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(-) Description

Title :  CRYSTAL STRUCTURE OF AMMONIA CHANNEL AMTB FROM E. COLI
 
Authors :  S. Khademi, J. O'Connell Iii, J. Remis, Y. Robles-Colmenares, L. J. W. R. M. Stroud
Date :  03 Aug 04  (Deposition) - 21 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Right Handed Helical Bundle, Transmembrane Helices, Ammonia Channnel, Membrane Protein, Rh Protein, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Khademi, J. O'Connell Iii, J. Remis, Y. Robles-Colmenares, L. J. W. Miercke, R. M. Stroud
Mechanism Of Ammonia Transport By Amt/Mep/Rh: Structure Of Amtb At 1. 35 A
Science V. 305 1587 2004
PubMed-ID: 15361618  |  Reference-DOI: 10.1126/SCIENCE.1101952

(-) Compounds

Molecule 1 - PROBABLE AMMONIUM TRANSPORTER
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29B
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AMTB
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (3x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric Unit (4, 16)
No.NameCountTypeFull Name
1BOG1Ligand/IonB-OCTYLGLUCOSIDE
2MSE11Mod. Amino AcidSELENOMETHIONINE
3NH33Ligand/IonAMMONIA
4NH41Ligand/IonAMMONIUM ION
Biological Unit 1 (4, 48)
No.NameCountTypeFull Name
1BOG3Ligand/IonB-OCTYLGLUCOSIDE
2MSE33Mod. Amino AcidSELENOMETHIONINE
3NH39Ligand/IonAMMONIA
4NH43Ligand/IonAMMONIUM ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:249 , LEU A:252 , ARG A:253 , LEU A:259 , SER A:263 , LEU A:296 , THR A:300 , LYS A:303 , ASP A:313 , GLU A:344 , HOH A:527 , HOH A:604 , HOH A:708 , HOH A:769 , HOH A:773 , HOH A:897BINDING SITE FOR RESIDUE BOG A 400
2AC2SOFTWAREPHE A:107 , TRP A:148 , SER A:219 , HOH A:573 , HOH A:587BINDING SITE FOR RESIDUE NH4 A 404
3AC3SOFTWAREILE A:28 , LEU A:114 , LEU A:208 , ILE A:266 , HIS A:318 , NH3 A:403BINDING SITE FOR RESIDUE NH3 A 401
4AC4SOFTWAREMSE A:23 , HIS A:168 , TRP A:212 , PHE A:215 , NH3 A:403BINDING SITE FOR RESIDUE NH3 A 402
5AC5SOFTWARELEU A:114 , HIS A:168 , TRP A:212 , HIS A:318 , NH3 A:401 , NH3 A:402BINDING SITE FOR RESIDUE NH3 A 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U7G)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Ile A:25 -Pro A:26

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U7G)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AMMONIUM_TRANSPPS01219 Ammonium transporters signature.AMTB_ECOLI182-207  1A:160-185
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AMMONIUM_TRANSPPS01219 Ammonium transporters signature.AMTB_ECOLI182-207  3A:160-185

(-) Exons   (0, 0)

(no "Exon" information available for 1U7G)

(-) 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:383
 aligned with AMTB_ECOLI | P69681 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:383
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404   
           AMTB_ECOLI    25 AVADKADNAFMMICTALVLFMTIPGIALFYGGLIRGKNVLSMLTQVTVTFALVCILWVVYGYSLAFGEGNNFFGNINWLMLKNIELTAVMGSIYQYIHVAFQGSFACITVGLIVGALAERIRFSAVLIFVVVWLTLSYIPIAHMVWGGGLLASHGALDFAGGTVVHINAAIAGLVGAYLIGKRVGFGKEAFKPHNLPMVFTGTAILYIGWFGFNAGSAGTANEIAALAFVNTVVATAAAILGWIFGEWALRGKPSLLGACSGAIAGLVGVTPACGYIGVGGALIIGVVAGLAGLWGVTMLKRLLRVDDPCDVFGVHGVCGIVGCIMTGIFAASSLGGVGFAEGVTMGHQLLVQLESIAITIVWSGVVAFIGYKLADLTVGLRV 407
               SCOP domains d1u7ga_ A: Ammonium transporter AmtB                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1u7gA00 A:3-385 Ammonium transporter AmtB like domains                                                                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains --------Ammonium_transp-1u7gA01 A:11-385                                                                                                                                                                                                                                                                                                                                                        Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh......ee..eehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh.........hhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------AMMONIUM_TRANSP           -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1u7g A   3 AVADKADNAFmmICTALVLFmTIPGIALFYGGLIRGKNVLSmLTQVTVTFALVCILWVVYGYSLASGEGNNFFGNINWLmLKNIELTAVmGSIYQYIHVAFQGSFACITVGLIVGALAERIRFPAVLIFVVVWLTLSYIPIAHmVWGGGLLASHGALDFAGGTVVHINAAIAGLVGAYLIGKRVGFGKEAFKPHNLPmVFTGTAILYIGWFGFNAGSAGTANEIAALAFVNTVVATAAAILGWIFGEWALRGLPSLLGACSGAIAGLVGVTPACGYIGVGGALIIGVVAGLAGLWGVTmLKRLLRVDDPCDVFGVHGVCGIVGCImTGIFAASSLGGVGFAEGVTmGHQLLVQLESIAITIVWSGVVAFIGYKLADLTVGLRV 385
                                    12||      22|       32        42 |      52        62        72        82        92       102       112       122       132       142   |   152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322     | 332       342     | 352       362       372       382   
                                     13-MSE    23-MSE               44-MSE                                82-MSE    92-MSE                                               146-MSE                                               200-MSE                                                                                              301-MSE                    328-MSE             348-MSE                                 
                                      14-MSE
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: Ammonium_transp] (12)

(-) Gene Ontology  (12, 12)

Asymmetric Unit(hide GO term definitions)
Chain A   (AMTB_ECOLI | P69681)
molecular function
    GO:0008519    ammonium transmembrane transporter activity    Enables the transfer of ammonium from one side of a membrane to the other. Ammonium is the cation NH4+ which is formed from N2 by root-nodule bacteria in leguminous plants and is an excretory product in ammonotelic animals.
    GO:0015292    uniporter activity    Catalysis of the transport of a single molecular species across a membrane; transport is independent of the movement of any other molecular species.
biological process
    GO:0072488    ammonium transmembrane transport    The directed movement of ammonium across a membrane by means of some agent such as a transporter or pore. Ammonium is the cation NH4+.
    GO:0015696    ammonium transport    The directed movement of ammonium into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Ammonium is the cation NH4+ which is formed from N2 by root-nodule bacteria in leguminous plants and is an excretory product in ammonotelic animals.
    GO:0015670    carbon dioxide transport    The directed movement of carbon dioxide (CO2) into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0019740    nitrogen utilization    A series of processes that forms an integrated mechanism by which a cell or an organism detects the depletion of primary nitrogen source, usually ammonia, and then activates genes to scavenge the last traces of the primary nitrogen source and to transport and metabolize alternative nitrogen sources. The utilization process begins when the cell or organism detects nitrogen levels, includes the activation of genes whose products detect, transport or metabolize nitrogen-containing substances, and ends when nitrogen is incorporated into the cell or organism's metabolism.
    GO:0015695    organic cation transport    The directed movement of organic cations into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Organic cations are atoms or small molecules with a positive charge which contain carbon in covalent linkage.
    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:0005887    integral component of plasma membrane    The component of the plasma 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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 Related Entries

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

UniProtKB/Swiss-Prot
        AMTB_ECOLI | P69681: 1u77 1u7c 1xqe 1xqf 2nmr 2nop 2now 2npc 2npd 2npe 2npg 2npj 2npk 2ns1 2nuu 3c1g 3c1h 3c1i 3c1j

(-) Related Entries Specified in the PDB File

1u77 1u7c