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(-) Description

Title :  CRYSTAL STRUCTURE OF AN S. THERMOPHILUS NFEOB E67A MUTANT BOUND TO GDP
 
Authors :  M. R. Ash, M. J. Maher, J. M. Guss, M. Jormakka
Date :  15 Jul 11  (Deposition) - 02 Nov 11  (Release) - 18 Apr 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  G Protein, Iron Transport, Gtpase, Transmembrane, Potassium, Metal Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. R. Ash, M. J. Maher, J. M. Guss, M. Jormakka
A Suite Of Switch I And Switch Ii Mutant Structures From Th G-Protein Domain Of Feob
Acta Crystallogr. , Sect. D V. 67 973 2011
PubMed-ID: 22101824  |  Reference-DOI: 10.1107/S0907444911039461

(-) Compounds

Molecule 1 - FERROUS IRON UPTAKE TRANSPORTER PROTEIN B
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-4T-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: NFEOB, UNP RESIDUES 1-270
    Gene: FEOB
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS THERMOPHILUS
    Organism Taxid: 264199
    Strain: LMG 18311

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1GDP4Ligand/IonGUANOSINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1GDP1Ligand/IonGUANOSINE-5'-DIPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:9 , ASN A:11 , SER A:12 , GLY A:13 , LYS A:14 , THR A:15 , SER A:16 , ASN A:113 , MET A:114 , ASP A:116 , VAL A:117 , SER A:142 , ALA A:143 , LEU A:144 , HOH A:281 , HOH A:284 , HOH A:303 , HOH A:304BINDING SITE FOR RESIDUE GDP A 300
2AC2SOFTWAREASN B:11 , SER B:12 , GLY B:13 , LYS B:14 , THR B:15 , SER B:16 , ASN B:113 , MET B:114 , ASP B:116 , VAL B:117 , SER B:142 , ALA B:143 , HOH B:284 , HOH B:297BINDING SITE FOR RESIDUE GDP B 300
3AC3SOFTWAREASN C:9 , ASN C:11 , SER C:12 , GLY C:13 , LYS C:14 , THR C:15 , SER C:16 , ASN C:113 , MET C:114 , ASP C:116 , VAL C:117 , SER C:142 , ALA C:143 , LEU C:144 , HOH C:275 , HOH C:283BINDING SITE FOR RESIDUE GDP C 300
4AC4SOFTWAREASN D:9 , ASN D:11 , SER D:12 , GLY D:13 , LYS D:14 , THR D:15 , SER D:16 , ASN D:113 , MET D:114 , ASP D:116 , VAL D:117 , SER D:142 , ALA D:143 , LEU D:144 , HOH D:277 , HOH D:278BINDING SITE FOR RESIDUE GDP D 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3B1W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3B1W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3B1W)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3B1W)

(-) Exons   (0, 0)

(no "Exon" information available for 3B1W)

(-) Sequences/Alignments

Asymmetric 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:262
 aligned with Q5M586_STRT2 | Q5M586 from UniProtKB/TrEMBL  Length:712

    Alignment length:262
                             1                                                                                                                                                                                                                                                                    
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259  
         Q5M586_STRT2     - -MTEIALIGNPNSGKTSLFNLITGHNQRVGNWPGVTVERKSGLVKKNKDLEIQDLPGIYSMSPYSPEEKVARDYLLSQRADSILNVVDATNLERNLYLTTQLIETGIPVTIALNMIDVLDGQGKKINVDKLSYHLGVPVVATSALKQTGVDQVVKKAAHTTTSTVGDLAFPIYDDRLEAAISQILEVLGNSVPQRSARFYAIKLFEQDSLVEAELDLSQFQRKEIEDIIRITEEIFTEDAESIVINERYAFIERVCQMAESH 261
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhh..eeeee......eeeeeee..eeeeeeee..........hhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhh...eeeeee....hhhhh.eehhhhhhhhhh..eee.......hhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b1w A   0 SMTEIALIGNPNSGKTSLFNLITGHNQRVGNWPGVTVERKSGLVKKNKDLEIQDLPGIYSMSPYSPEAKVARDYLLSQRADSILNVVDATNLERNLYLTTQLIETGIPVTIALNMIDVLDGQGKKINVDKLSYHLGVPVVATSALKQTGVDQVVKKAAHTTTSTVGDLAFPIYDDRLEAAISQILEVLGNSVPQRSARFYAIKLFEQDSLVEAELDLSQFQRKEIEDIIRITEEIFTEDAESIVINERYAFIERVCQMAESH 261
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259  


Chain B from PDB  Type:PROTEIN  Length:260
 aligned with Q5M586_STRT2 | Q5M586 from UniProtKB/TrEMBL  Length:712

    Alignment length:260
                             1                                                                                                                                                                                                                                                                  
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259
         Q5M586_STRT2     - -MTEIALIGNPNSGKTSLFNLITGHNQRVGNWPGVTVERKSGLVKKNKDLEIQDLPGIYSMSPYSPEEKVARDYLLSQRADSILNVVDATNLERNLYLTTQLIETGIPVTIALNMIDVLDGQGKKINVDKLSYHLGVPVVATSALKQTGVDQVVKKAAHTTTSTVGDLAFPIYDDRLEAAISQILEVLGNSVPQRSARFYAIKLFEQDSLVEAELDLSQFQRKEIEDIIRITEEIFTEDAESIVINERYAFIERVCQMAE 259
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee....hhhhhhhhhhh..eeeee......eeeeee......eeeee..........hhhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhh...eeeeeehhhhhhhh....hhhhhhhhhh..eee.......hhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b1w B   0 SMTEIALIGNPNSGKTSLFNLITGHNQRVGNWPGVTVERKSGLVKKNKDLEIQDLPGIYSMSPYSPEAKVARDYLLSQRADSILNVVDATNLERNLYLTTQLIETGIPVTIALNMIDVLDGQGKKINVDKLSYHLGVPVVATSALKQTGVDQVVKKAAHTTTSTVGDLAFPIYDDRLEAAISQILEVLGNSVPQRSARFYAIKLFEQDSLVEAELDLSQFQRKEIEDIIRITEEIFTEDAESIVINERYAFIERVCQMAE 259
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259


Chain C from PDB  Type:PROTEIN  Length:258
 aligned with Q5M586_STRT2 | Q5M586 from UniProtKB/TrEMBL  Length:712

    Alignment length:260
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260
         Q5M586_STRT2     1 MTEIALIGNPNSGKTSLFNLITGHNQRVGNWPGVTVERKSGLVKKNKDLEIQDLPGIYSMSPYSPEEKVARDYLLSQRADSILNVVDATNLERNLYLTTQLIETGIPVTIALNMIDVLDGQGKKINVDKLSYHLGVPVVATSALKQTGVDQVVKKAAHTTTSTVGDLAFPIYDDRLEAAISQILEVLGNSVPQRSARFYAIKLFEQDSLVEAELDLSQFQRKEIEDIIRITEEIFTEDAESIVINERYAFIERVCQMAES 260
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhh..eeeee......eeeeeee..eeeeeeee..........hhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhhhh...eeeeeehhhhhhhh..eehhhhhhhhhh..eee.......hhhhhhhhhhh......--......hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhee Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b1w C   1 MTEIALIGNPNSGKTSLFNLITGHNQRVGNWPGVTVERKSGLVKKNKDLEIQDLPGIYSMSPYSPEAKVARDYLLSQRADSILNVVDATNLERNLYLTTQLIETGIPVTIALNMIDVLDGQGKKINVDKLSYHLGVPVVATSALKQTGVDQVVKKAAHTTTSTV--LAFPIYDDRLEAAISQILEVLGNSVPQRSARFYAIKLFEQDSLVEAELDLSQFQRKEIEDIIRITEEIFTEDAESIVINERYAFIERVCQMAES 260
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160   |  |170       180       190       200       210       220       230       240       250       260
                                                                                                                                                                                             164  |                                                                                             
                                                                                                                                                                                                167                                                                                             


Chain D from PDB  Type:PROTEIN  Length:254
 aligned with Q5M586_STRT2 | Q5M586 from UniProtKB/TrEMBL  Length:712

    Alignment length:257
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       
         Q5M586_STRT2     1 MTEIALIGNPNSGKTSLFNLITGHNQRVGNWPGVTVERKSGLVKKNKDLEIQDLPGIYSMSPYSPEEKVARDYLLSQRADSILNVVDATNLERNLYLTTQLIETGIPVTIALNMIDVLDGQGKKINVDKLSYHLGVPVVATSALKQTGVDQVVKKAAHTTTSTVGDLAFPIYDDRLEAAISQILEVLGNSVPQRSARFYAIKLFEQDSLVEAELDLSQFQRKEIEDIIRITEEIFTEDAESIVINERYAFIERVCQM 257
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....hhhhhhhhhhh..eeeee......eeeeeee..eeeeeeee..........hhhhhhhhhhhh.....eeeeeee..hhhhhhhhhhhhhhh...eeeeeehhhhhhhh....hhhhhhhhhh..eee.......hhhhhhhhhhh......---.....hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b1w D   1 MTEIALIGNPNSGKTSLFNLITGHNQRVGNWPGVTVERKSGLVKKNKDLEIQDLPGIYSMSPYSPEAKVARDYLLSQRADSILNVVDATNLERNLYLTTQLIETGIPVTIALNMIDVLDGQGKKINVDKLSYHLGVPVVATSALKQTGVDQVVKKAAHTTTSTV---AFPIYDDRLEAAISQILEVLGNSVPQRSARFYAIKLFEQDSLVEAELDLSQFQRKEIEDIIRITEEIFTEDAESIVINERYAFIERVCQM 257
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160   |   170       180       190       200       210       220       230       240       250       
                                                                                                                                                                                             164 168
   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 3B1W)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3B1W)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3B1W)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q5M586_STRT2 | Q5M586)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0015093    ferrous iron transmembrane transporter activity    Enables the transfer of ferrous iron (Fe(II) or Fe2+) ions from one side of a membrane to the other.
biological process
    GO:1903874    ferrous iron transmembrane transport    The directed movement of ferrous iron (iron(2+)) across a membrane.
    GO:0015684    ferrous iron transport    The directed movement of ferrous iron (Fe(II) or Fe2+) ions into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0055072    iron ion homeostasis    Any process involved in the maintenance of an internal steady state of iron ions within an organism or cell.
    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: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.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  3b1w
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 Related Entries

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

UniProtKB/TrEMBL
        Q5M586_STRT2 | Q5M586: 3b1v 3b1x 3b1y 3b1z 3lx5 3lx8 3ss8 3tah 4non

(-) Related Entries Specified in the PDB File

3b1v
3b1x
3b1y
3b1z
3lx5 WILD-TYPE PROTEIN COMPLEXED WITH MGMPPNP
3lx8 WILD-TYPE PROTEIN COMPLEXED WITH GDP
3ss8 WILD-TYPE PROTEIN COMPLEXED WITH GDP.ALF4- AND K+