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(-) Description

Title :  CRYSTAL STRUCTURE OF DEGP (HTRA)
 
Authors :  T. Krojer, M. Garrido-Franco, R. Huber, M. Ehrmann, T. Clausen
Date :  04 Feb 02  (Deposition) - 03 Apr 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (6x)
Biol. Unit 2:  B  (6x)
Keywords :  Protein Quality Control, Serine Protease, Trypsin, Chaperone, Pdz, Atp-Independent, Temperature-Regulated, Periplasm, Cage-Forming Protein, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. Krojer, M. Garrido-Franco, R. Huber, M. Ehrmann, T. Clausen
Crystal Structure Of Degp (Htra) Reveals A New Protease-Chaperone Machine.
Nature V. 416 455 2002
PubMed-ID: 11919638  |  Reference-DOI: 10.1038/416455A
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEASE DO
    ChainsA, B
    EC Number3.4.21.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneDEGP
    MutationYES
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    SynonymDEGP, HTRA

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (6x)A 
Biological Unit 2 (6x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 25)

Asymmetric Unit (1, 25)
No.NameCountTypeFull Name
1MSE25Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 72)
No.NameCountTypeFull Name
1MSE72Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 78)
No.NameCountTypeFull Name
1MSE78Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1KY9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KY9)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Mse A:42 -Pro A:43
2Ala A:230 -Pro A:231
3Mse B:42 -Pro B:43

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KY9)

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.DEGP_ECOLI280-371
 
377-466
 
  4A:254-345
B:254-345
A:351-353
B:351-440
Biological Unit 1 (1, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.DEGP_ECOLI280-371
 
377-466
 
  12A:254-345
-
A:351-353
-
Biological Unit 2 (1, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.DEGP_ECOLI280-371
 
377-466
 
  12-
B:254-345
-
B:351-440

(-) Exons   (0, 0)

(no "Exon" information available for 1KY9)

(-) 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:311
 aligned with DEGP_ECOLI | P0C0V0 from UniProtKB/Swiss-Prot  Length:474

    Alignment length:343
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376   
           DEGP_ECOLI    37 QMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRNFQQFFGDDSPFCQEGSPFQSSPFCQGGQGGNGGGQQQKFMALGSGVIIDADKGYVVTNNHVVDNATVIKVQLSDGRKFDAKMVGKDPRSDIALIQIQNPKNLTAIKMADSDALRVGDYTVAIGNPFGLGETVTSGIVSALGRSGLNAENYENFIQTDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLTSQMVEYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKQVNVNLE 379
               SCOP domains d1ky9a2 A:11-259 Protease Do (DegP, HtrA)                           , catalytic domain                                                                                                                                                                   d1ky9a1 A:260-353 Protease Do (DegP, HtrA), C-terminal domains                                 SCOP domains
               CATH domains --------------1ky9A01  ------------------                           --------1ky9A01 A:25-33,A:87-154,A:245-259 Trypsin-like serine proteases    1ky9A02 A:155-244 Trypsin-like seri     ne proteases                                      1ky9A01        -1ky9A03 A:261-353  [code=2.30.42.10, no name defined]                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh..eeeeeeeeeeee..............---------------------------.eeeeeeeeeeeeeee....eeeeehhhhh.eeeeeeee....eeeeeeeeee....eeeeee............hhhhh....eeeeee.......eeeeeeeeee....-----....eee...........eee.....eeeeee............eeeeehhhhhhhhhhhhhhh...............hhhhhh........ee...................ee..........hhhhhhhh.........eeeee....eee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDZ  PDB: A:254-345 UniProt: 280-371                                                        -----PDZ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ky9 A  11 QmPSLAPmLEKVmPSVVSINVEGSTTVNTPRmPRNFQQFFG---------------------------GQQQKFmALGSGVIIDADKGYVVTNNHVVDNATVIKVQLSDGRKFDAKmVGKDPRSDIALIQIQNPKNLTAIKmADSDALRVGDYTVAIGNPFGLGETVTSGIVSALGRSG-----YENFIQTDAAINRGNAGGALVNLNGELIGINTAILAPDGGNIGIGFAIPSNmVKNLTSQmVEYGQVKRGELGImGTELNSELAKAmKVDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTmPVGSKLTLGLLRDGKQVNVNLE 353
                             |     |20  |     30        40 |      50|        -         -        80    |   90       100       110       120      |130       140       150 |     160       170       180        |-    |  200       210       220       230       240     | 250   |   260       270       280       290       300       310       320       330|      340       350   
                             |     |    |                 42-MSE   51                          79     |                                       127-MSE                  152-MSE                              189   195                                                246-MSE 254-MSE       268-MSE     280-MSE                                            331-MSE                  
                            12-MSE |    |                                                            85-MSE                                                                                                                                                                                                                                                                        
                                  18-MSE|                                                                                                                                                                                                                                                                                                                                          
                                       23-MSE                                                                                                                                                                                                                                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:396
 aligned with DEGP_ECOLI | P0C0V0 from UniProtKB/Swiss-Prot  Length:474

    Alignment length:436
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466      
           DEGP_ECOLI    37 QMPSLAPMLEKVMPSVVSINVEGSTTVNTPRMPRNFQQFFGDDSPFCQEGSPFQSSPFCQGGQGGNGGGQQQKFMALGSGVIIDADKGYVVTNNHVVDNATVIKVQLSDGRKFDAKMVGKDPRSDIALIQIQNPKNLTAIKMADSDALRVGDYTVAIGNPFGLGETVTSGIVSALGRSGLNAENYENFIQTDAAINRGNSGGALVNLNGELIGINTAILAPDGGNIGIGFAIPSNMVKNLTSQMVEYGQVKRGELGIMGTELNSELAKAMKVDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTMPVGSKLTLGLLRDGKQVNVNLELQQSSQNQVDSSSIFNGIEGAEMSNKGKDQGVVVNNVKTGTPAAQIGLKKGDVIIGANQQAVKNIAELRKVLDSKPSVLALNIQRGDSTIYLL 472
               SCOP domains d1ky9b3 B:11-259 Protease Do (DegP, HtrA)                           , catalytic domain                                                                                                                                                                   d1ky9b1 B:260-358 Protease Do (DegP, HtrA), C-terminal domains                                     d1ky9b2 B:3     59-446 Protease Do (DegP, HtrA), C-terminal domains                      SCOP domains
               CATH domains -------------1ky9B01   ------------------                           -------1ky9B01 B:24-33,B:86-151 Trypsin-like serine proteases            -1ky9B02 B:153-244 Trypsin-like seri        ne proteases                                     ----------------1ky9B03 B:261-354  [code=2.30.42.10, no name defined]                                         ---------------     ---1ky9B04 B:378-446  [code=2.30.42.10, no name defined]                 CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh..eeeeeeeeeeee..............---------------------------.eeeeeeeeeeeeeee....eeeeehhhhh.eeeeeee.....eeeeeeeeee....eeeeeee...........hhhhh....eeeeee.......eeeeeeeeee..--------...eee...........eee.....eeeeee............eeeeehhhhhhhhhhhhhhh....ee..eeee...hhhhhh........eeeeee...hhhhhhh.....ee.ee..ee..hhhhhhhhhhhh.......ee......ee....ee...............-----.....................hhhhh.....eeeee..ee..hhhhhhhhh........eeee....eeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PDZ  PDB: B:254-345 UniProt: 280-371                                                        -----PDZ  PDB: B:351-440 UniProt: 377-466                                                      ------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ky9 B  11 QmPSLAPmLEKVmPSVVSINVEGSTTVNTPRmPRNFQQFFG---------------------------GQQQKFmALGSGVIIDADKGYVVTNNHVVDNATVIKVQLSDGRKFDAKmVGKDPRSDIALIQIQNPKNLTAIKmADSDALRVGDYTVAIGNPFGLGETVTSGIVSALGR--------ENFIQTDAAINRGNAGGALVNLNGELIGINTAILAPDGGNIGIGFAIPSNmVKNLTSQmVEYGQVKRGELGImGTELNSELAKAmKVDAQRGAFVSQVLPNSSAAKAGIKAGDVITSLNGKPISSFAALRAQVGTmPVGSKLTLGLLRDGKQVNVNLELQQSSQNQVDSSSIFN-----EmSNKGKDQGVVVNNVKTGTPAAQIGLKKGDVIIGANQQAVKNIAELRKVLDSKPSVLALNIQRGDSTIYLL 446
                             |     |20  |     30        40 |      50|        -         -        80    |   90       100       110       120      |130       140       150 |     160       170       180      |  -     | 200       210       220       230       240     | 250   |   260       270       280       290       300       310       320       330|      340       350       360        |-    || 380       390       400       410       420       430       440      
                            12-MSE |    |                 42-MSE   51                          79     |                                       127-MSE                  152-MSE                            187      196                                               246-MSE 254-MSE       268-MSE     280-MSE                                            331-MSE                               369   375|                                                                      
                                  18-MSE|                                                            85-MSE                                                                                                                                                                                                                                                                                            376-MSE                                                                  
                                       23-MSE                                                                                                                                                                                                                                                                                                                                                                                                                                   

   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  (2, 5)

Asymmetric Unit

(-) CATH Domains  (2, 7)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1KY9)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (DEGP_ECOLI | P0C0V0)
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:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    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:0006515    misfolded or incompletely synthesized protein catabolic process    The chemical reactions and pathways resulting in the breakdown of misfolded or attenuated proteins.
    GO:0006457    protein folding    The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0009266    response to temperature stimulus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a temperature stimulus.
cellular component
    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
        DEGP_ECOLI | P0C0V02zle 3cs0 3mh4 3mh5 3mh6 3mh7 3otp 3ou0 4a8d

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1KY9)