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(-) Description

Title :  CRYSTAL STRUCTURE OF CTPB(S309A) IN COMPLEX WITH A PEPTIDE HAVING A VAL-PRO-ALA C-TERMINUS
 
Authors :  M. Mastny, A. Heuck, R. Kurzbauer, T. Clausen
Date :  17 Aug 13  (Deposition) - 04 Dec 13  (Release) - 15 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Hydrolase-Peptide Complex, Pdz-Proteases, Allosteric Regulation, Conformational Switch, Sporulation, Proteolytic Tunnel (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Mastny, A. Heuck, R. Kurzbauer, A. Heiduk, P. Boisguerin, R. Volkmer, M. Ehrmann, C. D. A. Rodrigues, D. Z. Rudner, T. Clausen
Ctpb Assembles A Gated Protease Tunnel Regulating Cell-Cell Signaling During Spore Formation In Bacillus Subtilis.
Cell(Cambridge, Mass. ) V. 155 647 2013
PubMed-ID: 24243021  |  Reference-DOI: 10.1016/J.CELL.2013.09.050

(-) Compounds

Molecule 1 - CARBOXY-TERMINAL PROCESSING PROTEASE CTPB
    Chains: A
    EC Number: 3.4.21.102
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 46-478
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168
    Organism Taxid: 224308
    Synonym: CTPB, C-TERMINAL PROCESSING PROTEASE
 
Molecule 2 - PEPTIDE1
    Chains: B
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 511693
    Other Details: PEPTIDE CO-PURIFIED FROM E. COLI EXPRESSION
    Strain: BL21
 
Molecule 3 - CARBOXY-TERMINAL PROCESSING PROTEASE CTPB
    Chains: C
    EC Number: 3.4.21.102
    Fragment: RESIDUES 29-40
    Organism Scientific: BACILLUS SUBTILIS SUBSP. SUBTILIS STR. 168
    Organism Taxid: 224308
    Other Details: PEPTIDE NH2-EMDKPQTAAVPA-COOH
    Synonym: PEPTIDE VPA, CTPB, C-TERMINAL PROCESSING PROTEASE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4C2G)

(-) Sites  (0, 0)

(no "Site" information available for 4C2G)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C2G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4C2G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4C2G)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.CTPB_BACSU92-168  1A:92-168
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDZPS50106 PDZ domain profile.CTPB_BACSU92-168  2A:92-168

(-) Exons   (0, 0)

(no "Exon" information available for 4C2G)

(-) 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:434
 aligned with CTPB_BACSU | O35002 from UniProtKB/Swiss-Prot  Length:480

    Alignment length:434
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475    
           CTPB_BACSU    46 SERDKAMDKIEKAYELISNEYVEKVDREKLLEGAIQGMLSTLNDPYSVYMDKQTAKQFSDSLDSSFEGIGAEVGMEDGKIIIVSPFKKSPAEKAGLKPNDEIISINGESMAGKDLNHAVLKIRGKKGSSVSMKIQRPGTKKQLSFRIKRAEIPLETVFASEKKVQGHSVGYIAISTFSEHTAEDFAKALRELEKKEIEGLVIDVRGNPGGYLQSVEEILKHFVTKDQPYIQIAERNGDKKRYFSTLTHKKAYPVNVITDKGSASASEILAGALKEAGHYDVVGDTSFGKGTVQQAVPMGDGSNIKLTLYKWLTPNGNWIHKKGIEPTIAIKQPDYFSAGPLQLKEPLKVDMNNEDVKHAQVLLKGLSFDPGREDGYFSKDMKKAVMAFQDQNKLNKTGVIDTRTAETLNQQIEKKKSDEKNDLQLQTALKSLFV 479
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh......eeehhhhhhhhhhhh..eeee..eeeeee..eeeeeee...hhhhhhh.....eeeee..ee....hhhhhhhhhh.....eeeeeee.......eeeeee.eeee...eeeeeeee..eeeeeeee.....hhhhhhhhhhhhhhhh....eeee......eehhhhhhhhh.........eeee.......ee...........eeeee.....hhhhhhhhhhhhh...eeee.......eeeeeee.....eeeeeeeeee...............ee...hhhhhh..............hhhhhhhhhhhhhh...........hhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------PDZ  PDB: A:92-168 UniProt: 92-168                                           ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4c2g A  46 SERDKAMDKIEKAYELISNEYVEKVDREKLLEGAIQGMLSTLNDPYSVYMDKQTAKQFSDSLDSSFEGIGAEVGMEDGKIIIVSPFKKSPAEKAGLKPNDEIISINGESMAGKDLNHAVLKIRGKKGSSVSMKIQRPGTKKQLSFRIKRAEIPLETVFASEKKVQGHSVGYIAISTFSEHTAEDFAKALRELEKKEIEGLVIDVRGNPGGYLQSVEEILKHFVTKDQPYIQIAERNGDKKRYFSTLTHKKAYPVNVITDKGSAAASEILAGALKEAGHYDVVGDTSFGKGTVQQAVPMGDGSNIKLTLYKWLTPNGNWIHKKGIEPTIAIKQPDYFSAGPLQLKEPLKVDMNNEDVKHAQVLLKGLSFDPGREDGYFSKDMKKAVMAFQDQNKLNKTGVIDTRTAETLNQQIEKKKSDEKNDLQLQTALKSLFV 479
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475    


Chain B from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .eee Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 4c2g B   3 AAAA   6


Chain C from PDB  Type:PROTEIN  Length:4
 aligned with CTPB_BACSU | O35002 from UniProtKB/Swiss-Prot  Length:480

    Alignment length:4
           CTPB_BACSU    37 AVPA  40
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .ee. Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 4c2g C   2 AVPA   5
   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 4C2G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C2G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C2G)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (CTPB_BACSU | O35002)
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:0042277    peptide binding    Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
    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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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:0006518    peptide metabolic process    The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0030435    sporulation resulting in formation of a cellular spore    The process in which a relatively unspecialized cell acquires the specialized features of a cellular spore, a cell form that can be used for dissemination, for survival of adverse conditions because of its heat and dessication resistance, and/or for reproduction.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CTPB_BACSU | O35002: 4c2c 4c2d 4c2e 4c2f 4c2h

(-) Related Entries Specified in the PDB File

4c2c CRYSTAL STRUCTURE OF THE PROTEASE CTPB IN AN ACTIVE STATE
4c2d CRYSTAL STRUCTURE OF THE PROTEASE CTPB IN AN ACTIVE STATE
4c2e CRYSTAL STRUCTURE OF THE PROTEASE CTPB(S309A) PRESENT IN A RESTING STATE
4c2f CRYSTAL STRUCTURE OF THE CTPB R168A MUTANT PRESENT IN AN ACTIVE CONFORMATION
4c2h CRYSTAL STRUCTURE OF THE CTPB(V118Y) MUTANT