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(-) Description

Title :  CRYSTAL STRUCTURE OF GLTPH IN COMPLEX WITH L-ASPARTATE AND SODIUM IONS
 
Authors :  E. Gouaux, O. Boudker, R. Ryan, D. Yernool, K. Shimamoto
Date :  16 Nov 06  (Deposition) - 27 Feb 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.29
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Amino Acid Transporter, Transmembrane Transporter, Aspartate Transporter, Binding Site, Sodium Binding, Substrate Binding, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Boudker, R. M. Ryan, D. Yernool, K. Shimamoto, E. Gouaux
Coupling Substrate And Ion Binding To Extracellular Gate Of A Sodium-Dependent Aspartate Transporter.
Nature V. 445 387 2007
PubMed-ID: 17230192  |  Reference-DOI: 10.1038/NATURE05455
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 425AA LONG HYPOTHETICAL PROTON GLUTAMATE SYMPORT PROTEIN
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD24
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: PYROCOCCUS HORIKOSHII
    Organism Taxid: 53953

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
1ASP3Mod. Amino AcidASPARTIC ACID
2NA6Ligand/IonSODIUM ION
3PLM3Ligand/IonPALMITIC ACID

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:308 , MET A:311 , SER A:349 , ILE A:350 , THR A:352BINDING SITE FOR RESIDUE NA A 423
02AC2SOFTWARESER A:278 , GLY A:306 , ALA A:307 , ASN A:310 , ASN A:401 , ASP A:405BINDING SITE FOR RESIDUE NA A 424
03AC3SOFTWARETHR B:308 , MET B:311 , SER B:349 , ILE B:350 , THR B:352BINDING SITE FOR RESIDUE NA B 423
04AC4SOFTWARESER B:278 , GLY B:306 , ASN B:310 , ASN B:401 , ASP B:405BINDING SITE FOR RESIDUE NA B 424
05AC5SOFTWARETHR C:308 , MET C:311 , SER C:349 , ILE C:350 , THR C:352BINDING SITE FOR RESIDUE NA C 423
06AC6SOFTWARESER C:278 , GLY C:306 , ALA C:307 , ASN C:310 , ASN C:401 , ASP C:405BINDING SITE FOR RESIDUE NA C 424
07AC7SOFTWAREARG A:276 , SER A:278 , THR A:314 , THR A:352 , ALA A:353 , GLY A:354 , VAL A:355 , PRO A:356 , GLY A:359 , ASP A:394 , ARG A:397 , THR A:398 , ASN A:401BINDING SITE FOR RESIDUE ASP A 425
08AC8SOFTWAREARG B:276 , SER B:278 , THR B:314 , THR B:352 , ALA B:353 , GLY B:354 , VAL B:355 , PRO B:356 , GLY B:357 , GLY B:359 , ASP B:394 , ARG B:397 , THR B:398 , ASN B:401BINDING SITE FOR RESIDUE ASP A 426
09AC9SOFTWAREARG C:276 , SER C:278 , THR C:314 , THR C:352 , ALA C:353 , GLY C:354 , VAL C:355 , PRO C:356 , GLY C:359 , ASP C:394 , ARG C:397 , THR C:398 , ASN C:401BINDING SITE FOR RESIDUE ASP A 427
10BC1SOFTWAREILE A:350 , GLY A:351BINDING SITE FOR RESIDUE PLM A 428
11BC2SOFTWAREILE B:350BINDING SITE FOR RESIDUE PLM B 425

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2NWX)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2NWX)

(-) 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:400
 aligned with O59010_PYRHO | O59010 from UniProtKB/TrEMBL  Length:425

    Alignment length:405
                                    21        31        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       371       381       391       401       411     
         O59010_PYRHO    12 VLQKILIGLILGAIVGLILGHYGYADAVKTYVKPFGDLFVRLLKMLVMPIVFASLVVGAASISPARLGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVGGQQFQPKQAPPLVKILLDIVPTNPFGALANGQVLPTIFFAIILGIAITYLMNSENEKVRKSAETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVMAEQGVKVVGELAKVTAAVYVGLTLQILLVYFVLLKIYGIDPISFIKKAKDAMLTAFVTRSSSGTLPVTMRVAKEMGISEGIYSFTLPLGATINMDGTALYQGVCTFFIANALGSHLTVGQQLTIVLTAVLASIGTAGVPGAGAIMLAMVLESVGLPLTDPNVAAAYAMILGIDAILDMGRTMVNVTGDLTGTAIVAKTE 416
               SCOP domains d2nwxa1 A:12-416 Proton glutamate symport protein                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2nwxA00 A:12-416 Proton glutamate symport protein                                                                                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............-----..hhhhhh.....hhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh....hhhhhhhhhhhh.........hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nwx A  12 VLQKILIGLILGAIVGLILGHYGYAHAVHTYVKPFGDLFVRLLKMLVMPIVFASLVVGAASISPARLGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVGGQQF-----PPLVHILLDIVPTNPFGALANGQVLPTIFFAIILGIAITYLMNSENEKVRKSAETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVMAEQGVHVVGELAKVTAAVYVGLTLQILLVYFVLLKIYGIDPISFIKHAKDAMLTAFVTRSSSGTLPVTMRVAKEMGISEGIYSFTLPLGATINMDGTALYQGVCTFFIANALGSHLTVGQQLTIVLTAVLASIGTAGVPGAGAIMLAMVLHSVGLPLTDPNVAAAYAMILGIDAILDMGRTMVNVTGDLTGTAIVAKTE 416
                                    21        31        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       371       381       391       401       411     
                                                                                                                                        122   128                                                                                                                                                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:396
 aligned with O59010_PYRHO | O59010 from UniProtKB/TrEMBL  Length:425

    Alignment length:405
                                    21        31        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       371       381       391       401       411     
         O59010_PYRHO    12 VLQKILIGLILGAIVGLILGHYGYADAVKTYVKPFGDLFVRLLKMLVMPIVFASLVVGAASISPARLGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVGGQQFQPKQAPPLVKILLDIVPTNPFGALANGQVLPTIFFAIILGIAITYLMNSENEKVRKSAETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVMAEQGVKVVGELAKVTAAVYVGLTLQILLVYFVLLKIYGIDPISFIKKAKDAMLTAFVTRSSSGTLPVTMRVAKEMGISEGIYSFTLPLGATINMDGTALYQGVCTFFIANALGSHLTVGQQLTIVLTAVLASIGTAGVPGAGAIMLAMVLESVGLPLTDPNVAAAYAMILGIDAILDMGRTMVNVTGDLTGTAIVAKTE 416
               SCOP domains d2nwxb1 B:12-416 Proton glutamate symport protein                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2nwxB00 B:12-416 Proton glutamate symport protein                                                                                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........---------..hhhhhhhhh..hhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh....hhhhhhhhhhhh.........hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nwx B  12 VLQKILIGLILGAIVGLILGHYGYAHAVHTYVKPFGDLFVRLLKMLVMPIVFASLVVGAASISPARLGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVG---------PPLVHILLDIVPTNPFGALANGQVLPTIFFAIILGIAITYLMNSENEKVRKSAETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVMAEQGVHVVGELAKVTAAVYVGLTLQILLVYFVLLKIYGIDPISFIKHAKDAMLTAFVTRSSSGTLPVTMRVAKEMGISEGIYSFTLPLGATINMDGTALYQGVCTFFIANALGSHLTVGQQLTIVLTAVLASIGTAGVPGAGAIMLAMVLHSVGLPLTDPNVAAAYAMILGIDAILDMGRTMVNVTGDLTGTAIVAKTE 416
                                    21        31        41        51        61        71        81        91       101       111      |  -      |131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411     
                                                                                                                                    118       128                                                                                                                                                                                                                                                                                                


Chain C from PDB  Type:PROTEIN  Length:401
 aligned with O59010_PYRHO | O59010 from UniProtKB/TrEMBL  Length:425

    Alignment length:405
                                    21        31        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       371       381       391       401       411     
         O59010_PYRHO    12 VLQKILIGLILGAIVGLILGHYGYADAVKTYVKPFGDLFVRLLKMLVMPIVFASLVVGAASISPARLGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVGGQQFQPKQAPPLVKILLDIVPTNPFGALANGQVLPTIFFAIILGIAITYLMNSENEKVRKSAETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVMAEQGVKVVGELAKVTAAVYVGLTLQILLVYFVLLKIYGIDPISFIKKAKDAMLTAFVTRSSSGTLPVTMRVAKEMGISEGIYSFTLPLGATINMDGTALYQGVCTFFIANALGSHLTVGQQLTIVLTAVLASIGTAGVPGAGAIMLAMVLESVGLPLTDPNVAAAYAMILGIDAILDMGRTMVNVTGDLTGTAIVAKTE 416
               SCOP domains d2nwxc1 C:12-416 Proton glutamate symport protein                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2nwxC00 C:12-416 Proton glutamate symport protein                                                                                                                                                                                                                                                                                                                                                                     CATH domains
           Pfam domains (1) SDF-2nwxC01 C:12-415                                                                                                                                                                                                                                                                                                                                                                                                - Pfam domains (1)
           Pfam domains (2) SDF-2nwxC02 C:12-415                                                                                                                                                                                                                                                                                                                                                                                                - Pfam domains (2)
           Pfam domains (3) SDF-2nwxC03 C:12-415                                                                                                                                                                                                                                                                                                                                                                                                - Pfam domains (3)
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh................----..hhhhhhhhh..hhhhhhhh.hhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhh....hhhhhhhhhhhh.........hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2nwx C  12 VLQKILIGLILGAIVGLILGHYGYAHAVHTYVKPFGDLFVRLLKMLVMPIVFASLVVGAASISPARLGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVGGQQFQ----PPLVHILLDIVPTNPFGALANGQVLPTIFFAIILGIAITYLMNSENEKVRKSAETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVMAEQGVHVVGELAKVTAAVYVGLTLQILLVYFVLLKIYGIDPISFIKHAKDAMLTAFVTRSSSGTLPVTMRVAKEMGISEGIYSFTLPLGATINMDGTALYQGVCTFFIANALGSHLTVGQQLTIVLTAVLASIGTAGVPGAGAIMLAMVLHSVGLPLTDPNVAAAYAMILGIDAILDMGRTMVNVTGDLTGTAIVAKTE 416
                                    21        31        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       371       381       391       401       411     
                                                                                                                                         123  128
   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, 3)

Asymmetric/Biological Unit
(-)
Class: Membrane and cell surface proteins and peptides (2046)

(-) CATH Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: SDF] (5)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (O59010_PYRHO | O59010)
molecular function
    GO:0015293    symporter activity    Enables the active transport of a solute across a membrane by a mechanism whereby two or more species are transported together in the same direction in a tightly coupled process not directly linked to a form of energy other than chemiosmotic energy.
biological process
    GO:0055085    transmembrane transport    The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    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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  2nwx
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 Related Entries

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

UniProtKB/TrEMBL
        O59010_PYRHO | O59010: 1xfh 2nwl 2nww 3kbc 3v8f 3v8g 4izm 4oye 4oyf 4p19 4p1a 4p3j 4p6h 4x2s 5cfy

(-) Related Entries Specified in the PDB File

1xhf CRYSTAL STRUCTURE OF THE BEF3-ACTIVATED RECEIVER DOMAIN OF REDOX RESPONSE REGULATOR ARCA