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(-) Description

Title :  CRYSTAL STRUCTURE OF CYSTEINE PEPTIDASE (NP_982244.1) FROM BACILLUS CEREUS ATCC 10987 AT 2.50 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  30 Nov 09  (Deposition) - 15 Dec 09  (Release) - 10 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Cysteine Peptidase, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-2, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Xu, N. D. Rawlings, H. J. Chiu, L. Jaroszewski, H. E. Klock, M. W. Knuth, M. D. Miller, M. A. Elsliger, A. M. Deacon, A. Godzik, S. A. Lesley, I. A. Wilson
Structural Analysis Of Papain-Like Nlpc/P60 Superfamily Enzymes With A Circularly Permuted Topology Reveals Potential Lipid Binding Sites.
Plos One V. 6 22013 2011
PubMed-ID: 21799766  |  Reference-DOI: 10.1371/JOURNAL.PONE.0022013

(-) Compounds

Molecule 1 - CYSTEINE PEPTIDASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BCE_A0238
    Organism Scientific: BACILLUS CEREUS
    Organism Taxid: 222523
    Strain: ATCC 10987

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 28)

Asymmetric/Biological Unit (3, 28)
No.NameCountTypeFull Name
1CL9Ligand/IonCHLORIDE ION
2LYS4Mod. Amino AcidLYSINE
3MSE15Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:36 , ILE A:39 , SER A:48 , HIS A:49 , GLU A:67 , ASP A:68 , TYR A:83 , GLU A:84 , TYR A:90BINDING SITE FOR RESIDUE LYS A 201
02AC2SOFTWARETYR B:33 , SER B:36 , ILE B:39 , SER B:48 , HIS B:49 , GLU B:67 , ASP B:68 , TYR B:83 , GLU B:84 , TYR B:90 , HOH B:207BINDING SITE FOR RESIDUE LYS B 201
03AC3SOFTWAREVAL C:35 , SER C:36 , ILE C:39 , SER C:48 , HIS C:49 , GLU C:67 , ASP C:68 , TYR C:83 , GLU C:84 , TYR C:90 , HOH C:205BINDING SITE FOR RESIDUE LYS C 201
04AC4SOFTWARETYR D:33 , SER D:36 , ILE D:39 , SER D:48 , HIS D:49 , GLU D:67 , ASP D:68 , TYR D:83 , GLU D:84 , TYR D:90 , HOH D:212BINDING SITE FOR RESIDUE LYS D 201
05AC5SOFTWAREARG A:72 , HIS A:78 , GLU A:84BINDING SITE FOR RESIDUE CL A 202
06AC6SOFTWARELEU A:34 , GLN C:134BINDING SITE FOR RESIDUE CL A 203
07AC7SOFTWAREGLN A:134 , TYR C:33 , LEU C:34BINDING SITE FOR RESIDUE CL A 204
08AC8SOFTWAREARG B:72 , HIS B:78 , GLU B:84BINDING SITE FOR RESIDUE CL B 202
09AC9SOFTWAREGLN B:134 , LEU D:34BINDING SITE FOR RESIDUE CL B 203
10BC1SOFTWARETYR B:33 , LEU B:34 , GLN D:134BINDING SITE FOR RESIDUE CL B 204
11BC2SOFTWAREARG C:72 , HIS C:78 , GLU C:84BINDING SITE FOR RESIDUE CL C 202
12BC3SOFTWARELYS C:117 , HIS D:59BINDING SITE FOR RESIDUE CL C 203
13BC4SOFTWAREARG D:72 , HIS D:78 , GLU D:84BINDING SITE FOR RESIDUE CL D 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KW0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KW0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KW0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KW0)

(-) Exons   (0, 0)

(no "Exon" information available for 3KW0)

(-) 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:190
 aligned with Q74NK7_BACC1 | Q74NK7 from UniProtKB/TrEMBL  Length:195

    Alignment length:195
                                                                                                                                                                                                                           195 
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191   | 
         Q74NK7_BACC1     2 GTDKFNNIKIDKYENLINVLKTGDIFLCSGNYLVSKLIKKVSESMFSHTGIIVKWGEHTLIMESVEDDGVRIVPLEHYIKNYENSNNRYNGSLFIARHELLQNVNDDSEMIRNLIKVGFSLLNSGYDKNEIAQIVARIGLGIGRHEDNNEYICSEFVNECFKKIGVEFLTDSEGFIFPEHIAADHHVLPIAQIE-   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...eehhhhhh.......eeeeee.hhhhhhhhhhh.....eeeeeeee..eeeeeeee...eeeeeehhhhhhhhhhh.....eeeeeeee.hhh.....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..........hhhhhhhhhhhh......-----..hhhhhhhh..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kw0 A   2 GTDKFNNIKIDKYENLINVLKTGDIFLCSGNYLVSKLIKKVSESmFSHTGIIVKWGEHTLImESVEDDGVRIVPLEHYIKNYENSNNRYNGSLFIARHELLQNVNDDSEmIRNLIKVGFSLLNSGYDKNEIAQIVARIGLGIGRHEDNNEYICSEFVNECFKKIGVEFL-----FIFPEHIAADHHVLPIAQIEK 201
                                    11        21        31        41    |   51        61 |      71        81        91       101       111       121       131       141       151       161        |-    |  181       191   ||
                                                                       46-MSE           63-MSE                                         111-MSE                                                    170   176                195|
                                                                                                                                                                                                                            201


Chain B from PDB  Type:PROTEIN  Length:198
 aligned with Q74NK7_BACC1 | Q74NK7 from UniProtKB/TrEMBL  Length:195

    Alignment length:200
                                1                                                                                                                                                                                               195 
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186        |-
         Q74NK7_BACC1     - ----MGTDKFNNIKIDKYENLINVLKTGDIFLCSGNYLVSKLIKKVSESMFSHTGIIVKWGEHTLIMESVEDDGVRIVPLEHYIKNYENSNNRYNGSLFIARHELLQNVNDDSEMIRNLIKVGFSLLNSGYDKNEIAQIVARIGLGIGRHEDNNEYICSEFVNECFKKIGVEFLTDSEGFIFPEHIAADHHVLPIAQIE-   -
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhh...eehhhhhh.......eeeeee.hhhhhhhhhhhh....eeeeeeee..eeeeeeee...eeeeeehhhhhhhhhhh.....eeeeeeee.hhh.....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..........hhhhhhhhhhhh.........--..hhhhhhhh..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kw0 B  -3 YFQGmGTDKFNNIKIDKYENLINVLKTGDIFLCSGNYLVSKLIKKVSESmFSHTGIIVKWGEHTLImESVEDDGVRIVPLEHYIKNYENSNNRYNGSLFIARHELLQNVNDDSEmIRNLIKVGFSLLNSGYDKNEIAQIVARIGLGIGRHEDNNEYICSEFVNECFKKIGVEFLTDS--FIFPEHIAADHHVLPIAQIEK 201
                                |    6        16        26        36        46        56      | 66        76        86        96       106    |  116       126       136       146       156       166      |176       186       201
                                |                                           46-MSE           63-MSE                                         111-MSE                                                       173  |                195|
                                1-MSE                                                                                                                                                                        176                 201


Chain C from PDB  Type:PROTEIN  Length:198
 aligned with Q74NK7_BACC1 | Q74NK7 from UniProtKB/TrEMBL  Length:195

    Alignment length:201
                                 1                                                                                                                                                                                               195 
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195 
         Q74NK7_BACC1     - -----MGTDKFNNIKIDKYENLINVLKTGDIFLCSGNYLVSKLIKKVSESMFSHTGIIVKWGEHTLIMESVEDDGVRIVPLEHYIKNYENSNNRYNGSLFIARHELLQNVNDDSEMIRNLIKVGFSLLNSGYDKNEIAQIVARIGLGIGRHEDNNEYICSEFVNECFKKIGVEFLTDSEGFIFPEHIAADHHVLPIAQIE-   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh..eehhhhhh.......eeeeee.hhhhhhhhhhhh....eeeeeeee..eeeeeeee...eeeeeehhhhhhhhhhh.....eeeeeeee.........hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..........hhhhhhhhhhhh........---..hhhhhhhh..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kw0 C  -4 LYFQGmGTDKFNNIKIDKYENLINVLKTGDIFLCSGNYLVSKLIKKVSESmFSHTGIIVKWGEHTLImESVEDDGVRIVPLEHYIKNYENSNNRYNGSLFIARHELLQNVNDDSEmIRNLIKVGFSLLNSGYDKNEIAQIVARIGLGIGRHEDNNEYICSEFVNECFKKIGVEFLTD---FIFPEHIAADHHVLPIAQIEK 201
                                 |   5        15        25        35        45|       55       |65        75        85        95       105     | 115       125       135       145       155       165      |  -|      185       195|
                                 1-MSE                                       46-MSE           63-MSE                                         111-MSE                                                      172 176                195|
                                                                                                                                                                                                                                  201


Chain D from PDB  Type:PROTEIN  Length:191
 aligned with Q74NK7_BACC1 | Q74NK7 from UniProtKB/TrEMBL  Length:195

    Alignment length:197
                             1                                                                                                                                                                                               195 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189     | 
         Q74NK7_BACC1     - -MGTDKFNNIKIDKYENLINVLKTGDIFLCSGNYLVSKLIKKVSESMFSHTGIIVKWGEHTLIMESVEDDGVRIVPLEHYIKNYENSNNRYNGSLFIARHELLQNVNDDSEMIRNLIKVGFSLLNSGYDKNEIAQIVARIGLGIGRHEDNNEYICSEFVNECFKKIGVEFLTDSEGFIFPEHIAADHHVLPIAQIE-   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------------DUF830-3kw0D01 D:20-188                                                                                                                                                  -------- Pfam domains (1)
           Pfam domains (2) --------------------DUF830-3kw0D02 D:20-188                                                                                                                                                  -------- Pfam domains (2)
           Pfam domains (3) --------------------DUF830-3kw0D03 D:20-188                                                                                                                                                  -------- Pfam domains (3)
           Pfam domains (4) --------------------DUF830-3kw0D04 D:20-188                                                                                                                                                  -------- Pfam domains (4)
         Sec.struct. author hhhhhhhh...eehhhhhh.......eeeeee.hhhhhhhhhhhh....eeeeeeee..eeeeeeee...eeeeeehhhhhhhhhhh.....eeeeeeee.hhh.....hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh..........hhhhhhhhhhhh.....------..hhhhhhhh..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kw0 D   0 GmGTDKFNNIKIDKYENLINVLKTGDIFLCSGNYLVSKLIKKVSESmFSHTGIIVKWGEHTLImESVEDDGVRIVPLEHYIKNYENSNNRYNGSLFIARHELLQNVNDDSEmIRNLIKVGFSLLNSGYDKNEIAQIVARIGLGIGRHEDNNEYICSEFVNECFKKIGVEF------FIFPEHIAADHHVLPIAQIEK 201
                             |       9        19        29        39      | 49        59   |    69        79        89        99       109 |     119       129       139       149       159       169      |179       189     ||
                             |                                           46-MSE           63-MSE                                         111-MSE                                                   169    176                195|
                             1-MSE                                                                                                                                                                                            201
   Legend:   → Mismatch (orange background)
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    → 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 3KW0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KW0)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: Peptidase_CA (169)

(-) Gene Ontology  (0, 0)

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