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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

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

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	GOL	1	Ligand/Ion	GLYCEROL
3	SO4	3	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 15)

No.	Name	Count	Type	Full Name
1	ACT	3	Ligand/Ion	ACETATE ION
2	GOL	3	Ligand/Ion	GLYCEROL
3	SO4	9	Ligand/Ion	SULFATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:124 , PHE A:125 , SER A:126 , HOH A:867	BINDING SITE FOR RESIDUE SO4 A 501
2	AC2	SOFTWARE	ASN A:72 , ASN A:73 , PHE A:74	BINDING SITE FOR RESIDUE SO4 A 503
3	AC3	SOFTWARE	VAL A:147 , TRP A:148 , ALA A:158 , ASP A:160 , TYR A:278 , GOL A:801	BINDING SITE FOR RESIDUE ACT A 601
4	AC4	SOFTWARE	MET A:13 , HIS A:100 , PHE A:103 , GLN A:104 , GLY A:218 , SER A:219 , GLY A:221 , GOL A:801 , HOH A:878	BINDING SITE FOR RESIDUE SO4 A 701
5	AC5	SOFTWARE	PHE A:161 , SER A:219 , ACT A:601 , SO4 A:701	BINDING SITE FOR RESIDUE GOL A 801

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

Asymmetric Unit

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

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

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AMMONIUM_TRANSP	PS01219	Ammonium transporters signature.	AMTB_ECOLI	182-207	1	A:160-181

Biological Unit 1 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AMMONIUM_TRANSP	PS01219	Ammonium transporters signature.	AMTB_ECOLI	182-207	3	A:160-181

(no "Exon" information available for 2NPG)

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:366
 aligned with AMTB_ECOLI | P69681 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:385
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403     
           AMTB_ECOLI    24 PAVADKADNAFMMICTALVLFMTIPGIALFYGGLIRGKNVLSMLTQVTVTFALVCILWVVYGYSLAFGEGNNFFGNINWLMLKNIELTAVMGSIYQYIHVAFQGSFACITVGLIVGALAERIRFSAVLIFVVVWLTLSYIPIAHMVWGGGLLASHGALDFAGGTVVHINAAIAGLVGAYLIGKRVGFGKEAFKPHNLPMVFTGTAILYIGWFGFNAGSAGTANEIAALAFVNTVVATAAAILGWIFGEWALRGKPSLLGACSGAIAGLVGVTPACGYIGVGGALIIGVVAGLAGLWGVTMLKRLLRVDDPCDVFGVHGVCGIVGCIMTGIFAASSLGGVGFAEGVTMGHQLLVQLESIAITIVWSGVVAFIGYKLADLTVGLRVP 408
               SCOP domains d2npga_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2npgA00 A:2-386 Ammonium transporter AmtB like domains                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh......ee..eehhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.........hhhhhhhhhhhhhhh-------------..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh.------hhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------AMMONIUM_TRANSP           --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2npg A   2 PAVADKADNAFMMICTALVLFMTIPGIALFYGGLIRGKNVLSMLTQVTVTFALVCILWVVYGYSLAFGEGNNFFGNINWLMLKNIELTAVMGSIYQYIHVAFQGSFACITVGLIVGALAERIRFSAVLIFVVVWLTLSYIPIAHMVWGGGLLASHGALDFAGGTVVHINAAIAGLVGAYL-------------PHNLPMVFTGTAILYIGWFGFNAGSAGTANEIAALAFVNTVVATAAAILGWIFGEWALRGKPSLLGACSGAIAGLVGVTPACGYIGVGGALIIGVVAGLAGLWGVTMLK------DPCDVFGVFGVCGIVGCIMTGIFAASSLGGVGFAEGVTMGHQLLVQLESIAITIVWSGVVAFIGYKLADLTVGLRVP 386
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181         -   |   201       211       221       231       241       251       261       271       281       291       301 |     311       321       331       341       351       361       371       381     
                                                                                                                                                                                                             181           195                                                                                                         303    310

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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Membrane and cell surface proteins and peptides (2046)

Fold: Ammonium transporter (24)

Superfamily: Ammonium transporter (24)

Family: automated matches (19)

Protein domain: automated matches (19)

Escherichia coli [TaxId: 562] (14)

d2npga_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Ammonium transporter fold (31)

Homologous Superfamily: Ammonium transporter AmtB like domains (31)

Escherichia coli. Organism_taxid: 562. (16)

2npgA00

A:2-386

(no "Pfam Domain" information available for 2NPG)

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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
		ACT	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GOL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
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		AC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Ile A:25 - Pro A:26	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2npg
		Family and Domain Information	:	ProDom \| SYSTERS
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	AMTB_ECOLI \| P69681
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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
2npj	AMTB(H318F) IN THE PRESENCE OF AMMONIUM SPACE GROUP P63 WITH IMIDAZOLE
2npk	AMTB(H168A/H318A) IN THE PRESENCE OF AMMONIUM SPACE GROUP P63 WITH IMIDAZOLE

Description

Compounds

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Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

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