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------Trypsin-3lgiC04 C:    50-245                                                                                                                                                                        --PDZ-3lgiC Pfam domains (1)
           Pfam domains (2) ------------Trypsin-3lgiC05 C:    50-245                                                                                                                                                                        --PDZ-3lgiC Pfam domains (2)
           Pfam domains (3) ------------Trypsin-3lgiC06 C:    50-245                                                                                                                                                                        --PDZ-3lgiC Pfam domains (3)
         Sec.struct. author .........hhhhhhhhh..eeeeeeeee.----..eeeeeeeeeee......eeeehhhhh...eeeee.....eeeeeeeeee....eeeeee.....................eeeeeehhhhh..eeeeeeeeeeee..........eeee...........eeee....eeeeeeee.............eeeeehhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lgi C  38 DSTDETPASYNLAVRRAAPAVVNVYNRGLN----NQLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPFQLATKIMDKLIRDGRVIR 256
                                    47        57        67    |   77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247         
                                                        67   72
   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
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 6)

Asymmetric/Biological Unit
(-)
Clan: PDZ-like (184)
(-)
Family: PDZ (172)
(-)
Escherichia coli (strain K12) (21)
1aPDZ-3lgiC01C:248-256
1bPDZ-3lgiC02C:248-256
1cPDZ-3lgiC03C:248-256
(-)
Clan: Peptidase_PA (797)

(-) 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 | P0AEE3: 1sot 1soz 1te0 1vcw 2qf0 2qf3 2qgr 2r3u 2r3y 2rce 3b8j 3gcn 3gco 3gds 3gdu 3gdv 3lgt 3lgu 3lgv 3lgw 3lgy 3lh1 3lh3 4rqy 4rqz 4rr0 4rr1

(-) Related Entries Specified in the PDB File

2qf3 SAME STRUCTURE AT LOWER RESOLUTION
3lgt
3lgu
3lgv
3lgw
3lgy
3lh1
3lh3