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(-) Description

Title :  CRYSTAL STRUCTURE OF THE STREPTOCOCCUS PYOGENES NAD+ GLYCOHYDROLASE SPN IN COMPLEX WITH IFS, THE IMMUNITY FACTOR FOR SPN
 
Authors :  C. L. Smith, J. Stine Elam, T. Ellenberger, J. Ghosh, J. S. Pinkner, S. J. Hultgren, M. G. Caparon
Date :  19 Nov 10  (Deposition) - 02 Mar 11  (Release) - 02 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Glycohydrolase, Nad+, Virulence Factor, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. L. Smith, J. Ghosh, J. S. Elam, J. S. Pinkner, S. J. Hultgren, M. G. Caparon, T. Ellenberger
Structural Basis Of Streptococcus Pyogenes Immunity To Its Nad(+) Glycohydrolase Toxin.
Structure V. 19 192 2011
PubMed-ID: 21300288  |  Reference-DOI: 10.1016/J.STR.2010.12.013

(-) Compounds

Molecule 1 - NAD+-GLYCOHYDROLASE
    Chains: A, C
    EC Number: 3.2.2.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 191-451
    Gene: SPN
    Organism Scientific: STREPTOCOCCUS PYOGENES
    Organism Taxid: 1314
 
Molecule 2 - IMMUNITY FACTOR FOR SPN
    Chains: B, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: IFS
    Organism Scientific: STREPTOCOCCUS PYOGENES
    Organism Taxid: 1314
    Synonym: SPN IMMUNITY FACTOR

 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  (1, 25)

Asymmetric Unit (1, 25)
No.NameCountTypeFull Name
1MSE25Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 13)
No.NameCountTypeFull Name
1MSE13Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 12)
No.NameCountTypeFull Name
1MSE12Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 3PNT)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3PNT)

(-) 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:250
 aligned with D7S065_STRPY | D7S065 from UniProtKB/TrEMBL  Length:451

    Alignment length:250
                                   205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445
         D7S065_STRPY   196 ERDLFEKKFKEIKDKWVTDKQADEFIETADKYADKAVQMSAVASRAEYYRMYVSRKYQYKKEFVEKLKQVYKESGASHVTSKKDLMLAFDDAKRKSTIGRQENGLFVTSFAEDMALLFTDQGKLKSADQIENIKGVDSGKYSDGVYQYEYDSELTKNIDKLGYIRTASGDTPGANSLNIPGCQTWSGKHIENSESELIFPSISVKDLKSKAVLAEIDAKGYFEIIDPTIIAPNGDHKKVTGRFKIKKMQD 445
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh....hhhhhhhhhhhhhhhheeeeehhhhhhhhhhhhhhh.ee.hhhhheeeeehhhhhhhhh.......hhhhhhhhh...........eeeeehhhhhhhhhhhh..........................hhhhh...eee.eee....hhhhhhhhhhhhh..eee..eee.....eee...eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pnt A 196 ERDLFEKKFKEIKDKWVTDKQADEFIETADKYADKAVQmSAVASRAEYYRmYVSRKYQYKKEFVEKLKQVYKESGASHVTSKKDLmLAFDDAKRKSTIGRQENGLFVTSFAEDmALLFTDQGKLKSADQIENIKGVDSGKYSDGVYQYEYDSELTKNIDKLGYIRTASGDTPGANSLNIPGCQTWSGKHIENSESELIFPSISVKDLKSKAVLAEIDAKGYFEIIDPTIIAPNGDHKKVTGRFKIKKmQD 445
                                   205       215       225       235       245|      255       265       275     | 285       295       305   |   315       325       335       345       355       365       375       385       395       405       415       425       435       445
                                                                234-MSE     246-MSE                            281-MSE                     309-MSE                                                                                                                               443-MSE


Chain B from PDB  Type:PROTEIN  Length:161
 aligned with Q2VJ58_STRPY | Q2VJ58 from UniProtKB/TrEMBL  Length:161

    Alignment length:161
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160 
         Q2VJ58_STRPY     1 MYKVPKGLEHYQKMFQKEVTVNDLKKYLIGSDKEYRITRRDSYMGDISDPEVILEYGVYPAFIKGYTQLKANIEEALLEMSNSGQALDIYQAVQTLNAENMLLNYYESLPFYLNRQSILANITKALKDAHIREAMAHYKLGEFAHYQDTMLDMVERTIETF 161
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhh....hhhhhhhhhhh.hhhhh............hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.hhhhhhhhhh..hhhhhhh..hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pnt B   1 mYKVPKGLEHYQKmFQKEVTVNDLKKYLIGSDKEYRITRRDSYmGDISDPEVILEYGVYPAFIKGYTQLKANIEEALLEmSNSGQALDIYQAVQTLNAENmLLNYYESLPFYLNRQSILANITKALKDAHIREAmAHYKLGEFAHYQDTmLDmVERTIETF 161
                            |       10   |    20        30        40   |    50        60        70        80        90       100|      110       120       130    |  140       150  |    160 
                            |           14-MSE                        44-MSE                              80-MSE              101-MSE                           135-MSE        150-MSE       
                            1-MSE                                                                                                                                                 153-MSE    


Chain C from PDB  Type:PROTEIN  Length:250
 aligned with D7S065_STRPY | D7S065 from UniProtKB/TrEMBL  Length:451

    Alignment length:250
                                   205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445
         D7S065_STRPY   196 ERDLFEKKFKEIKDKWVTDKQADEFIETADKYADKAVQMSAVASRAEYYRMYVSRKYQYKKEFVEKLKQVYKESGASHVTSKKDLMLAFDDAKRKSTIGRQENGLFVTSFAEDMALLFTDQGKLKSADQIENIKGVDSGKYSDGVYQYEYDSELTKNIDKLGYIRTASGDTPGANSLNIPGCQTWSGKHIENSESELIFPSISVKDLKSKAVLAEIDAKGYFEIIDPTIIAPNGDHKKVTGRFKIKKMQD 445
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) NADase_NGA-3pntC01 C:196-445                                                                                                                                                                                                                               Pfam domains (1)
           Pfam domains (2) NADase_NGA-3pntC02 C:196-445                                                                                                                                                                                                                               Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh....hhhhhhhhhhhhhhhheeeeehhhhhhhhhhhhhhh.ee.hhhhheeeeehhhhhh..........hhhhhhhhhh..........eeeeehhhhhhhhhhhh..........................hhhhh...eee.eee....hhhhhhhhhhhhheeeee..eee.....eee...eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pnt C 196 ERDLFEKKFKEIKDKWVTDKQADEFIETADKYADKAVQmSAVASRAEYYRmYVSRKYQYKKEFVEKLKQVYKESGASHVTSKKDLmLAFDDAKRKSTIGRQENGLFVTSFAEDmALLFTDQGKLKSADQIENIKGVDSGKYSDGVYQYEYDSELTKNIDKLGYIRTASGDTPGANSLNIPGCQTWSGKHIENSESELIFPSISVKDLKSKAVLAEIDAKGYFEIIDPTIIAPNGDHKKVTGRFKIKKmQD 445
                                   205       215       225       235       245|      255       265       275     | 285       295       305   |   315       325       335       345       355       365       375       385       395       405       415       425       435       445
                                                                234-MSE     246-MSE                            281-MSE                     309-MSE                                                                                                                               443-MSE


Chain D from PDB  Type:PROTEIN  Length:160
 aligned with Q2VJ58_STRPY | Q2VJ58 from UniProtKB/TrEMBL  Length:161

    Alignment length:160
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161
         Q2VJ58_STRPY     2 YKVPKGLEHYQKMFQKEVTVNDLKKYLIGSDKEYRITRRDSYMGDISDPEVILEYGVYPAFIKGYTQLKANIEEALLEMSNSGQALDIYQAVQTLNAENMLLNYYESLPFYLNRQSILANITKALKDAHIREAMAHYKLGEFAHYQDTMLDMVERTIETF 161
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhh...hhhhhhhhhhh.hhhhh............hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh.hhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pnt D   2 YKVPKGLEHYQKmFQKEVTVNDLKKYLIGSDKEYRITRRDSYmGDISDPEVILEYGVYPAFIKGYTQLKANIEEALLEmSNSGQALDIYQAVQTLNAENmLLNYYESLPFYLNRQSILANITKALKDAHIREAmAHYKLGEFAHYQDTmLDmVERTIETF 161
                                    11  |     21        31        41  |     51        61        71        81        91       101       111       121       131   |   141       151 |     161
                                       14-MSE                        44-MSE                              80-MSE              101-MSE                           135-MSE        150-MSE       
                                                                                                                                                                                 153-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 3PNT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: NADase_NGA] (1)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (D7S065_STRPY | D7S065)
molecular function
    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.

Chain B,D   (Q2VJ58_STRPY | Q2VJ58)

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 Related Entries

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        Q2VJ58_STRPY | Q2VJ58: 3qb2

(-) Related Entries Specified in the PDB File

3qb2 THE CRYSTAL STRUCTURE OF IMMUNITY FACTOR FOR SPN (IFS)