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(-) Description

Title :  CRYSTAL STRUCTURE OF M. TUBERCULOSIS CLPP1P1
 
Authors :  K. R. Schmitz, D. W. Carney, J. K. Sello, R. T. Sauer
Date :  11 Jul 14  (Deposition) - 08 Oct 14  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.25
Chains :  Asym. Unit :  A,B,C,D,E,F,G
Biol. Unit 1:  A,B,C,D,E,F,G  (2x)
Keywords :  Hydrolase, Peptidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. R. Schmitz, D. W. Carney, J. K. Sello, R. T. Sauer
Crystal Structure Of Mycobacterium Tuberculosis Clpp1P2 Suggests A Model For Peptidase Activation By Aaa+ Partner Binding And Substrate Delivery.
Proc. Natl. Acad. Sci. Usa V. 111 E4587 2014
PubMed-ID: 25267638  |  Reference-DOI: 10.1073/PNAS.1417120111

(-) Compounds

Molecule 1 - ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT 1
    Chains: A, B, C, D, E, F, G
    EC Number: 3.4.21.92
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: MATURE ENZYME
    Gene: CLPP1, CLPP, RV2461C, MTV008.17C
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 83332
    Strain: ATCC 25618 / H37RV
    Synonym: ENDOPEPTIDASE CLP 1

 Structural Features

(-) Chains, Units

  1234567
Asymmetric Unit : ABCDEFG
Biological Unit 1 (2x): ABCDEFG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 63)

Asymmetric Unit (2, 63)
No.NameCountTypeFull Name
1MSE49Mod. Amino AcidSELENOMETHIONINE
2SO414Ligand/IonSULFATE ION
Biological Unit 1 (2, 126)
No.NameCountTypeFull Name
1MSE98Mod. Amino AcidSELENOMETHIONINE
2SO428Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:70 , ILE A:71 , SER A:72binding site for residue SO4 A 301
02AC2SOFTWAREARG A:171 , ARG A:173binding site for residue SO4 A 302
03AC3SOFTWARESER C:70 , ILE C:71 , SER C:72 , GLY C:127 , PHE C:143binding site for residue SO4 C 301
04AC4SOFTWAREARG C:171 , ARG C:173 , TRP C:174binding site for residue SO4 C 302
05AC5SOFTWARESER D:70 , ILE D:71 , SER D:72 , GLY D:127 , PHE D:143binding site for residue SO4 D 301
06AC6SOFTWAREARG D:164binding site for residue SO4 D 302
07AC7SOFTWAREARG D:171 , ARG D:173binding site for residue SO4 D 303
08AC8SOFTWAREARG D:173binding site for residue SO4 D 304
09AC9SOFTWARESER E:70 , SER E:72 , GLY E:127 , PHE E:143binding site for residue SO4 E 301
10AD1SOFTWAREARG E:171 , ARG E:173binding site for residue SO4 E 302
11AD2SOFTWAREARG E:164 , ARG E:173 , GLU E:182 , TYR E:183binding site for residue SO4 E 303
12AD3SOFTWARESER G:70 , ILE G:71 , SER G:72 , PHE G:143binding site for residue SO4 G 301
13AD4SOFTWAREARG G:171 , ARG G:173binding site for residue SO4 G 302
14AD5SOFTWAREGLN G:160 , ARG G:164 , ARG G:173binding site for residue SO4 G 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4U0H)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4U0H)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4U0H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4U0H)

(-) Exons   (0, 0)

(no "Exon" information available for 4U0H)

(-) 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:178
                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeeehhhhhhhhh.....eee....eee...........hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..eehhhhhhhhh...ee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u0h A  14 LSLTDSVYERLLSERIIFLGSEVNDEIANRLCAQILLLAAEDASKDISLYINSPGGSISAGmAIYDTmVLAPCDIATYAmGmAASmGEFLLAAGTKGKRYALPHARILmHQPLGGGSAADIAIQAEQFAVIKKEmFRLNAEFTGQPIERIEADSDRDRWFTAAEALEYGFVDHIITRA 193
                                    23        33        43        53        63        73 |     |83        93 |   | 103       113       123    || 135       145    |  155       165       175       185        
                                                                                        75-MSE |          93-MSE |                    122-MSE28|                150-MSE                                       
                                                                                              81-MSE        95-MSE                           131                                                              
                                                                                                                99-MSE                                                                                        


Chain B from PDB  Type:PROTEIN  Length:175
                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeeehhhhhhhhh.....eee....eee.......hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..eehhhhhhhhh...ee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u0h B  14 LSLTDSVYERLLSERIIFLGSEVNDEIANRLCAQILLLAAEDASKDISLYINSPGGSISAGmAIYDTmVLAPCDIATYAmGmAASmGEFLLAAGTKGKRYALPHARILmHQPLGADIAIQAEQFAVIKKEmFRLNAEFTGQPIERIEADSDRDRWFTAAEALEYGFVDHIITRAH 194
                                    23        33        43        53        63        73 |     |83        93 |   | 103       113       123   ||  139       149|      159       169       179       189     
                                                                                        75-MSE |          93-MSE |                    122-MSE7|             150-MSE                                        
                                                                                              81-MSE        95-MSE                          134                                                            
                                                                                                                99-MSE                                                                                     


Chain C from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeeehhhhhhhhh.....eee....eee.........hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..eehhhhhhhhh...ee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u0h C  14 LSLTDSVYERLLSERIIFLGSEVNDEIANRLCAQILLLAAEDASKDISLYINSPGGSISAGmAIYDTmVLAPCDIATYAmGmAASmGEFLLAAGTKGKRYALPHARILmHQPLGGAADIAIQAEQFAVIKKEmFRLNAEFTGQPIERIEADSDRDRWFTAAEALEYGFVDHIITRA 193
                                    23        33        43        53        63        73 |     |83        93 |   | 103       113       123    || 137       147  |    157       167       177       187      
                                                                                        75-MSE |          93-MSE |                    122-MSE28|              150-MSE                                       
                                                                                              81-MSE        95-MSE                           133                                                            
                                                                                                                99-MSE                                                                                      


Chain D from PDB  Type:PROTEIN  Length:177
                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeeehhhhhhhhh.....eee....eee........hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..eehhhhhhhhh...ee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u0h D  14 LSLTDSVYERLLSERIIFLGSEVNDEIANRLCAQILLLAAEDASKDISLYINSPGGSISAGmAIYDTmVLAPCDIATYAmGmAASmGEFLLAAGTKGKRYALPHARILmHQPLGGADIAIQAEQFAVIKKEmFRLNAEFTGQPIERIEADSDRDRWFTAAEALEYGFVDHIITRAHV 195
                                    23        33        43        53        63        73 |     |83        93 |   | 103       113       123    || 138       148 |     158       168       178       188       
                                                                                        75-MSE |          93-MSE |                    122-MSE28|             150-MSE                                         
                                                                                              81-MSE        95-MSE                           134                                                             
                                                                                                                99-MSE                                                                                       


Chain E from PDB  Type:PROTEIN  Length:178
                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeeehhhhhhhhh.....eee....eee..........hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..eehhhhhhhhh...ee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4u0h E  14 LSLTDSVYERLLSERIIFLGSEVNDEIANRLCAQILLLAAEDASKDISLYINSPGGSISAGmAIYDTmVLAPCDIATYAmGmAASmGEFLLAAGTKGKRYALPHARILmHQPLGGVTADIAIQAEQFAVIKKEmFRLNAEFTGQPIERIEADSDRDRWFTAAEALEYGFVDHIITRAH 194
                                    23        33        43        53        63        73 |     |83        93 |   | 103       113       123      |136       146   |   156       166       176       186        
                                                                                        75-MSE |          93-MSE |                    122-MSE 130|             150-MSE                                        
                                                                                              81-MSE        95-MSE                             134                                                            
                                                                                                                99-MSE                                                                                        


Chain F from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeeehhhhhhhhh.....eee....eee......hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..eehhhhhhhhh...ee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4u0h F  14 LSLTDSVYERLLSERIIFLGSEVNDEIANRLCAQILLLAAEDASKDISLYINSPGGSISAGmAIYDTmVLAPCDIATYAmGmAASmGEFLLAAGTKGKRYALPHARILmHQPLADIAIQAEQFAVIKKEmFRLNAEFTGQPIERIEADSDRDRWFTAAEALEYGFVDHIITRAH 194
                                    23        33        43        53        63        73 |     |83        93 |   | 103       113       123  ||   140       150       160       170       180       190    
                                                                                        75-MSE |          93-MSE |                    122-MSE|             150-MSE                                        
                                                                                              81-MSE        95-MSE                         134                                                            
                                                                                                                99-MSE                                                                                    


Chain G from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeeehhhhhhhhh.....eee....eee.......hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..eehhhhhhhhh...ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4u0h G  14 LSLTDSVYERLLSERIIFLGSEVNDEIANRLCAQILLLAAEDASKDISLYINSPGGSISAGmAIYDTmVLAPCDIATYAmGmAASmGEFLLAAGTKGKRYALPHARILmHQPLGADIAIQAEQFAVIKKEmFRLNAEFTGQPIERIEADSDRDRWFTAAEALEYGFVDHIITRA 193
                                    23        33        43        53        63        73 |     |83        93 |   | 103       113       123   ||  139       149|      159       169       179       189    
                                                                                        75-MSE |          93-MSE |                    122-MSE7|             150-MSE                                       
                                                                                              81-MSE        95-MSE                          134                                                           
                                                                                                                99-MSE
   Legend:   → Mismatch (orange background)
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  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 4U0H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4U0H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4U0H)

(-) Gene Ontology  (8, 8)

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  4u0h
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        CLPP1_MYCTU | P9WPC5: 2c8t 2cby 2ce3 4u0g 5dzk 5e0s

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