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(-) Description

Title :  CRYSTAL STRUCTURE OF A PTS DEPENDENT N-ACETYL-GALACTOSAMINE-IIB COMPONENT (AGAV, SPY_0631) FROM STREPTOCOCCUS PYOGENES AT 1.65 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  05 Oct 10  (Deposition) - 27 Oct 10  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pts Iib Component, Phosphotransferase, Sugar Transport, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of A Pts Dependent N-Acetyl-Galactosamine-Iib Component (Agav, Spy_0631) From Streptococcus Pyogenes At 1. 65 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PTS SYSTEM, N-ACETYLGALACTOSAMINE-SPECIFIC IIB COMPONENT
    Chains: A, B
    EC Number: 2.7.1.69
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AGAV, M5005_SPY0521, SPY_0631
    Organism Scientific: STREPTOCOCCUS PYOGENES SEROTYPE M1
    Organism Taxid: 301447
    Synonym: PUTATIVE PTS DEPENDENT N-ACETYL-GALACTOSAMINE-IIB COMPONENT

 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  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1MSE6Mod. Amino AcidSELENOMETHIONINE
2PEG3Ligand/IonDI(HYDROXYETHYL)ETHER
3PGE1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
3PGE-1Ligand/IonTRIETHYLENE GLYCOL
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
3PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:13 , LYS A:85BINDING SITE FOR RESIDUE PEG A 202
2AC2SOFTWAREARG B:60 , GLN B:78 , ASP B:112 , VAL B:115BINDING SITE FOR RESIDUE PGE B 200
3AC3SOFTWAREILE A:117 , GLU B:95 , HOH B:327BINDING SITE FOR RESIDUE PEG B 201
4AC4SOFTWAREILE B:7 , ASN B:143 , LYS B:145 , SER B:152BINDING SITE FOR RESIDUE PEG B 203

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P3V)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln A:3 -Pro A:4

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P3V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P3V)

(-) Exons   (0, 0)

(no "Exon" information available for 3P3V)

(-) 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:162
 aligned with Q9A0T4_STRP1 | Q9A0T4 from UniProtKB/TrEMBL  Length:162

    Alignment length:162
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
         Q9A0T4_STRP1     1 MTQPNIIMTRVDERLIHGQGQLWVKFLNCNTVIVANDAVSEDKIQQSLMKTVIPSSIAIRFFSIQKVIDIIHKASPAQSIFIVVKDLQDAKLLVEGGVPITEINIGNIHKTDDKVAITQFISLGETDKSAIRCLAHDHHVVFNTKTTPAGNSASDVDILDYI 162
               SCOP domains d3p3va_ A: automated matches                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeeee.hhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhh....eeeeee.hhhhhhhhhhh.....eeeeee.......ee.....eehhhhhhhhhhhhhh...eee.......hhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p3v A   1 mTQPNIImTRVDERLIHGQGQLWVKFLNCNTVIVANDAVSEDKIQQSLmKTVIPSSIAIRFFSIQKVIDIIHKASPAQSIFIVVKDLQDAKLLVEGGVPITEINIGNIHKTDDKVAITQFISLGETDKSAIRCLAHDHHVVFNTKTTPAGNSASDVDILDYI 162
                            |      |10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160  
                            |      8-MSE                                   49-MSE                                                                                                             
                            1-MSE                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:163
 aligned with Q9A0T4_STRP1 | Q9A0T4 from UniProtKB/TrEMBL  Length:162

    Alignment length:163
                             1                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159   
         Q9A0T4_STRP1     - -MTQPNIIMTRVDERLIHGQGQLWVKFLNCNTVIVANDAVSEDKIQQSLMKTVIPSSIAIRFFSIQKVIDIIHKASPAQSIFIVVKDLQDAKLLVEGGVPITEINIGNIHKTDDKVAITQFISLGETDKSAIRCLAHDHHVVFNTKTTPAGNSASDVDILDYI 162
               SCOP domains d3p3vb_ B: automated matches                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----PTSIIB_sorb-3p3vB01 B:5-154                                                                                                                           -------- Pfam domains (1)
           Pfam domains (2) -----PTSIIB_sorb-3p3vB02 B:5-154                                                                                                                           -------- Pfam domains (2)
         Sec.struct. author ......eeeeeee.hhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhh......eeeeehhhhhhhhhhhh.....eeeee.hhhhhhhhhhh.....eeeeee.......ee.....eehhhhhhhhhhhhhh...eee.......hhhhh.hhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p3v B   0 GmTQPNIImTRVDERLIHGQGQLWVKFLNCNTVIVANDAVSEDKIQQSLmKTVIPSSIAIRFFSIQKVIDIIHKASPAQSIFIVVKDLQDAKLLVEGGVPITEINIGNIHKTDDKVAITQFISLGETDKSAIRCLAHDHHVVFNTKTTPAGNSASDVDILDYI 162
                             |      |9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159   
                             1-MSE  8-MSE                                   49-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P3V)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: PTSIIB_sorb] (6)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q9A0T4_STRP1 | Q9A0T4)
molecular function
    GO:0008982    protein-N(PI)-phosphohistidine-sugar phosphotransferase activity    Catalysis of the PEP-dependent, phosphoryl transfer-driven transport of substances across a membrane. The transport happens by catalysis of the reaction: protein N-phosphohistidine + sugar(out) = protein histidine + sugar phosphate(in). This differs from primary and secondary active transport in that the solute is modified during transport.
biological process
    GO:0034219    carbohydrate transmembrane transport    The process in which a carbohydrate is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0009401    phosphoenolpyruvate-dependent sugar phosphotransferase system    The uptake and phosphorylation of specific carbohydrates from the extracellular environment; uptake and phosphorylation are coupled, making the PTS a link between the uptake and metabolism of sugars; phosphoenolpyruvate is the original phosphate donor; phosphoenolpyruvate passes the phosphate via a signal transduction pathway, to enzyme 1 (E1), which in turn passes it on to the histidine protein, HPr; the next step in the system involves sugar-specific membrane-bound complex, enzyme 2 (EII), which transports the sugar into the cell; it includes the sugar permease, which catalyzes the transport reactions; EII is usually divided into three different domains, EIIA, EIIB, and EIIC.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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