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(-) Description

Title :  CRYSTAL STRUCTURE OF GLTPH K55C-A364C MUTANT CROSSLINKED WITH DIVALENT MERCURY
 
Authors :  N. Reyes, C. Ginter, O. Boudker
Date :  20 Oct 09  (Deposition) - 01 Dec 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.51
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Amino Acid Transporter, Transmembrane Transporter, Aspartate Transporter, Transport Protein, Cysteine Cross-Link, Inward-Facing (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Reyes, C. Ginter, O. Boudker
Transport Mechanism Of A Bacterial Homologue Of Glutamate Transporters.
Nature V. 462 880 2009
PubMed-ID: 19924125  |  Reference-DOI: 10.1038/NATURE08616

(-) 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
    Gene: PH1295
    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
2HG3Ligand/IonMERCURY (II) ION
3NA6Ligand/IonSODIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:276 , SER A:277 , SER A:278 , MET A:311 , THR A:314 , THR A:352 , GLY A:354 , VAL A:355 , ALA A:358 , GLY A:359 , ASP A:394 , ARG A:397 , THR A:398 , ASN A:401BINDING SITE FOR RESIDUE ASP A 500
02AC2SOFTWAREARG B:276 , SER B:277 , SER B:278 , MET B:311 , THR B:314 , THR B:352 , GLY B:354 , VAL B:355 , ALA B:358 , GLY B:359 , ASP B:394 , ARG B:397 , THR B:398 , ASN B:401BINDING SITE FOR RESIDUE ASP B 500
03AC3SOFTWAREARG C:276 , SER C:277 , SER C:278 , MET C:311 , THR C:314 , THR C:352 , GLY C:354 , VAL C:355 , ALA C:358 , GLY C:359 , ASP C:394 , ARG C:397 , THR C:398 , ASN C:401BINDING SITE FOR RESIDUE ASP C 500
04AC4SOFTWARECYS A:55 , CYS A:364 , LEU A:374 , TYR A:383BINDING SITE FOR RESIDUE HG A 501
05AC5SOFTWAREGLY A:306 , ILE A:309 , ASN A:310 , ASN A:401 , ASP A:405BINDING SITE FOR RESIDUE NA A 454
06AC6SOFTWARETHR A:308 , MET A:311 , SER A:349 , ILE A:350 , GLY A:351 , THR A:352BINDING SITE FOR RESIDUE NA A 453
07AC7SOFTWARECYS B:55 , CYS B:364 , LEU B:374 , TYR B:383BINDING SITE FOR RESIDUE HG B 501
08AC8SOFTWAREGLY B:306 , ILE B:309 , ASN B:310 , ASN B:401 , ASP B:405BINDING SITE FOR RESIDUE NA B 454
09AC9SOFTWARETHR B:308 , MET B:311 , SER B:349 , ILE B:350 , GLY B:351 , THR B:352BINDING SITE FOR RESIDUE NA B 453
10BC1SOFTWARECYS C:55 , CYS C:364 , LEU C:374 , TYR C:383BINDING SITE FOR RESIDUE HG C 501
11BC2SOFTWAREGLY C:306 , ILE C:309 , ASN C:310 , ASN C:401 , ASP C:405BINDING SITE FOR RESIDUE NA C 454
12BC3SOFTWARETHR C:308 , MET C:311 , SER C:349 , ILE C:350 , GLY C:351 , THR C:352BINDING SITE FOR RESIDUE NA C 453

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Pro A:75 -Ala A:76
2Pro B:75 -Ala B:76
3Pro C:75 -Ala C:76

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3KBC)

(-) 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:412
 aligned with O59010_PYRHO | O59010 from UniProtKB/TrEMBL  Length:425

    Alignment length:413
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415   
         O59010_PYRHO     6 KYIEYPVLQKILIGLILGAIVGLILGHYGYADAVKTYVKPFGDLFVRLLKMLVMPIVFASLVVGAASISPARLGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVGGQQFQPKQAPPLVKILLDIVPTNPFGALANGQVLPTIFFAIILGIAITYLMNSENEKVRKSAETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVMAEQGVKVVGELAKVTAAVYVGLTLQILLVYFVLLKIYGIDPISFIKKAKDAMLTAFVTRSSSGTLPVTMRVAKEMGISEGIYSFTLPLGATINMDGTALYQGVCTFFIANALGSHLTVGQQLTIVLTAVLASIGTAGVPGAGAIMLAMVLESVGLPLTDPNVAAAYAMILGIDAILDMGRTMVNVTGDLTGTAIVAKTEGE 418
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhh....hhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..hhhhhh..........hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh......hhhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.-. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kbc A   6 KYIEYPVLQKILIGLILGAIVGLILGHYGYAHAVHTYVKPFGDLFVRLLCMLVMPIVFASLVVGAASISPARLGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVGGQQFQPHQAPPLVHILLDIVPTNPFGALANGQVLPTIFFAIILGIAITYLMNSENEKVRKSAETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVMAEQGVHVVGELAKVTAAVYVGLTLQILLVYFVLLKIYGIDPISFIKHAKDAMLTAFVTRSSSGTLPVTMRVAKEMGISEGIYSFTLPLGATINMDGTALYQGVATFFIANALGSHLTVGQQLTIVLTAVLASIGTAGVPGAGAIMLCMVLHSVGLPLTDPNVAAAYAMILGIDAILDMGRTMVNVTGDLTGTAIVAKTE-D 500
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415| |
                                                                                                                                                                                                                                                                                                                                                                                                                                                    416 |
                                                                                                                                                                                                                                                                                                                                                                                                                                                      500


Chain B from PDB  Type:PROTEIN  Length:412
 aligned with O59010_PYRHO | O59010 from UniProtKB/TrEMBL  Length:425

    Alignment length:412
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415  
         O59010_PYRHO     6 KYIEYPVLQKILIGLILGAIVGLILGHYGYADAVKTYVKPFGDLFVRLLKMLVMPIVFASLVVGAASISPARLGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVGGQQFQPKQAPPLVKILLDIVPTNPFGALANGQVLPTIFFAIILGIAITYLMNSENEKVRKSAETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVMAEQGVKVVGELAKVTAAVYVGLTLQILLVYFVLLKIYGIDPISFIKKAKDAMLTAFVTRSSSGTLPVTMRVAKEMGISEGIYSFTLPLGATINMDGTALYQGVCTFFIANALGSHLTVGQQLTIVLTAVLASIGTAGVPGAGAIMLAMVLESVGLPLTDPNVAAAYAMILGIDAILDMGRTMVNVTGDLTGTAIVAKTEG 417
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhh....hhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..hhhhhh..........hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh......hhhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kbc B   6 KYIEYPVLQKILIGLILGAIVGLILGHYGYAHAVHTYVKPFGDLFVRLLCMLVMPIVFASLVVGAASISPARLGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVGGQQFQPHQAPPLVHILLDIVPTNPFGALANGQVLPTIFFAIILGIAITYLMNSENEKVRKSAETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVMAEQGVHVVGELAKVTAAVYVGLTLQILLVYFVLLKIYGIDPISFIKHAKDAMLTAFVTRSSSGTLPVTMRVAKEMGISEGIYSFTLPLGATINMDGTALYQGVATFFIANALGSHLTVGQQLTIVLTAVLASIGTAGVPGAGAIMLCMVLHSVGLPLTDPNVAAAYAMILGIDAILDMGRTMVNVTGDLTGTAIVAKTED 500
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415||
                                                                                                                                                                                                                                                                                                                                                                                                                                                    416|
                                                                                                                                                                                                                                                                                                                                                                                                                                                     500


Chain C from PDB  Type:PROTEIN  Length:412
 aligned with O59010_PYRHO | O59010 from UniProtKB/TrEMBL  Length:425

    Alignment length:412
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415  
         O59010_PYRHO     6 KYIEYPVLQKILIGLILGAIVGLILGHYGYADAVKTYVKPFGDLFVRLLKMLVMPIVFASLVVGAASISPARLGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVGGQQFQPKQAPPLVKILLDIVPTNPFGALANGQVLPTIFFAIILGIAITYLMNSENEKVRKSAETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVMAEQGVKVVGELAKVTAAVYVGLTLQILLVYFVLLKIYGIDPISFIKKAKDAMLTAFVTRSSSGTLPVTMRVAKEMGISEGIYSFTLPLGATINMDGTALYQGVCTFFIANALGSHLTVGQQLTIVLTAVLASIGTAGVPGAGAIMLAMVLESVGLPLTDPNVAAAYAMILGIDAILDMGRTMVNVTGDLTGTAIVAKTEG 417
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------SDF-3kbcC01 C:12-415                                                                                                                                                                                                                                                                                                                                                                                                -- Pfam domains (1)
           Pfam domains (2) ------SDF-3kbcC02 C:12-415                                                                                                                                                                                                                                                                                                                                                                                                -- Pfam domains (2)
           Pfam domains (3) ------SDF-3kbcC03 C:12-415                                                                                                                                                                                                                                                                                                                                                                                                -- Pfam domains (3)
         Sec.struct. author .....hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhh....hhhhhhhh.hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhh..hhhhhh..........hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh......hhhhhhhhhhhhh......hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kbc C   6 KYIEYPVLQKILIGLILGAIVGLILGHYGYAHAVHTYVKPFGDLFVRLLCMLVMPIVFASLVVGAASISPARLGRVGVKIVVYYLLTSAFAVTLGIIMARLFNPGAGIHLAVGGQQFQPHQAPPLVHILLDIVPTNPFGALANGQVLPTIFFAIILGIAITYLMNSENEKVRKSAETLLDAINGLAEAMYKIVNGVMQYAPIGVFALIAYVMAEQGVHVVGELAKVTAAVYVGLTLQILLVYFVLLKIYGIDPISFIKHAKDAMLTAFVTRSSSGTLPVTMRVAKEMGISEGIYSFTLPLGATINMDGTALYQGVATFFIANALGSHLTVGQQLTIVLTAVLASIGTAGVPGAGAIMLCMVLHSVGLPLTDPNVAAAYAMILGIDAILDMGRTMVNVTGDLTGTAIVAKTED 500
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415||
                                                                                                                                                                                                                                                                                                                                                                                                                                                    416|
                                                                                                                                                                                                                                                                                                                                                                                                                                                     500
   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 3KBC)

(-) CATH Domains  (0, 0)

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

(-) 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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  3kbc
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  O59010_PYRHO | O59010
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

1xfh CRYSTAL STRUCTURE OF GLUTAMATE TRANSPORTER HOMOLOG FROM PYROCOCCUS HORIKOSHII
2nwl CRYSTAL STRUCTURE OF GLTPH IN COMPLEX WITH L-ASP
2nww CRYSTAL STRUCTURE OF GLTPH IN COMPLEX WITH TBOA
2nwx CRYSTAL STRUCTURE OF GLTPH IN COMPLEX WITH L-ASPARTATE AND SODIUM IONS