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(-) Description

Title :  CRYSTAL STRUCTURE OF A PERIPLASMIC HIS/GLU/GLN/ARG/OPINE FAMILY-BINDING PROTEIN FROM SILICIBACTER POMEROYI IN COMPLEX WITH LYSINE
 
Authors :  J. B. Bonanno, M. Rutter, K. T. Bain, S. Miller, R. Romero, J. M. Sauder, S. K. Burley, S. C. Almo, New York Sgx Research Center For Struct Genomics (Nysgxrc)
Date :  07 Jul 09  (Deposition) - 21 Jul 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Transporter, Psi-2, Protein Structure Initiative, New York Sgx Research Center For Structural Genomics, Nysgxrc, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. B. Bonanno, M. Rutter, K. T. Bain, S. Miller, R. Romero, J. M. Sauder, S. K. Burley, S. C. Almo
Crystal Structure Of A Periplasmic His/Glu/Gln/Arg/Opine Family-Binding Protein From Silicibacter Pomeroyi In Comple With Lysine
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PERIPLASMIC HIS/GLU/GLN/ARG/OPINE FAMILY-BINDING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MODIFIED PET26
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector: PET
    Expression System Vector Type: PLASMID
    Fragment: SEQUENCE DATABASE RESIDUES 50-270
    Gene: SPO1306
    Organism Scientific: SILICIBACTER POMEROYI
    Organism Taxid: 89184
    Synonym: HIS/GLU/GLN/ARG/OPINE FAMILY ABC TRANSPORTER

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2LYS1Mod. Amino AcidLYSINE
3NA1Ligand/IonSODIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:14 , HOH A:31 , GLU A:58 , TYR A:61 , TRP A:99 , GLY A:117 , MET A:118 , SER A:119 , ARG A:124 , GLN A:158 , THR A:161 , ILE A:162 , GLN A:163 , PRO A:180BINDING SITE FOR RESIDUE LYS A 1
2AC2SOFTWAREASP A:125 , ILE A:128 , ASP A:129 , GLU A:232BINDING SITE FOR RESIDUE NA A 279
3AC3SOFTWAREHOH A:20 , HOH A:27 , ILE A:120 , THR A:121 , ASP A:122 , GLU A:236BINDING SITE FOR RESIDUE GOL A 280

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3I6V)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Pro A:62 -Pro A:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3I6V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3I6V)

(-) Exons   (0, 0)

(no "Exon" information available for 3I6V)

(-) 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:219
 aligned with Q5LTV6_RUEPO | Q5LTV6 from UniProtKB/TrEMBL  Length:270

    Alignment length:219
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261         
         Q5LTV6_RUEPO    52 TVRMGTEGAYPPYNFINDAGEVDGFERELGDELCKRAGLTCEWVKNDWDSIIPNLVSGNYDTIIAGMSITDERDEVIDFTQNYIPPTASSYVATSDGADLSGIVAAQTATIQAGYIAESGATLVEFATPEETIAAVRNGEADAVFADRDYLVPIVAESGGELMFVGDDVPLGGGVGMGLRESDGELRGKFDAAITSMKEDGTLNTMIKKWFGEDAAVYE 270
               SCOP domains d3i6va_ A: automated matches                                                                                                                                                                                                SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..ee...eee.....eehhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhh....ee......hhhhhh..eeeeeee...eeeeee.........eeeee..hhhhhhhhhh..eeeee.hhhhhhhhhhh....eeeeehhhhhhhhhhh....eeeeeeee....eeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3i6v A  52 TVRMGTEGAYPPYNFINDAGEVDGFERELGDELCKRAGLTCEWVKNDWDSIIPNLVSGNYDTIIAGMSITDERDEVIDFTQNYIPPTASSYVATSDGADLSGIVAAQTATIQAGYIAESGATLVEFATPEETIAAVRNGEADAVFADRDYLVPIVAESGGELMFVGDDVPLGGGVGMGLRESDGELRGKFDAAITSMKEDGTLNTMIKKWFGEDAAVYK   1
                                    61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       ||
                                                                                                                                                                                                                                                   269|
                                                                                                                                                                                                                                                      1
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3I6V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3I6V)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q5LTV6_RUEPO | Q5LTV6)
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.
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.
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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