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(-) Description

Title :  STRUCTURE OF THE C. DIFFICILE TCDB CYSTEINE PROTEASE DOMAIN
 
Authors :  P. J. Lupardus, K. C. Garcia
Date :  26 Oct 10  (Deposition) - 16 Feb 11  (Release) - 31 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Clan Cd Cysteine Protease, Protease, Inositol Hexakisphosphate, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Shen, P. J. Lupardus, M. M. Gersch, A. W. Puri, V. E. Albrow, K. C. Garcia, M. Bogyo
Defining An Allosteric Circuit In The Cysteine Protease Domain Of Clostridium Difficile Toxins.
Nat. Struct. Mol. Biol. V. 18 364 2011
PubMed-ID: 21317893  |  Reference-DOI: 10.1038/NSMB.1990

(-) Compounds

Molecule 1 - TOXIN B
    Chains: B, A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 544-797
    Gene: CD0660, TCDB
    Organism Scientific: CLOSTRIDIUM DIFFICILE
    Organism Taxid: 272563
    Strain: 630

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2IHP2Ligand/IonINOSITOL HEXAKISPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2IHP1Ligand/IonINOSITOL HEXAKISPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2IHP1Ligand/IonINOSITOL HEXAKISPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREIHP A:255 , HOH A:307 , IHP B:256 , HOH B:282BINDING SITE FOR RESIDUE CA B 255
2AC2SOFTWAREIHP A:255 , HOH A:307 , ARG B:28 , ARG B:32 , TYR B:34 , LEU B:54 , LYS B:57 , LYS B:104 , ARG B:208 , ARG B:209 , LYS B:221 , LYS B:232 , LYS B:249 , CA B:255 , HOH B:257 , HOH B:264 , HOH B:265 , HOH B:282 , HOH B:284 , HOH B:287 , HOH B:290 , HOH B:292 , HOH B:296 , HOH B:298 , HOH B:299 , HOH B:322 , HOH B:339 , HOH B:341BINDING SITE FOR RESIDUE IHP B 256
3AC3SOFTWAREARG A:28 , ARG A:32 , TYR A:34 , LEU A:54 , LYS A:57 , LYS A:104 , ARG A:208 , ARG A:209 , LYS A:221 , LYS A:232 , TYR A:234 , LYS A:249 , HOH A:257 , HOH A:265 , HOH A:272 , HOH A:280 , HOH A:284 , HOH A:286 , HOH A:292 , HOH A:307 , HOH A:315 , HOH A:350 , HOH A:371 , HOH A:372 , HOH A:374 , HOH A:377 , CA B:255 , IHP B:256 , HOH B:282BINDING SITE FOR RESIDUE IHP A 255

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3PEE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PEE)

(-) Exons   (0, 0)

(no "Exon" information available for 3PEE)

(-) 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:244
 aligned with Q189K3_PEPD6 | Q189K3 from UniProtKB/TrEMBL  Length:2366

    Alignment length:244
                                   560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790    
         Q189K3_PEPD6   551 FSQNIVVDKEYLLEKISSLARSSERGYIHYIVQLQGDKISYEAACNLFAKTPYDSVLFQKNIEDSEIAYYYNPGDGEIQEIDKYKIPSIISDRPKIKLTFIGHGKDEFNTDIFAGFDVDSLSTEIEAAIDLAKEDISPKSIEINLLGCNMFSYSINVEETYPGKLLLKVKDKISELMPSISQDSIIVSANQYEVRINSEGRRELLDHSGEWINKEESIIKDISSKEYISFNPKENKITVKSKNL 794
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhh.......eeeeee...hhhhhhhhhhhhhhh...eeeee.......eeeeee....eeeeee............eeeeeee..........ee..eehhhhhhhhhhhhhhhh......eeeeeee.........hhhhhhhhhhhhhhhhhhhhhh.......eeeee....eee.....eeee.....eehhhhhhhh.....eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pee A   8 FSQNIVVDKEYLLEKISSLARSSERGYIHYIVQLQGDKISYEAACNLFAKTPYDSVLFQKNIEDSEIAYYYNPGDGEIQEIDKYKIPSIISDRPKIKLTFIGHGKDEFNTDIFAGFDVDSLSTEIEAAIDLAKEDISPKSIEINLLGCNMFSYSINVEETYPGKLLLKVKDKISELMPSISQDSIIVSANQYEVRINSEGRRELLDHSGEWINKEESIIKDISSKEYISFNPKENKITVKSKNL 251
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247    


Chain B from PDB  Type:PROTEIN  Length:243
 aligned with Q189K3_PEPD6 | Q189K3 from UniProtKB/TrEMBL  Length:2366

    Alignment length:243
                                   561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791   
         Q189K3_PEPD6   552 SQNIVVDKEYLLEKISSLARSSERGYIHYIVQLQGDKISYEAACNLFAKTPYDSVLFQKNIEDSEIAYYYNPGDGEIQEIDKYKIPSIISDRPKIKLTFIGHGKDEFNTDIFAGFDVDSLSTEIEAAIDLAKEDISPKSIEINLLGCNMFSYSINVEETYPGKLLLKVKDKISELMPSISQDSIIVSANQYEVRINSEGRRELLDHSGEWINKEESIIKDISSKEYISFNPKENKITVKSKNL 794
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhh.......eeeeee...hhhhhhhhhhhhhhh...eeeee.......eeeeee....eeeeee............eeeeeee..........ee..eehhhhhhhhhhhhhhhh......eeeeeee.........hhhhhhhhhhhhhhhhhhhhhh.......eeeee....eee.....eeee.....eehhhhhhhh.....eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pee B   9 SQNIVVDKEYLLEKISSLARSSERGYIHYIVQLQGDKISYEAACNLFAKTPYDSVLFQKNIEDSEIAYYYNPGDGEIQEIDKYKIPSIISDRPKIKLTFIGHGKDEFNTDIFAGFDVDSLSTEIEAAIDLAKEDISPKSIEINLLGCNMFSYSINVEETYPGKLLLKVKDKISELMPSISQDSIIVSANQYEVRINSEGRRELLDHSGEWINKEESIIKDISSKEYISFNPKENKITVKSKNL 251
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248
   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 3PEE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q189K3_PEPD6 | Q189K3)
molecular function
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.

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        Q189K3_PEPD6 | Q189K3: 3pa8

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