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(-) Description

Title :  RE-REFINEMENT OF 1SOZ, CRYSTAL STRUCTURE OF DEGS PROTEASE IN COMPLEX WITH AN ACTIVATING PEPTIDE
 
Authors :  R. T. Sauer, R. A. Grant
Date :  05 Nov 14  (Deposition) - 11 Mar 15  (Release) - 18 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Stress Response, Protein Quality Control, Pdz, Upr, Htra, Hydrolase, Hydrolase-Peptide Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. K. De Regt, S. Kim, J. Sohn, R. A. Grant, T. A. Baker, R. T. Sauer
A Conserved Activation Cluster Is Required For Allosteric Communication In Htra-Family Proteases.
Structure V. 23 517 2015
PubMed-ID: 25703375  |  Reference-DOI: 10.1016/J.STR.2015.01.012

(-) Compounds

Molecule 1 - PROTEASE DEGS
    ChainsA, B, C
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid562
    FragmentPROTEASE AND PDZ DOMAINS
    GeneDEGS, P12B_C3347
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
 
Molecule 2 - ACTIVATING PEPTIDE
    ChainsD, E, F
    EngineeredYES
    FragmentSYNTHETIC ACTIVATING PEPTIDE
    Other DetailsSYNTHETIC PEPTIDE
    SyntheticYES

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit ABCDEF

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4RQZ)

(-) Sites  (0, 0)

(no "Site" information available for 4RQZ)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RQZ)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4RQZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RQZ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RQZ)

(-) Exons   (0, 0)

(no "Exon" information available for 4RQZ)

(-) 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:272
                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh..eeeeeeee.........eeeeeeeeee.....eeeeehhhhh...eeeee.....eeeeeeeeee....eeeee......................eeeeeehhhhh..eeeeeeeee..............eee...........eee.....eeeeeeee.............eeeeehhhhhhhhhhhhhhh....ee.....hhhhhhh....ee..ee..hhhhhhhhhhh....eeeee..eeee.ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rqz A  42 MTPASYNLAVRRAAPAVVNVYNRGLNTNSHNQLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPFQLATKIMDKLIRDGRVIRGYIVVNDGPAANAGDLIISVDNKPASALETMDQVAEIRPGSVIPVVVTLQVTIQEYP 352
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251      |284||     302       312|      323       333 ||    350  
                                                                                                                                                                                                                                                  258|  ||    297|       312|                  335|         
                                                                                                                                                                                                                                                   282  ||     302        314                   343         
                                                                                                                                                                                                                                                      285|                                                  
                                                                                                                                                                                                                                                       290                                                  

Chain B from PDB  Type:PROTEIN  Length:274
                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh..eeeeeeee...eeeeeeeeeeee...eeeeehhhhh...eeeee.....eeeeeeeeee....eeeee......................eeeeeehhhhh..eeeeeeeee..............eee...........eeee....eeeeeeee.............eeeeehhhhhhhhhhhhhhh....ee.........hhhhhhh...eeeee..ee..hhhhhhhhhhhh....eeeeeee.eeee.ee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rqz B  42 MTPASYNLAVRRAAPAVVNVYNRGLNLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPFQLATKIMDKLIRDGRVIRGYIGIIVVNPDGPAANAGVNDLIISVDNKPAISALETMDQVAEIRPGSVIPVVVMTLQVTIQEYP 352
                                    51        61     || 77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257   ||  290      |302       312       322       332   ||  348    
                                                    67|                                                                                                                                                                                        261|  ||     297|                                 336|         
                                                     74                                                                                                                                                                                         282  ||      300                                  343         
                                                                                                                                                                                                                                                   285|                                                       
                                                                                                                                                                                                                                                    289                                                       

Chain C from PDB  Type:PROTEIN  Length:271
                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh..eeeeeeeee.......eeeeeeeeeee.....eeeeehhhhh...eeeee.....eee.eeeeee....eeeee......................eeeeeehhhhh..eeeeeeeeeeee..........eeee...........eee.....eeeeeeee.............eeeeehhhhhhhhhhhhhhh....ee.....................ee..ee..hhhhhhhhh....ee...ee.ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rqz C  42 MTPASYNLAVRRAAPAVVNVYNRGLNTNSHNQLEIRTLGSGVIMDQRGYIITNKHVINDADQIIVALQDGRVFEALLVGSDSLTDLAVLKINATGGLPTIPINARRVPHIGDVVLAIGNPYNLGQTITQGIISATGRIGLNPTGRQNFLQTDASINHGNSGGALVNSLGELMGINTLSFDKSNDGETPEGIGFAIPFQLATKIMDKLIRDGRVIRGYIGIIVVNPDGPAAIQVNDLIISVDNKPALETMDQVAEIRPGSVIPLQVTIQEYP 352
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261|  ||  294|      307    || 320       330 ||    351 
                                                                                                                                                                                                                                                     261|  ||  294|           312|             332|        
                                                                                                                                                                                                                                                      282  ||   298            316              344        
                                                                                                                                                                                                                                                         285|                                              
                                                                                                                                                                                                                                                          289                                              

Chain D from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 4rqz D 408 YQF 410

Chain E from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 4rqz E 407 VYQF 410

Chain F from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 4rqz F 408 YQF 410

   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 4RQZ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RQZ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RQZ)

(-) Gene Ontology  (13, 16)

Asymmetric/Biological Unit(hide GO term definitions)

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(no "Cis Peptide Bonds" information available for 4rqz)
 

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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 2r3u 2r3y 2rce 3b8j 3gcn 3gco 3gds 3gdu 3gdv 3lgi 3lgt 3lgu 3lgv 3lgw 3lgy 3lh1 3lh3 4rqy 4rr0 4rr1
        H9UXC8_ECOLX | H9UXC84rqy 4rr0 4rr1

(-) Related Entries Specified in the PDB File

1soz THE DEPOSITED STRUCTURE FACTORS FROM ENTRY 1SOZ WERE USED TO RE-REFINE THE STRUCTURE TO IMPROVE MODEL GEOMETRY