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(-) Description

Title :  AN UNUSUAL TWIN-HIS ARRANGEMENT IN THE PORE OF AMMONIA CHANNELS IS ESSENTIAL FOR SUBSTRATE CONDUCTANCE
 
Authors :  D. Lupo, F. K. Winkler
Date :  27 Oct 06  (Deposition) - 14 Nov 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Membrane Protein, Ammonia Transport, Histidine Mutant, Amtb, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Javelle, D. Lupo, L. Zheng, X. -D. Li, F. K. Winkler, M. Merrick
An Unusual Twin-His Arrangement In The Pore Of Ammonia Channels Is Essential For Substrate Conductance
J. Biol. Chem. V. 281 39492 2006
PubMed-ID: 17040913  |  Reference-DOI: 10.1074/JBC.M608325200

(-) Compounds

Molecule 1 - AMMONIA CHANNEL
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B-AMTBH318F
    Expression System Strain: C43 (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: AMTB
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: AMMONIA TRANSPORTER

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2IMD2Ligand/IonIMIDAZOLE
Biological Unit 1 (2, 9)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2IMD6Ligand/IonIMIDAZOLE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:147 , ALA A:158 , LEU A:159 , ASP A:160 , TYR A:278BINDING SITE FOR RESIDUE ACT A 601
2AC2SOFTWAREGLN A:104 , PHE A:107 , TRP A:148 , PHE A:161 , SER A:219 , HOH A:827BINDING SITE FOR RESIDUE IMD A 701
3AC3SOFTWAREHIS A:100 , PHE A:103 , GLN A:104 , SER A:219 , GLY A:221 , HOH A:845 , HOH A:888BINDING SITE FOR RESIDUE IMD A 801

(-) SS Bonds  (0, 0)

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

(-) 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 2NPJ)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AMMONIUM_TRANSPPS01219 Ammonium transporters signature.AMTB_ECOLI182-207  1A:160-181
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1AMMONIUM_TRANSPPS01219 Ammonium transporters signature.AMTB_ECOLI182-207  3A:160-181

(-) Exons   (0, 0)

(no "Exon" information available for 2NPJ)

(-) 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:363
 aligned with AMTB_ECOLI | P69681 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:384
                                    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 AVADKADNAFMMICTALVLFMTIPGIALFYGGLIRGKNVLSMLTQVTVTFALVCILWVVYGYSLAFGEGNNFFGNINWLMLKNIELTAVMGSIYQYIHVAFQGSFACITVGLIVGALAERIRFSAVLIFVVVWLTLSYIPIAHMVWGGGLLASHGALDFAGGTVVHINAAIAGLVGAYLIGKRVGFGKEAFKPHNLPMVFTGTAILYIGWFGFNAGSAGTANEIAALAFVNTVVATAAAILGWIFGEWALRGKPSLLGACSGAIAGLVGVTPACGYIGVGGALIIGVVAGLAGLWGVTMLKRLLRVDDPCDVFGVHGVCGIVGCIMTGIFAASSLGGVGFAEGVTMGHQLLVQLESIAITIVWSGVVAFIGYKLADLTVGLRVP 408
               SCOP domains d2npja_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2npjA00 A:3-386 Ammonium transporter AmtB like domains                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains --------Ammonium_transp-2npjA01 A:11-386                                                                                                                                                                                                                                                                                                                                                         Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh......ee..eehhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.........hhhhhhhhhhhhhhh-------------..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh.--------..hhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------AMMONIUM_TRANSP           --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2npj A   3 AVADKADNAFMMICTALVLFMTIPGIALFYGGLIRGKNVLSMLTQVTVTFALVCILWVVYGYSLAFGEGNNFFGNINWLMLKNIELTAVMGSIYQYIHVAFQGSFACITVGLIVGALAERIRFSAVLIFVVVWLTLSYIPIAHMVWGGGLLASHGALDFAGGTVVHINAAIAGLVGAYL-------------PHNLPMVFTGTAILYIGWFGFNAGSAGTANEIAALAFVNTVVATAAAILGWIFGEWALRGKPSLLGACSGAIAGLVGVTPACGYIGVGGALIIGVVAGLAGLWGVTML--------PCDVFGVFGVCGIVGCIMTGIFAASSLGGVGFAEGVTMGHQLLVQLESIAITIVWSGVVAFIGYKLADLTVGLRVP 386
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172        |-         -  |    202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382    
                                                                                                                                                                                                            181           195                                                                                                        302      311
   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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  AMTB_ECOLI | P69681
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 Related Entries

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

UniProtKB/Swiss-Prot
        AMTB_ECOLI | P69681: 1u77 1u7c 1u7g 1xqe 1xqf 2nmr 2nop 2now 2npc 2npd 2npe 2npg 2npk 2ns1 2nuu 3c1g 3c1h 3c1i 3c1j

(-) Related Entries Specified in the PDB File

1u7g TRIPLE MUTANT OF AMTB
1xqe WILD-TYPE AMTB IN THE PRESENCE OF AMMONIUM SPACE GROUP R3
1xqf WILD-TYPE AMTB IN THE PRESENCE OF MAGNESIUM
2nmr AMTB(WILD-TYPE) IN THE PRESENCE OF AMMONIUM SPACE GROUP P63
2nop AMTB(WILD-TYPE) IN THE PRESENCE OF AMMONIUM SPACE GROUP P63 WITH IMIDAZOLE
2now AMTB(H168E) IN THE PRESENCE OF AMMONIUM SPACE GROUP P63
2npc AMTB(H168A) IN THE PRESENCE OF AMMONIUM SPACE GROUP P63 WITH IMIDAZOLE
2npd AMTB(H168F) IN THE PRESENCE OF AMMONIUM SPACE GROUP P63 WITH IMIDAZOLE
2npe AMTB(H318A) SPACE GROUP P63
2npg AMTB(H318F) IN THE PRESENCE OF AMMONIUM SPACE GROUP P63
2npk AMTB(H168A/H318A) IN THE PRESENCE OF AMMONIUM SPACE GROUP P63 WITH IMIDAZOLE