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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MATURE STREPTOCOCCAL CYSTEINE PROTEASE, MSPEB
 
Authors :  J. G. Olsen, R. Dagil, L. M. Niclasen, O. E. Soerensen, B. B. Kragelund
Date :  16 Sep 08  (Deposition) - 08 Sep 09  (Release) - 07 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Proteinase, Papain Family, Cysteine Protease, Hydrolase, Dimer, Clan Ca, Exotoxin, Family 10, Peptidase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. G. Olsen, R. Dagil, L. M. Niclasen, O. E. Soerensen, B. B. Kragelund
Structure Of The Mature Streptococcal Cysteine Protease Exotoxin Mspeb In Its Active Dimeric Form.
J. Mol. Biol. V. 393 693 2009
PubMed-ID: 19712682  |  Reference-DOI: 10.1016/J.JMB.2009.08.046

(-) Compounds

Molecule 1 - STREPTOPAIN
    ChainsA, B
    EC Number3.4.22.10
    Organism ScientificSTREPTOCOCCUS PYOGENES
    Organism Taxid1314
    Other DetailsCYSTEINE PROTEASE INHIBITOR E64 LINKED TO CYSTEINE 47
    Other Details - SourcePROTEIN WAS PURIFIED FROM NATURAL SOURCE.
    StrainALAB49
    SynonymMATURE STREPTOCOCCAL PYROGENIC EXOTOXIN B, STREPTOCOCCAL CYSTEINE PROTEINASE, STREPTOCOCCUS PEPTIDASE A, SPP, EXOTOXIN TYPE B, SPE B

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1E642Ligand/IonN-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1E641Ligand/IonN-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1E641Ligand/IonN-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:17 , CYS A:47 , ASP A:130 , GLY A:136 , SER A:137 , GLY A:188 , GLY A:194 , HIS A:195 , HOH A:2165 , HOH A:2166 , GLN B:36 , SER B:37BINDING SITE FOR RESIDUE E64 A1254
2AC2SOFTWAREGLN A:36 , SER A:37 , GLN B:17 , CYS B:47 , VAL B:48 , ASP B:128 , ASP B:130 , SER B:135 , GLY B:136 , SER B:137 , ALA B:138 , GLN B:187 , GLY B:194 , HIS B:195 , HOH B:2018 , HOH B:2092 , HOH B:2099 , HOH B:2166 , HOH B:2167BINDING SITE FOR RESIDUE E64 B1254

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2UZJ)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Asn A:19 -Pro A:20
2Gln A:36 -Ser A:37
3Tyr A:61 -Pro A:62
4His A:82 -Pro A:83
5Asn B:19 -Pro B:20
6Gln B:36 -Ser B:37
7Tyr B:61 -Pro B:62
8His B:82 -Pro B:83

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (7, 13)

Asymmetric Unit (7, 13)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_SPEB_STRPY_005 *D154NSPEB_STRPY  ---  ---A/BD9N
2UniProtVAR_SPEB_STRPY_006 *L211VSPEB_STRPY  ---  ---A/BL66V
3UniProtVAR_SPEB_STRPY_007 *I305VSPEB_STRPY  ---  ---A/BI160V
4UniProtVAR_SPEB_STRPY_008 *S308GSPEB_STRPY  ---  ---A/BS163G
5UniProtVAR_SPEB_STRPY_009 *A317SSPEB_STRPY  ---  ---A/BA172S
6UniProtVAR_SPEB_STRPY_010 *G384DSPEB_STRPY  ---  ---AG239D
7UniProtVAR_SPEB_STRPY_011 *V394ISPEB_STRPY  ---  ---A/BV249I
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (7, 7)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_SPEB_STRPY_005 *D154NSPEB_STRPY  ---  ---AD9N
2UniProtVAR_SPEB_STRPY_006 *L211VSPEB_STRPY  ---  ---AL66V
3UniProtVAR_SPEB_STRPY_007 *I305VSPEB_STRPY  ---  ---AI160V
4UniProtVAR_SPEB_STRPY_008 *S308GSPEB_STRPY  ---  ---AS163G
5UniProtVAR_SPEB_STRPY_009 *A317SSPEB_STRPY  ---  ---AA172S
6UniProtVAR_SPEB_STRPY_010 *G384DSPEB_STRPY  ---  ---AG239D
7UniProtVAR_SPEB_STRPY_011 *V394ISPEB_STRPY  ---  ---AV249I
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_SPEB_STRPY_005 *D154NSPEB_STRPY  ---  ---BD9N
2UniProtVAR_SPEB_STRPY_006 *L211VSPEB_STRPY  ---  ---BL66V
3UniProtVAR_SPEB_STRPY_007 *I305VSPEB_STRPY  ---  ---BI160V
4UniProtVAR_SPEB_STRPY_008 *S308GSPEB_STRPY  ---  ---BS163G
5UniProtVAR_SPEB_STRPY_009 *A317SSPEB_STRPY  ---  ---BA172S
7UniProtVAR_SPEB_STRPY_011 *V394ISPEB_STRPY  ---  ---BV249I
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2UZJ)

(-) Exons   (0, 0)

(no "Exon" information available for 2UZJ)

(-) 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:249
 aligned with SPEB_STRP6 | Q5X9P3 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:253
                                   155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395   
           SPEB_STRP6   146 QPVVKSLLDSKGIHYNQGNPYNLLTPVIEKVKPGEQSFVGQHAATGCVATATAQIMKYHNYPNKGLKDYTYTLSSNNPYFNHPKNLFAAISTRQYNWNNILPTYSGRESNVQKMAISELMADVGISVDMDYGPSSGSAGSSRVQRALKENFGYNQSVHQINRSDFSKQDWEAQIDKELSQNQPVYYQGVGKVGGHAFVIDGADGRNFYHVNWGWGGVSDGFFRLDALNPSALGTGGGAGGFNGYQSAVVGIKP 398
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhh..................................hhhhhhhhhhhhhhh........eeee............eeeehhhhh...............hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhhhhh...eeeeeee..eeeeeeeeeee....eeee........eee......hhhhh----.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------N--------------------------------------------------------V---------------------------------------------------------------------------------------------V--G--------S------------------------------------------------------------------D---------I---- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uzj A   1 QPVVKSLLDSKGIHYNQGNPYNLLTPVIEKVKPGEQSFVGQHAATGCVATATAQIMKYHNYPNKGLKDYTYTLSSNNPYFNHPKNLFAAISTRQYNWNNILPTYSGRESNVQKMAISELMADVGISVDMDYGPSSGSAGSSRVQRALKENFGYNQSVHQINRSDFSKQDWEAQIDKELSQNQPVYYQGVGKVGGHAFVIDGADGRNFYHVNWGWGGVSDGFFRLDALNPSALG----AGGFNGYQSAVVGIKP 253
                                    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   
                                                                                                                                                                                                                                                                  233  238               

Chain A from PDB  Type:PROTEIN  Length:249
 aligned with SPEB_STRPY | P0C0J0 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:253
                                   155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395   
           SPEB_STRPY   146 QPVVKSLLDSKGIHYNQGNPYNLLTPVIEKVKPGEQSFVGQHAATGCVATATAQIMKYHNYPNKGLKDYTYTLSSNNPYFNHPKNLFAAISTRQYNWNNILPTYSGRESNVQKMAISELMADVGISVDMDYGPSSGSAGSSRVQRALKENFGYNQSVHQINRSDFSKQDWEAQIDKELSQNQPVYYQGVGKVGGHAFVIDGADGRNFYHVNWGWGGVSDGFFRLDALNPSALGTGGGAGGFNGYQSAVVGIKP 398
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee.hhhhhh..................................hhhhhhhhhhhhhhh........eeee............eeeehhhhh...............hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhhhhh...eeeeeee..eeeeeeeeeee....eeee........eee......hhhhh----.....eeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------N--------------------------------------------------------V---------------------------------------------------------------------------------------------V--G--------S------------------------------------------------------------------D---------I---- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uzj A   1 QPVVKSLLDSKGIHYNQGNPYNLLTPVIEKVKPGEQSFVGQHAATGCVATATAQIMKYHNYPNKGLKDYTYTLSSNNPYFNHPKNLFAAISTRQYNWNNILPTYSGRESNVQKMAISELMADVGISVDMDYGPSSGSAGSSRVQRALKENFGYNQSVHQINRSDFSKQDWEAQIDKELSQNQPVYYQGVGKVGGHAFVIDGADGRNFYHVNWGWGGVSDGFFRLDALNPSALG----AGGFNGYQSAVVGIKP 253
                                    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   
                                                                                                                                                                                                                                                                  233  238               

Chain B from PDB  Type:PROTEIN  Length:247
 aligned with SPEB_STRP6 | Q5X9P3 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:253
                                   155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395   
           SPEB_STRP6   146 QPVVKSLLDSKGIHYNQGNPYNLLTPVIEKVKPGEQSFVGQHAATGCVATATAQIMKYHNYPNKGLKDYTYTLSSNNPYFNHPKNLFAAISTRQYNWNNILPTYSGRESNVQKMAISELMADVGISVDMDYGPSSGSAGSSRVQRALKENFGYNQSVHQINRSDFSKQDWEAQIDKELSQNQPVYYQGVGKVGGHAFVIDGADGRNFYHVNWGWGGVSDGFFRLDALNPSALGTGGGAGGFNGYQSAVVGIKP 398
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Inhibitor_I---Peptidase_C10-2uzjB01 B:15-223                                                                                                                                                                                   ------------------------------ Pfam domains (1)
           Pfam domains (2) Inhibitor_I---Peptidase_C10-2uzjB02 B:15-223                                                                                                                                                                                   ------------------------------ Pfam domains (2)
         Sec.struct. author .....hhhhhh..................................hhhhhhhhhhhhhhh........eeee............eeeehhhhh...............hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhhhhh...eeeeeee..eeeeeeeeee....eeeee........eeee.....hhhhh------...eeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------N--------------------------------------------------------V---------------------------------------------------------------------------------------------V--G--------S----------------------------------------------------------------------------I---- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uzj B   1 QPVVKSLLDSKGIHYNQGNPYNLLTPVIEKVKPGEQSFVGQHAATGCVATATAQIMKYHNYPNKGLKDYTYTLSSNNPYFNHPKNLFAAISTRQYNWNNILPTYSGRESNVQKMAISELMADVGISVDMDYGPSSGSAGSSRVQRALKENFGYNQSVHQINRSDFSKQDWEAQIDKELSQNQPVYYQGVGKVGGHAFVIDGADGRNFYHVNWGWGGVSDGFFRLDALNPSALG------GFNGYQSAVVGIKP 253
                                    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   
                                                                                                                                                                                                                                                                  233    240             

Chain B from PDB  Type:PROTEIN  Length:247
 aligned with SPEB_STRPY | P0C0J0 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:253
                                   155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395   
           SPEB_STRPY   146 QPVVKSLLDSKGIHYNQGNPYNLLTPVIEKVKPGEQSFVGQHAATGCVATATAQIMKYHNYPNKGLKDYTYTLSSNNPYFNHPKNLFAAISTRQYNWNNILPTYSGRESNVQKMAISELMADVGISVDMDYGPSSGSAGSSRVQRALKENFGYNQSVHQINRSDFSKQDWEAQIDKELSQNQPVYYQGVGKVGGHAFVIDGADGRNFYHVNWGWGGVSDGFFRLDALNPSALGTGGGAGGFNGYQSAVVGIKP 398
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) Inhibitor_I---Peptidase_C10-2uzjB01 B:15-223                                                                                                                                                                                   ------------------------------ Pfam domains (1)
           Pfam domains (2) Inhibitor_I---Peptidase_C10-2uzjB02 B:15-223                                                                                                                                                                                   ------------------------------ Pfam domains (2)
         Sec.struct. author .....hhhhhh..................................hhhhhhhhhhhhhhh........eeee............eeeehhhhh...............hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh.......eeee.hhhhhhhhhhhhhhhhhh...eeeeeee..eeeeeeeeee....eeeee........eeee.....hhhhh------...eeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------N--------------------------------------------------------V---------------------------------------------------------------------------------------------V--G--------S----------------------------------------------------------------------------I---- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2uzj B   1 QPVVKSLLDSKGIHYNQGNPYNLLTPVIEKVKPGEQSFVGQHAATGCVATATAQIMKYHNYPNKGLKDYTYTLSSNNPYFNHPKNLFAAISTRQYNWNNILPTYSGRESNVQKMAISELMADVGISVDMDYGPSSGSAGSSRVQRALKENFGYNQSVHQINRSDFSKQDWEAQIDKELSQNQPVYYQGVGKVGGHAFVIDGADGRNFYHVNWGWGGVSDGFFRLDALNPSALG------GFNGYQSAVVGIKP 253
                                    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   
                                                                                                                                                                                                                                                                  233    240             

   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 2UZJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2UZJ)

(-) Pfam Domains  (2, 4)

Asymmetric Unit

(-) Gene Ontology  (7, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SPEB_STRPY | P0C0J0)
molecular function
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
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.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0035897    proteolysis in other organism    The chemical reactions and pathways performed by an organism resulting in the hydrolysis of proteins in another organism by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

Chain A,B   (SPEB_STRP6 | Q5X9P3)
molecular function
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    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:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
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.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        SPEB_STRPY | P0C0J01dki 1pvj

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2UZJ)