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(-) Description

Title :  STRUCTURAL BASIS FOR HIGH ARGININE SPECIFICITY IN SALMONELLA TYPHIMURIUM PERIPLASMIC BINDING PROTEIN STM4351.
 
Authors :  A. L. Stamp, P. Owen, K. El Omari, M. Lockyer, H. K. Lamb, I. G. Charles, A. R. Hawkins, D. K. Stammers
Date :  31 Jan 11  (Deposition) - 11 May 11  (Release) - 22 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Arginine-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. L. Stamp, P. Owen, K. El Omari, M. Lockyer, H. K. Lamb, I. G. Charles, A. R. Hawkins, D. K. Stammers
Crystallographic And Microcalorimetric Analyses Reveal The Structural Basis For High Arginine Specificity In The Salmonella Enterica Serovar Typhimurium Periplasmic Binding Protein Stm4351.
Proteins V. 79 2352 2011
PubMed-ID: 21560168  |  Reference-DOI: 10.1002/PROT.23060

(-) Compounds

Molecule 1 - STM4351
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21A
    Expression System Strain: BL21-AI
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 18-246
    Organism Scientific: SALMONELLA ENTERICA SUBSP. ENTERICA
    Organism Taxid: 90371
    Strain: SEROVAR TYPHIMURIUM

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2ARG2Mod. Amino AcidARGININE
3GOL2Ligand/IonGLYCEROL
4ZN6Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:30 , THR A:32 , TYR A:33 , GLU A:37 , PHE A:71 , ALA A:88 , GLY A:89 , ASP A:91 , ARG A:96 , GLU A:135 , THR A:138 , THR A:139 , HIS A:140 , ASP A:177BINDING SITE FOR RESIDUE ARG A1245
02AC2SOFTWAREASP A:72 , ASP A:157BINDING SITE FOR RESIDUE ZN A1246
03AC3SOFTWAREHIS A:26 , ASP A:84 , HOH A:2150BINDING SITE FOR RESIDUE ZN A1247
04AC4SOFTWAREASP A:40 , ASP A:42BINDING SITE FOR RESIDUE ZN A1248
05AC5SOFTWARETHR A:93 , LYS A:95 , THR A:138 , ARG A:142 , HOH A:2071 , HOH A:2151 , HOH A:2152BINDING SITE FOR RESIDUE ACT A1249
06AC6SOFTWAREGLY A:119 , TYR A:121 , HIS A:122 , ALA A:192 , MET A:194 , ASP A:195 , HOH A:2108 , HOH A:2153BINDING SITE FOR RESIDUE GOL A1250
07AC7SOFTWARESER B:30 , THR B:32 , TYR B:33 , GLU B:37 , PHE B:71 , ALA B:88 , GLY B:89 , ASP B:91 , ARG B:96 , GLU B:135 , THR B:138 , THR B:139 , HIS B:140 , ASP B:177 , HOH B:2036BINDING SITE FOR RESIDUE ARG B1245
08AC8SOFTWAREASP B:72 , ASP B:157 , HOH B:2069BINDING SITE FOR RESIDUE ZN B2246
09AC9SOFTWAREHIS B:26 , ASP B:84 , HOH B:2070BINDING SITE FOR RESIDUE ZN B2247
10BC1SOFTWARETHR B:93 , ARG B:96 , THR B:138 , ARG B:142BINDING SITE FOR RESIDUE ACT B2248
11BC2SOFTWAREGLY B:119 , TYR B:121 , HIS B:122 , MET B:194 , ASP B:195 , HOH B:2071BINDING SITE FOR RESIDUE GOL B2249
12BC3SOFTWAREHOH B:2064 , HOH B:2065 , HOH B:2066 , HOH B:2067 , HOH B:2068BINDING SITE FOR RESIDUE ZN B2250

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y7I)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:34 -Pro A:35
2Ala B:34 -Pro B:35

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y7I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y7I)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y7I)

(-) 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:229
 aligned with Q8ZKA9_SALTY | Q8ZKA9 from UniProtKB/TrEMBL  Length:246

    Alignment length:229
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237         
        Q8ZKA9_SALTY     18 ASVSARTLHFGTSATYAPYEFVDADNKIVGFDIDVANAVCKEMQAECSFTNQSFDSLIPSLRFKKFDAVIAGMDMTPKREQQVSFSQPYYEGLSAVVVTRKGAYHTFADLKGKKVGLENGTTHQRYLQDKQQAITPVAYDSYLNAFTDLKNNRLEGVFGDVAAIGKWLKNNPDYAIMDERASDPDYYGKGLGIAVRKDNDALLQEINAALDKVKASPEYAQMQEKWFTQ  246
               SCOP domains d2y7ia_ A: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeeee........ee.....eehhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh....ee......hhhhhh..ee.........eeeeee......hhhhh..eeeee..hhhhhhhhhhh...eeeee.hhhhhhhhhhh....eeeeehhhhhhhhh....eee.................ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2y7i A   18 ASVSARTLHFGTSATYAPYEFVDADNKIVGFDIDVANAVCKEMQAECSFTNQSFDSLIPSLRFKKFDAVIAGMDMTPKREQQVSFSQPYYEGLSAVVVTRKGAYHTFADLKGKKVGLENGTTHQRYLQDKQQAITPVAYDSYLNAFTDLKNNRLEGVFGDVAAIGKWLKNNPDYAIMDERASDPDYYGKGLGIAVRKDNDALLQEINAALDKVKASPEYAQMQEKWFTR 1245
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       ||
                                                                                                                                                                                                                                                             245|
                                                                                                                                                                                                                                                             1245


Chain B from PDB  Type:PROTEIN  Length:225
 aligned with Q8ZKA9_SALTY | Q8ZKA9 from UniProtKB/TrEMBL  Length:246

    Alignment length:225
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241     
        Q8ZKA9_SALTY     22 ARTLHFGTSATYAPYEFVDADNKIVGFDIDVANAVCKEMQAECSFTNQSFDSLIPSLRFKKFDAVIAGMDMTPKREQQVSFSQPYYEGLSAVVVTRKGAYHTFADLKGKKVGLENGTTHQRYLQDKQQAITPVAYDSYLNAFTDLKNNRLEGVFGDVAAIGKWLKNNPDYAIMDERASDPDYYGKGLGIAVRKDNDALLQEINAALDKVKASPEYAQMQEKWFTQ  246
               SCOP domains d2y7ib_ B: automated matches                                                                                                                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---SBP_bac_3-2y7iB01 B:25-1245                                                                                                                                                                                                    Pfam domains (1)
           Pfam domains (2) ---SBP_bac_3-2y7iB02 B:25-1245                                                                                                                                                                                                    Pfam domains (2)
         Sec.struct. author ..eeeeee........ee.....eehhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh....ee......hhhhhh..ee.........eeeeee.....hhhhhh..eeeee..hhhhhhhhhhh...eeeee.hhhhhhhhhhh....eeeeehhhhhhhhh....eee.................ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2y7i B   22 ARTLHFGTSATYAPYEFVDADNKIVGFDIDVANAVCKEMQAECSFTNQSFDSLIPSLRFKKFDAVIAGMDMTPKREQQVSFSQPYYEGLSAVVVTRKGAYHTFADLKGKKVGLENGTTHQRYLQDKQQAITPVAYDSYLNAFTDLKNNRLEGVFGDVAAIGKWLKNNPDYAIMDERASDPDYYGKGLGIAVRKDNDALLQEINAALDKVKASPEYAQMQEKWFTR 1245
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241   ||
                                                                                                                                                                                                                                                         245|
                                                                                                                                                                                                                                                         1245
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y7I)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: PBP (391)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q8ZKA9_SALTY | Q8ZKA9)
molecular function
    GO:0004970    ionotropic glutamate receptor activity    Catalysis of the transmembrane transfer of an ion by a channel that opens when glutamate has been bound by the channel complex or one of its constituent parts.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0035235    ionotropic glutamate receptor signaling pathway    A series of molecular signals initiated by glutamate binding to a glutamate receptor on the surface of the target cell, followed by the movement of ions through a channel in the receptor complex. Ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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