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(-) Description

Title :  XAA-PRO DIPEPTIDASE FROM BACILLUS ANTHRACIS.
 
Authors :  J. Osipiuk, M. Makowska-Grzyska, L. Papazisi, W. F. Anderson, A. Joach Center For Structural Genomics Of Infectious Diseases (Csgi
Date :  31 Dec 10  (Deposition) - 02 Feb 11  (Release) - 19 Sep 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.97
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Structural Genomics, Csgid, Center For Structural Genomics Of Infectious Diseases, Aminopeptidase, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, M. Makowska-Grzyska, L. Papazisi, W. F. Anderson, A. Joachimiak
Xaa-Pro Dipeptidase From Bacillus Anthracis.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROLINE DIPEPTIDASE
    Chains: A, B, C, D
    EC Number: 3.4.13.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BAS4102, BA_4422, GBAA4422, GBAA_4422, PEPQ1
    Organism Common: ANTHRAX,ANTHRAX BACTERIUM
    Organism Scientific: BACILLUS ANTHRACIS
    Organism Taxid: 198094
    Strain: AMES
    Synonym: X-PRO DIPEPTIDASE, XAA-PRO DIPEPTIDASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL1Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL-1Ligand/IonGLYCEROL
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL-1Ligand/IonGLYCEROL
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2GOL-1Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:262 , PHE A:301 , HOH A:697 , HOH A:731 , HOH A:755 , HOH A:765 , LYS D:345 , SER D:346 , LYS D:348BINDING SITE FOR RESIDUE GOL A 501
2AC2SOFTWAREASP A:212 , ASP A:223 , GLU A:316 , GLU A:330 , HOH A:601BINDING SITE FOR RESIDUE CA A 502
3AC3SOFTWAREASP B:212 , ASP B:223 , GLU B:316 , GLU B:330 , HOH B:547 , HOH B:677BINDING SITE FOR RESIDUE CA B 401
4AC4SOFTWAREASP C:212 , ASP C:223 , GLU C:316 , GLU C:330 , HOH C:532 , HOH C:586BINDING SITE FOR RESIDUE CA C 401
5AC5SOFTWAREASP D:212 , ASP D:223 , GLU D:316 , GLU D:330 , HOH D:506 , HOH D:619BINDING SITE FOR RESIDUE CA D 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3Q6D)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:296 -Pro A:297
2Ala B:296 -Pro B:297
3Ala C:296 -Pro C:297
4Ala D:296 -Pro D:297

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3Q6D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3Q6D)

(-) Exons   (0, 0)

(no "Exon" information available for 3Q6D)

(-) 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:355
 aligned with Q81M33_BACAN | Q81M33 from UniProtKB/TrEMBL  Length:353

    Alignment length:355
                              1                                                                                                                                                                                                                                                                                                                                                                
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348     
         Q81M33_BACAN     - --MEKIERLRSAFDEAGIDGILLTNEHSRRYMANFTGTAGVVLISKKRAQFITDFRYVEQASKQAVGYEIVQHAGLIIDEVAKQVKELGIQKLGFEQDTLTYSSYSAHKEAIDAEFIPTSGLVEKLRLIKTDSEIKILKEAAQIADAAFEHILSFIRPGVSEIEVSNELEFFMRKQGATSSSFDIIVASGLRSALPHGVASEKVIETGDFVTLDFGAYYKGYCSDITRTIAVGEPSDKLKEIYNIVLEAQLRGVNGIKAGLTGREADALTRDYITEKGYGEYFGHSTGHGIGLEIHEAPGLAFRSDTVLEPGMAVTVEPGIYIPGIGGVRIEDDIIVTSEGNEVITKSPKELIIL 353
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhh......eeeee...eeeeehhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhh..eeeee.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh...ee....eeee.hhhhh..............eeeeee.eee..ee..eeeeee....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhh....eee......eeeee............eeee..eeee...eeee..eeeee....eee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q6d A  -1 NAMEKIERLRSAFDEAGIDGILLTNEHSRRYMANFTGTAGVVLISKKRAQFITDFRYVEQASKQAVGYEIVQHAGLIIDEVAKQVKELGIQKLGFEQDTLTYSSYSAHKEAIDAEFIPTSGLVEKLRLIKTDSEIKILKEAAQIADAAFEHILSFIRPGVSEIEVSNELEFFMRKQGATSSSFDIIVASGLRSALPHGVASEKVIETGDFVTLDFGAYYKGYCSDITRTIAVGEPSDKLKEIYNIVLEAQLRGVNGIKAGLTGREADALTRDYITEKGYGEYFGHSTGHGIGLEIHEAPGLAFRSDTVLEPGMAVTVEPGIYIPGIGGVRIEDDIIVTSEGNEVITKSPKELIIL 353
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348     


Chain B from PDB  Type:PROTEIN  Length:355
 aligned with Q81M33_BACAN | Q81M33 from UniProtKB/TrEMBL  Length:353

    Alignment length:355
                              1                                                                                                                                                                                                                                                                                                                                                                
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348     
         Q81M33_BACAN     - --MEKIERLRSAFDEAGIDGILLTNEHSRRYMANFTGTAGVVLISKKRAQFITDFRYVEQASKQAVGYEIVQHAGLIIDEVAKQVKELGIQKLGFEQDTLTYSSYSAHKEAIDAEFIPTSGLVEKLRLIKTDSEIKILKEAAQIADAAFEHILSFIRPGVSEIEVSNELEFFMRKQGATSSSFDIIVASGLRSALPHGVASEKVIETGDFVTLDFGAYYKGYCSDITRTIAVGEPSDKLKEIYNIVLEAQLRGVNGIKAGLTGREADALTRDYITEKGYGEYFGHSTGHGIGLEIHEAPGLAFRSDTVLEPGMAVTVEPGIYIPGIGGVRIEDDIIVTSEGNEVITKSPKELIIL 353
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhh......eeeee...eeeeehhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhh..eeeee.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh...ee....eeee.hhhhh.............eeeeeee.eee..ee..eeeeeee...hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhh....eee......eeeee............eeee..eeee...eeee..eeeee....eee........... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q6d B  -1 NAMEKIERLRSAFDEAGIDGILLTNEHSRRYMANFTGTAGVVLISKKRAQFITDFRYVEQASKQAVGYEIVQHAGLIIDEVAKQVKELGIQKLGFEQDTLTYSSYSAHKEAIDAEFIPTSGLVEKLRLIKTDSEIKILKEAAQIADAAFEHILSFIRPGVSEIEVSNELEFFMRKQGATSSSFDIIVASGLRSALPHGVASEKVIETGDFVTLDFGAYYKGYCSDITRTIAVGEPSDKLKEIYNIVLEAQLRGVNGIKAGLTGREADALTRDYITEKGYGEYFGHSTGHGIGLEIHEAPGLAFRSDTVLEPGMAVTVEPGIYIPGIGGVRIEDDIIVTSEGNEVITKSPKELIIL 353
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348     


Chain C from PDB  Type:PROTEIN  Length:353
 aligned with Q81M33_BACAN | Q81M33 from UniProtKB/TrEMBL  Length:353

    Alignment length:353
                             1                                                                                                                                                                                                                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349   
         Q81M33_BACAN     - -MEKIERLRSAFDEAGIDGILLTNEHSRRYMANFTGTAGVVLISKKRAQFITDFRYVEQASKQAVGYEIVQHAGLIIDEVAKQVKELGIQKLGFEQDTLTYSSYSAHKEAIDAEFIPTSGLVEKLRLIKTDSEIKILKEAAQIADAAFEHILSFIRPGVSEIEVSNELEFFMRKQGATSSSFDIIVASGLRSALPHGVASEKVIETGDFVTLDFGAYYKGYCSDITRTIAVGEPSDKLKEIYNIVLEAQLRGVNGIKAGLTGREADALTRDYITEKGYGEYFGHSTGHGIGLEIHEAPGLAFRSDTVLEPGMAVTVEPGIYIPGIGGVRIEDDIIVTSEGNEVITKSPKELII 352
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh..eeee.hhhhhhhhh.......eeeee...eeeeehhhhhhhhhhhh...eeee...hhhhhhhhhhhhhh..eeeee....hhhhhhhhhh....eeeee.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...ee....eeee.hhhhh.............eeeeeee.eee..ee..eeeeeee...hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhh....eee......eeeee............eeee..eeee...eeee..eeeee....eee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q6d C   0 AMEKIERLRSAFDEAGIDGILLTNEHSRRYMANFTGTAGVVLISKKRAQFITDFRYVEQASKQAVGYEIVQHAGLIIDEVAKQVKELGIQKLGFEQDTLTYSSYSAHKEAIDAEFIPTSGLVEKLRLIKTDSEIKILKEAAQIADAAFEHILSFIRPGVSEIEVSNELEFFMRKQGATSSSFDIIVASGLRSALPHGVASEKVIETGDFVTLDFGAYYKGYCSDITRTIAVGEPSDKLKEIYNIVLEAQLRGVNGIKAGLTGREADALTRDYITEKGYGEYFGHSTGHGIGLEIHEAPGLAFRSDTVLEPGMAVTVEPGIYIPGIGGVRIEDDIIVTSEGNEVITKSPKELII 352
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349   


Chain D from PDB  Type:PROTEIN  Length:353
 aligned with Q81M33_BACAN | Q81M33 from UniProtKB/TrEMBL  Length:353

    Alignment length:353
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350   
         Q81M33_BACAN     1 MEKIERLRSAFDEAGIDGILLTNEHSRRYMANFTGTAGVVLISKKRAQFITDFRYVEQASKQAVGYEIVQHAGLIIDEVAKQVKELGIQKLGFEQDTLTYSSYSAHKEAIDAEFIPTSGLVEKLRLIKTDSEIKILKEAAQIADAAFEHILSFIRPGVSEIEVSNELEFFMRKQGATSSSFDIIVASGLRSALPHGVASEKVIETGDFVTLDFGAYYKGYCSDITRTIAVGEPSDKLKEIYNIVLEAQLRGVNGIKAGLTGREADALTRDYITEKGYGEYFGHSTGHGIGLEIHEAPGLAFRSDTVLEPGMAVTVEPGIYIPGIGGVRIEDDIIVTSEGNEVITKSPKELIIL 353
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --Creatinase_N-3q6dD01 D:3-127                                                                                                 ------Peptidase_M24-3q6dD05 D:134-337                                                                                                                                                                             ---------------- Pfam domains (1)
           Pfam domains (2) --Creatinase_N-3q6dD02 D:3-127                                                                                                 ------Peptidase_M24-3q6dD06 D:134-337                                                                                                                                                                             ---------------- Pfam domains (2)
           Pfam domains (3) --Creatinase_N-3q6dD03 D:3-127                                                                                                 ------Peptidase_M24-3q6dD07 D:134-337                                                                                                                                                                             ---------------- Pfam domains (3)
           Pfam domains (4) --Creatinase_N-3q6dD04 D:3-127                                                                                                 ------Peptidase_M24-3q6dD08 D:134-337                                                                                                                                                                             ---------------- Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhh..eeee.hhhhhhhhhh......eeeee...eeee.hhhhhhhhhhhh...eee....hhhhhhhhhhhhh...eeeee....hhhhhhhhhhhh..eeeee.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh...ee....eeee.hhhhh..............eeeeee.eee..ee..eeeeee....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.hhhhh....eee......eeeee............eeee..eeee...eeee..eeeee....eee........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q6d D   1 MEKIERLRSAFDEAGIDGILLTNEHSRRYMANFTGTAGVVLISKKRAQFITDFRYVEQASKQAVGYEIVQHAGLIIDEVAKQVKELGIQKLGFEQDTLTYSSYSAHKEAIDAEFIPTSGLVEKLRLIKTDSEIKILKEAAQIADAAFEHILSFIRPGVSEIEVSNELEFFMRKQGATSSSFDIIVASGLRSALPHGVASEKVIETGDFVTLDFGAYYKGYCSDITRTIAVGEPSDKLKEIYNIVLEAQLRGVNGIKAGLTGREADALTRDYITEKGYGEYFGHSTGHGIGLEIHEAPGLAFRSDTVLEPGMAVTVEPGIYIPGIGGVRIEDDIIVTSEGNEVITKSPKELIIL 353
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350
   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 3Q6D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3Q6D)

(-) Pfam Domains  (2, 8)

Asymmetric Unit
(-)
Clan: AMP_N-like (22)
(-)
Clan: no clan defined [family: Peptidase_M24] (23)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q81M33_BACAN | Q81M33)
molecular function
    GO:0016805    dipeptidase activity    Catalysis of the hydrolysis of a dipeptide.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0102009    proline dipeptidase activity    Catalysis of the reaction: H2O + a dipeptide with proline at the C-terminal <=> L-proline + a standard alpha amino acid.
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.

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  3q6d
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