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(-) Description

Title :  CRYSTAL STRUCTURE OF AN XXA-PRO AMINOPEPTIDASE FROM STREPTOCOCCUS PYOGENES
 
Authors :  A. Joachimiak, N. E. C. Duke, L. Volkart, S. Clancy, Midwest Center Fo Structural Genomics (Mcsg)
Date :  16 Sep 10  (Deposition) - 03 Nov 10  (Release) - 03 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Joachimiak, N. E. C. Duke, L. Volkart, S. Clancy, Midwest Center For Structural Genomics (Mcsg)
Crystal Structure Of An Xxa-Pro Aminopeptidase From Streptococcus Pyogenes
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - AMINOPEPTIDASE P, XAA-PRO 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
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: M28_SPY1536, SPY_1824
    Organism Scientific: STREPTOCOCCUS PYOGENES
    Organism Taxid: 160490
    Strain: M1 GAS

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 12)

Asymmetric/Biological Unit (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3OVK)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3OVK)

(-) 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:129
 aligned with Q48RL4_STRPM | Q48RL4 from UniProtKB/TrEMBL  Length:370

    Alignment length:129
                                    23        33        43        53        63        73        83        93       103       113       123       133         
         Q48RL4_STRPM    14 MSGFLEQRLGHCLRQMAEKGLEALLVTHLTNSYYLTGFSGTAATVLITAKRRVLITDSRYTLLAKASVEGFDIIESRTPLKVVAELLEADQIDCLGFEDQVSFSFYQAMQAELSGITLLAQSGFVEHLR 142
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhh......eeeee...eeeee...hhhhhhhhh...eeee..hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh...eeeee...hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ovk A   1 mSGFLEQRLGHCLRQmAEKGLEALLVTHLTNSYYLTGFSGTAATVLITAKRRVLITDSRYTLLAKASVEGFDIIESRTPLKVVAELLEADQIDCLGFEDQVSFSFYQAmQAELSGITLLAQSGFVEHLR 129
                            |       10     |  20        30        40        50        60        70        80        90       100       110       120         
                            |             16-MSE                                                                                      109-MSE                
                            1-MSE                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:129
 aligned with Q48RL4_STRPM | Q48RL4 from UniProtKB/TrEMBL  Length:370

    Alignment length:129
                                    23        33        43        53        63        73        83        93       103       113       123       133         
         Q48RL4_STRPM    14 MSGFLEQRLGHCLRQMAEKGLEALLVTHLTNSYYLTGFSGTAATVLITAKRRVLITDSRYTLLAKASVEGFDIIESRTPLKVVAELLEADQIDCLGFEDQVSFSFYQAMQAELSGITLLAQSGFVEHLR 142
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhh......eeeee...eeeee...hhhhhhhhh...eeee..hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh...eeeee...hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ovk B   1 mSGFLEQRLGHCLRQmAEKGLEALLVTHLTNSYYLTGFSGTAATVLITAKRRVLITDSRYTLLAKASVEGFDIIESRTPLKVVAELLEADQIDCLGFEDQVSFSFYQAmQAELSGITLLAQSGFVEHLR 129
                            |       10     |  20        30        40        50        60        70        80        90       100       110       120         
                            1-MSE         16-MSE                                                                                      109-MSE                


Chain C from PDB  Type:PROTEIN  Length:129
 aligned with Q48RL4_STRPM | Q48RL4 from UniProtKB/TrEMBL  Length:370

    Alignment length:129
                                    23        33        43        53        63        73        83        93       103       113       123       133         
         Q48RL4_STRPM    14 MSGFLEQRLGHCLRQMAEKGLEALLVTHLTNSYYLTGFSGTAATVLITAKRRVLITDSRYTLLAKASVEGFDIIESRTPLKVVAELLEADQIDCLGFEDQVSFSFYQAMQAELSGITLLAQSGFVEHLR 142
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhh......eeeee...eeeeehhhhhhhhhh.....eeee..hhhhhhhhhhhhh...eeeee...hhhhhhhhhhhh...eeeee...hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ovk C   1 mSGFLEQRLGHCLRQmAEKGLEALLVTHLTNSYYLTGFSGTAATVLITAKRRVLITDSRYTLLAKASVEGFDIIESRTPLKVVAELLEADQIDCLGFEDQVSFSFYQAmQAELSGITLLAQSGFVEHLR 129
                            |       10     |  20        30        40        50        60        70        80        90       100       110       120         
                            1-MSE         16-MSE                                                                                      109-MSE                


Chain D from PDB  Type:PROTEIN  Length:129
 aligned with Q48RL4_STRPM | Q48RL4 from UniProtKB/TrEMBL  Length:370

    Alignment length:129
                                    23        33        43        53        63        73        83        93       103       113       123       133         
         Q48RL4_STRPM    14 MSGFLEQRLGHCLRQMAEKGLEALLVTHLTNSYYLTGFSGTAATVLITAKRRVLITDSRYTLLAKASVEGFDIIESRTPLKVVAELLEADQIDCLGFEDQVSFSFYQAMQAELSGITLLAQSGFVEHLR 142
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------Creatinase_N-3ovkD01 D:8-129                                                                                               Pfam domains (1)
           Pfam domains (2) -------Creatinase_N-3ovkD02 D:8-129                                                                                               Pfam domains (2)
           Pfam domains (3) -------Creatinase_N-3ovkD03 D:8-129                                                                                               Pfam domains (3)
           Pfam domains (4) -------Creatinase_N-3ovkD04 D:8-129                                                                                               Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhh......eeeee...eeeee...hhhhhhhhh...eeee..hhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhh...eeeee...hhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ovk D   1 mSGFLEQRLGHCLRQmAEKGLEALLVTHLTNSYYLTGFSGTAATVLITAKRRVLITDSRYTLLAKASVEGFDIIESRTPLKVVAELLEADQIDCLGFEDQVSFSFYQAmQAELSGITLLAQSGFVEHLR 129
                            |       10     |  20        30        40        50        60        70        80        90       100       110       120         
                            1-MSE         16-MSE                                                                                      109-MSE
   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 3OVK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: AMP_N-like (22)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (Q48RL4_STRPM | Q48RL4)
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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