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(-) Description

Title :  CRYSTAL STRUCTURE OF CLPP IN HEPTAMERIC FORM FROM STAPHYLOCOCCUS AUREUS
 
Authors :  J. Zhang, F. Ye, L. Lan, H. Jiang, C. Luo, C. -G. Yang
Date :  09 Jul 11  (Deposition) - 07 Sep 11  (Release) - 25 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.43
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G
Keywords :  Atpase-Dependent Protease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Zhang, F. Ye, L. Lan, H. Jiang, C. Luo, C. -G. Yang
Structural Switching Of Staphylococcus Aureus Clp Protease: A Key To Understanding Protease Dynamics
J. Biol. Chem. V. 286 37590 2011
PubMed-ID: 21900233  |  Reference-DOI: 10.1074/JBC.M111.277848

(-) Compounds

Molecule 1 - ATP-DEPENDENT CLP PROTEASE PROTEOLYTIC SUBUNIT
    Chains: A, B, C, D, E, F, G
    EC Number: 3.4.21.92
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: CLPP
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 196620
    Strain: MW2
    Synonym: ENDOPEPTIDASE CLP

 Structural Features

(-) Chains, Units

  1234567
Asymmetric/Biological Unit : ABCDEFG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL
3SO42Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:123 , ASP A:172 , HIS C:123 , ASP C:172BINDING SITE FOR RESIDUE SO4 A 196
2AC2SOFTWAREASP B:59BINDING SITE FOR RESIDUE CA B 196
3AC3SOFTWARELYS C:149 , ARG C:152 , HOH C:230 , PRO D:116 , GLU F:178 , VAL F:189BINDING SITE FOR RESIDUE GOL C 196
4AC4SOFTWARETYR A:78 , GLU D:178 , LYS D:181 , PRO F:116 , ASN F:117BINDING SITE FOR RESIDUE SO4 D 196

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ST9)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu F:193 -Thr F:194

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3ST9)

(-) PROSITE Motifs  (2, 14)

Asymmetric/Biological Unit (2, 14)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CLP_PROTEASE_SERPS00381 Endopeptidase Clp serine active site.CLPP_STAAW90-101
 
 
 
 
 
 		  7A:90-101
B:90-101
C:90-101
D:90-101
E:90-101
F:90-101
G:90-101
2CLP_PROTEASE_HISPS00382 Endopeptidase Clp histidine active site.CLPP_STAAW112-125
 
 
 
 
 
 		  7A:112-125
B:112-125
C:112-125
D:112-125
E:112-125
F:112-125
G:112-125

(-) Exons   (0, 0)

(no "Exon" information available for 3ST9)

(-) 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:170
 aligned with CLPP_STAAW | P63786 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:175
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187     
           CLPP_STAAW    18 YDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDTIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP 192
               SCOP domains d3st9a_ A: Clp protease, ClpP subunit                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeeehhhhhhhh......eee....eee....-----...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..eehhhhhhhh....ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------CLP_PROTEASE----------CLP_PROTEASE_H------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3st9 A  18 YDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDTIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQP-----GQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP 192
                                    27        37        47        57        67        77        87        97       107       117       | -   |   137       147       157       167       177       187     
                                                                                                                                     125   131                                                             


Chain B from PDB  Type:PROTEIN  Length:170
 aligned with CLPP_STAAW | P63786 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:175
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187     
           CLPP_STAAW    18 YDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDTIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP 192
               SCOP domains d3st9b_ B: Clp protease, ClpP subunit                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeeehhhhhhhhh.....eee....eee....-----...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..eehhhhhhhh....ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------CLP_PROTEASE----------CLP_PROTEASE_H------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3st9 B  18 YDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDTIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQP-----GQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP 192
                                    27        37        47        57        67        77        87        97       107       117       | -   |   137       147       157       167       177       187     
                                                                                                                                     125   131                                                             


Chain C from PDB  Type:PROTEIN  Length:171
 aligned with CLPP_STAAW | P63786 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:175
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187     
           CLPP_STAAW    18 YDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDTIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP 192
               SCOP domains d3st9c_ C: Clp protease, ClpP subunit                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh...eeee....hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeeehhhhhhhhh.....eee....eee....----....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh....eehhhhhhhh....ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------CLP_PROTEASE----------CLP_PROTEASE_H------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3st9 C  18 YDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDTIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQP----QGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP 192
                                    27        37        47        57        67        77        87        97       107       117       | -  |    137       147       157       167       177       187     
                                                                                                                                     125  130                                                              


Chain D from PDB  Type:PROTEIN  Length:171
 aligned with CLPP_STAAW | P63786 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:175
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187     
           CLPP_STAAW    18 YDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDTIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP 192
               SCOP domains d3st9d_ D: Clp protease, ClpP subunit                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeeehhhhhhhh......eee....eee....----....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..eehhhhhhhh....ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------CLP_PROTEASE----------CLP_PROTEASE_H------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3st9 D  18 YDIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDTIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQP----QGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP 192
                                    27        37        47        57        67        77        87        97       107       117       | -  |    137       147       157       167       177       187     
                                                                                                                                     125  130                                                              


Chain E from PDB  Type:PROTEIN  Length:172
 aligned with CLPP_STAAW | P63786 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:174
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188    
           CLPP_STAAW    19 DIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDTIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP 192
               SCOP domains d3st9e_ E: Clp protease, ClpP subunit                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeeehhhhhhhhh.....eee....eee.....--.....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh....eehhhhhhhh....ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------CLP_PROTEASE----------CLP_PROTEASE_H------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3st9 E  19 DIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDTIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPL--AQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVP 192
                                    28        38        48        58        68        78        88        98       108       118       | -|      138       148       158       168       178       188    
                                                                                                                                     126  |                                                               
                                                                                                                                        129                                                               


Chain F from PDB  Type:PROTEIN  Length:173
 aligned with CLPP_STAAW | P63786 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:176
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188      
           CLPP_STAAW    19 DIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDTIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPET 194
               SCOP domains d3st9f_ F: Clp protease, ClpP subunit                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhh.eeee....hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeeehhhhhhhh......eee....eee....---.....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhh...eeehhhhhhh....ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------CLP_PROTEASE----------CLP_PROTEASE_H--------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3st9 F  19 DIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDTIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQP---AQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPET 194
                                    28        38        48        58        68        78        88        98       108       118      |  -|      138       148       158       168       178       188      
                                                                                                                                    125 129                                                                 


Chain G from PDB  Type:PROTEIN  Length:173
 aligned with CLPP_STAAW | P63786 from UniProtKB/Swiss-Prot  Length:195

    Alignment length:175
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188     
           CLPP_STAAW    19 DIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDTIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLGGAQGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE 193
               SCOP domains d3st9g_ G: Clp protease, ClpP subunit                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh...eeee....hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhhh...eeeeeeeeeehhhhhhhhh.....eee....eee......--....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh....eehhhhhhhh....ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------CLP_PROTEASE----------CLP_PROTEASE_H-------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3st9 G  19 DIYSRLLKDRIIMLGSQIDDNVANSIVSQLLFLQAQDSEKDIYLYINSPGGSVTAGFAIYDTIQHIKPDVQTICIGMAASMGSFLLAAGAKGKRFALPNAEVMIHQPLG--QGQATEIEIAANHILKTREKLNRILSERTGQSIEKIQKDTDRDNFLTAEEAKEYGLIDEVMVPE 193
                                    28        38        48        58        68        78        88        98       108       118        |- |     138       148       158       168       178       188     
                                                                                                                                      127  |                                                               
                                                                                                                                         130
   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  (1, 7)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ST9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ST9)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G   (CLPP_STAAW | P63786)
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: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:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  CLPP_STAAW | P63786
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  3.4.21.92
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 Related Entries

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

UniProtKB/Swiss-Prot
        CLPP_STAAW | P63786: 3sta 4emm 4emp

(-) Related Entries Specified in the PDB File

3sta