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(-) Description

Title :  CRYSTAL STRUCTURE OF A CLOSTRIPAIN (PARMER_00083) FROM PARABACTEROIDES MERDAE ATCC 43184 AT 1.70 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  02 Dec 11  (Deposition) - 13 Jun 12  (Release) - 11 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Clostripain Family Protein, Peptidase_c11, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Mcluskey, J. S. Grewal, D. Das, A. Godzik, S. A. Lesley, A. M. Deacon, G. H. Coombs, M. A. Elsliger, I. A. Wilson, J. C. Mottram
Crystal Structure And Activity Studies Of The C11 Cysteine Peptidase From Parabacteroides Merdae In The Human Gut Microbiome.
J. Biol. Chem. V. 291 9482 2016
PubMed-ID: 26940874  |  Reference-DOI: 10.1074/JBC.M115.706143

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: PB1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 23-147
    Gene: PARMER_00083
    Organism Scientific: PARABACTEROIDES MERDAE
    Organism Taxid: 411477
    Strain: ATCC 43184
 
Molecule 2 - HYPOTHETICAL PROTEIN
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: PB1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 148-375
    Gene: PARMER_00083
    Organism Scientific: PARABACTEROIDES MERDAE
    Organism Taxid: 411477
    Strain: ATCC 43184

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 31)

Asymmetric Unit (2, 31)
No.NameCountTypeFull Name
1EDO7Ligand/Ion1,2-ETHANEDIOL
2MSE24Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (2, 15)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2MSE12Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (2, 16)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:196 , LEU B:223 , GLN B:224 , LEU B:225 , GLU B:226 , HOH B:575BINDING SITE FOR RESIDUE EDO B 401
2AC2SOFTWARELYS B:268 , ILE B:273 , TYR B:370 , HOH B:535 , HOH B:582BINDING SITE FOR RESIDUE EDO B 402
3AC3SOFTWAREASP B:168 , ASP B:169 , ASN B:192 , LYS C:147BINDING SITE FOR RESIDUE EDO B 403
4AC4SOFTWARESER C:48 , ILE C:51 , TYR C:72 , LYS C:93 , HOH C:398BINDING SITE FOR RESIDUE EDO C 201
5AC5SOFTWAREASP C:106 , ASP C:108 , HOH C:326 , PRO D:216 , GLN D:217 , LYS D:227 , HOH D:673BINDING SITE FOR RESIDUE EDO C 202
6AC6SOFTWAREASP A:124 , HOH A:306 , HIS C:133 , HOH C:327 , GLN D:151BINDING SITE FOR RESIDUE EDO C 203
7AC7SOFTWARETYR D:196 , LEU D:223 , GLN D:224 , LEU D:225 , HOH D:531BINDING SITE FOR RESIDUE EDO D 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3UWS)

(-) 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:124
 aligned with A7A9N3_9PORP | A7A9N3 from UniProtKB/TrEMBL  Length:375

    Alignment length:124
                                    33        43        53        63        73        83        93       103       113       123       133       143    
         A7A9N3_9PORP    24 TPEPRTTRTILVYMMANNSLNSFASKNIESMIEGATSKNLNGGNLIVYYAPAGSPPELLRIKEENGVVKKIHLKDYEKQNSADPDVMRSVIGEVVSQYPADSYGLVLWSHGTAWLPSDYQNKLK 147
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeee..eeeeeeeee.......hhhhhhhhhhhhhhhh.eeeeeeeee.........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3uws A  24 TPEPRTTRTILVYmmANNSLNSFASKNIESmIEGATSKNLNGGNLIVYYAPAGSPPELLRIKEENGVVKKIHLKDYEKQNSADPDVmRSVIGEVVSQYPADSYGLVLWSHGTAWLPSDYQNKLK 147
                                    33   ||   43        53|       63        73        83        93       103      |113       123       133       143    
                                        37-MSE           54-MSE                                                 110-MSE                                 
                                         38-MSE                                                                                                         


Chain B from PDB  Type:PROTEIN  Length:228
 aligned with A7A9N3_9PORP | A7A9N3 from UniProtKB/TrEMBL  Length:375

    Alignment length:228
                                   157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367        
         A7A9N3_9PORP   148 AFGQDGNNWMEIDDLAKGLPDDLFDFILFDACYMASVECTYELRNKAEYILASPTETMADGWPYEEMMPQLFATDLQLEKVGETFYNHYLNNTYPYATVSLTKTSELDNLKSAIHDILADKTESDIYSLDPKNMQRLEYLYRSPGMLYDFNDYIKQLATAEQYDRFISCLDKAVVYKAHTPKSYYAAIGNALPIKSYCGLTIFVPQESLPKMLEWYKQRVGWYKAVYE 375
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeehhhhhhhhh....eeeeeee.....hhhhhhhh...eeeeee..........hhhhhhhhhh....hhhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhhhh..hhhhhhh.hhhhh............eeehhhhhhhhhhhhhhhhhhhhhhhheeeeee..eeee....eeee.......eee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3uws B 148 AFGQDGNNWmEIDDLAKGLPDDLFDFILFDACYmASVECTYELRNKAEYILASPTETmADGWPYEEmmPQLFATDLQLEKVGETFYNHYLNNTYPYATVSLTKTSELDNLKSAIHDILADKTESDIYSLDPKNmQRLEYLYRSPGmLYDFNDYIKQLATAEQYDRFISCLDKAVVYKAHTPKSYYAAIGNALPIKSYCGLTIFVPQESLPKmLEWYKQRVGWYKAVYE 375
                                   157       167       177   |   187       197       207      |217       227       237       247       257       267       277   |   287     | 297       307       317       327       337       347       357 |     367        
                                   157-MSE                 181-MSE                 205-MSE  214-MSE                                                            281-MSE     293-MSE                                                           359-MSE            
                                                                                             215-MSE                                                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:120
 aligned with A7A9N3_9PORP | A7A9N3 from UniProtKB/TrEMBL  Length:375

    Alignment length:120
                                    37        47        57        67        77        87        97       107       117       127       137       147
         A7A9N3_9PORP    28 RTTRTILVYMMANNSLNSFASKNIESMIEGATSKNLNGGNLIVYYAPAGSPPELLRIKEENGVVKKIHLKDYEKQNSADPDVMRSVIGEVVSQYPADSYGLVLWSHGTAWLPSDYQNKLK 147
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeee......eeeeeeee..eeeeeeeee.......hhhhhhhhhhhhhhhh...eeeeeee.........hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3uws C  28 RTTRTILVYmmANNSLNSFASKNIESmIEGATSKNLNGGNLIVYYAPAGSPPELLRIKEENGVVKKIHLKDYEKQNSADPDVmRSVIGEVVSQYPADSYGLVLWSHGTAWLPSDYQNKLK 147
                                    37|       47      | 57        67        77        87        97       107  |    117       127       137       147
                                    37-MSE           54-MSE                                                 110-MSE                                 
                                     38-MSE                                                                                                         


Chain D from PDB  Type:PROTEIN  Length:228
 aligned with A7A9N3_9PORP | A7A9N3 from UniProtKB/TrEMBL  Length:375

    Alignment length:228
                                   157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367        
         A7A9N3_9PORP   148 AFGQDGNNWMEIDDLAKGLPDDLFDFILFDACYMASVECTYELRNKAEYILASPTETMADGWPYEEMMPQLFATDLQLEKVGETFYNHYLNNTYPYATVSLTKTSELDNLKSAIHDILADKTESDIYSLDPKNMQRLEYLYRSPGMLYDFNDYIKQLATAEQYDRFISCLDKAVVYKAHTPKSYYAAIGNALPIKSYCGLTIFVPQESLPKMLEWYKQRVGWYKAVYE 375
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee..eeehhhhhhhhh....eeeeeee.....hhhhhhhh...eeeeee..........hhhhhhhhhh....hhhhhhhhhhhhhhh......eeeeee..hhhhhhhhhhhhhh..hhhhhhh.hhhhh............eeehhhhhhhhhhhhhhhhhhhhhhhheeeeee..eeee....eeee.......eee.....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3uws D 148 AFGQDGNNWmEIDDLAKGLPDDLFDFILFDACYmASVECTYELRNKAEYILASPTETmADGWPYEEmmPQLFATDLQLEKVGETFYNHYLNNTYPYATVSLTKTSELDNLKSAIHDILADKTESDIYSLDPKNmQRLEYLYRSPGmLYDFNDYIKQLATAEQYDRFISCLDKAVVYKAHTPKSYYAAIGNALPIKSYCGLTIFVPQESLPKmLEWYKQRVGWYKAVYE 375
                                   157       167       177   |   187       197       207      |217       227       237       247       257       267       277   |   287     | 297       307       317       327       337       347       357 |     367        
                                   157-MSE                 181-MSE                 205-MSE  214-MSE                                                            281-MSE     293-MSE                                                           359-MSE            
                                                                                             215-MSE
   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 3UWS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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