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(-) Description

Title :  CRYSTAL STRUCTURES OF A SODIUM-ALPHA-KETO ACID BINDING SUBUNIT FROM A TRAP TRANSPORTER IN ITS CLOSED FORMS
 
Authors :  S. Gonin, P. Arnoux, B. Pierru, B. Alonso, M. Sabaty, D. Pignol
Date :  09 Aug 06  (Deposition) - 03 Apr 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Trap Transporter, Periplasmic Subunit, Ligand Binding, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Gonin, P. Arnoux, B. Pierru, J. Lavergne, B. Alonso, M. Sabaty, D. Pignol
Crystal Structures Of An Extracytoplasmic Solute Receptor From A Trap Transporter In Its Open And Closed Forms Reveal A Helix-Swapped Dimer Requiring A Cation For Alpha-Keto Acid Binding.
Bmc Struct. Biol. V. 7 11 2007
PubMed-ID: 17362499  |  Reference-DOI: 10.1186/1472-6807-7-11
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TRAP-T FAMILY SORBITOL/MANNITOL TRANSPORTER, PERIPLASMIC BINDING PROTEIN, SMOM
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET101
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: SKAP
    Organism Scientific: RHODOBACTER SPHAEROIDES 2.4.1
    Organism Taxid: 272943
    Strain: ATCC 17023

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
2PYR3Ligand/IonPYRUVIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:156 , GLU A:214 , TRP A:215 , GLU A:240 , PYR A:601BINDING SITE FOR RESIDUE NA A 500
2AC2SOFTWAREGLN B:156 , GLU B:214 , TRP B:215 , GLU B:240 , PYR B:602BINDING SITE FOR RESIDUE NA B 501
3AC3SOFTWAREILE A:47 , TYR A:99 , TYR A:100 , GLN A:156 , ARG A:177 , GLU A:214 , TRP A:215 , VAL A:216 , GLU A:240 , NA A:500BINDING SITE FOR RESIDUE PYR A 601
4AC4SOFTWARETYR B:99 , TYR B:100 , GLN B:156 , ARG B:177 , GLU B:214 , TRP B:215 , VAL B:216 , GLU B:240 , NA B:501BINDING SITE FOR RESIDUE PYR B 602
5AC5SOFTWAREPHE B:116 , PHE B:310 , ALA B:313 , ASN B:314 , TYR B:317 , ARG B:338 , HOH B:689BINDING SITE FOR RESIDUE PYR B 603

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:235 -Pro A:236
2Tyr B:235 -Pro B:236

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2HZL)

(-) 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:334
 aligned with TAKP_RHOS4 | Q3J1R2 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:334
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361    
           TAKP_RHOS4    32 VTWRLASSFPKSLDTIFGGAEVLSKMLSEATDGNFQIQVFSAGELVPGLQAADAVTEGTVECCHTVGYYYWGKDPTFALAAAVPFSLSARGINAWHYHGGGIDLYNEFLSQHNIVAFPGGNTGVQMGGWFRREINTVADMQGLKMRVGGFAGKVMERLGVVPQQIAGGDIYPALEKGTIDATEWVGPYDDEKLGFFKVAPYYYYPGWWEGGPTVHFMFNKSAYEGLTPTYQSLLRTACHAADANMLQLYDWKNPTAIKSLVAQGTQLRPFSPEILQACFEAANEVYAEMEASNPAFKKIWDSIKAFRSEHYTWAQIAEYNYDTFMMVQQNAGKL 365
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.........hhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhh....eeeehhhhhh..hhhhhh........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.......ee......hhhhh..eee...hhhhhhhh...eee.....hhhhhhhh....ee...hhhhhhhhhhhhh..eeee........eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hzl A  32 VTWRLASSFPKSLDTIFGGAEVLSKMLSEATDGNFQIQVFSAGELVPGLQAADAVTEGTVECCHTVGYYYWGKDPTFALAAAVPFSLSARGINAWHYHGGGIDLYNEFLSQHNIVAFPGGNTGVQMGGWFRREINTVADMQGLKMRVGGFAGKVMERLGVVPQQIAGGDIYPALEKGTIDATEWVGPYDDEKLGFFKVAPYYYYPGWWEGGPTVHFMFNKSAYEGLTPTYQSLLRTACHAADANMLQLYDWKNPTAIKSLVAQGTQLRPFSPEILQACFEAANEVYAEMEASNPAFKKIWDSIKAFRSEHYTWAQIAEYNYDTFMMVQQNAGKL 365
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361    


Chain B from PDB  Type:PROTEIN  Length:337
 aligned with TAKP_RHOS4 | Q3J1R2 from UniProtKB/Swiss-Prot  Length:365

    Alignment length:337
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       
           TAKP_RHOS4    29 APKVTWRLASSFPKSLDTIFGGAEVLSKMLSEATDGNFQIQVFSAGELVPGLQAADAVTEGTVECCHTVGYYYWGKDPTFALAAAVPFSLSARGINAWHYHGGGIDLYNEFLSQHNIVAFPGGNTGVQMGGWFRREINTVADMQGLKMRVGGFAGKVMERLGVVPQQIAGGDIYPALEKGTIDATEWVGPYDDEKLGFFKVAPYYYYPGWWEGGPTVHFMFNKSAYEGLTPTYQSLLRTACHAADANMLQLYDWKNPTAIKSLVAQGTQLRPFSPEILQACFEAANEVYAEMEASNPAFKKIWDSIKAFRSEHYTWAQIAEYNYDTFMMVQQNAGKL 365
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.........hhhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhh....eeeehhhhhh..hhhhhh........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.......ee.....hhhhhh..eee...hhhhhhhhh..eee..hhhhhhhhhhh....ee...hhhhhhhhhhhhh..eeee........eeeeeeehhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hzl B  29 APKVTWRLASSFPKSLDTIFGGAEVLSKMLSEATDGNFQIQVFSAGELVPGLQAADAVTEGTVECCHTVGYYYWGKDPTFALAAAVPFSLSARGINAWHYHGGGIDLYNEFLSQHNIVAFPGGNTGVQMGGWFRREINTVADMQGLKMRVGGFAGKVMERLGVVPQQIAGGDIYPALEKGTIDATEWVGPYDDEKLGFFKVAPYYYYPGWWEGGPTVHFMFNKSAYEGLTPTYQSLLRTACHAADANMLQLYDWKNPTAIKSLVAQGTQLRPFSPEILQACFEAANEVYAEMEASNPAFKKIWDSIKAFRSEHYTWAQIAEYNYDTFMMVQQNAGKL 365
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358
   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 2HZL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HZL)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TAKP_RHOS4 | Q3J1R2)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0043177    organic acid binding    Interacting selectively and non-covalently with an organic acid, any acidic compound containing carbon in covalent linkage.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0071702    organic substance transport    The directed movement of organic substances into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter or pore. An organic substance is a molecular entity that contains carbon.
    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:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
    GO:0042597    periplasmic space    The region between the inner (cytoplasmic) and outer membrane (Gram-negative Bacteria) or cytoplasmic membrane and cell wall (Fungi and Gram-positive Bacteria).
    GO:0031317    tripartite ATP-independent periplasmic transporter complex    A complex consisting of two membrane proteins and one extracytoplasmic solute receptor. Such transporters transport a variety of substrates without direct ATP power, instead using energy from ion gradients.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TAKP_RHOS4 | Q3J1R2: 2hzk

(-) Related Entries Specified in the PDB File

2hzk OPEN UNLIGANDED FORM