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Title :   CRYSTAL STRUCTURE OF THE ATPASE DOMAIN OF TAP1 WITH ATP (D645N MUTANT)

Authors :   E. Procko, I. Ferrin-O'Connell, S. -L. Ng, R. Gaudet

Date :   07 Jul 06 (Deposition) - 11 Oct 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,D

Keywords :   Abc Atpase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. Procko, I. Ferrin-O'Connell, S. -L. Ng, R. Gaudet
Distinct Structural And Functional Properties Of The Atpase Sites In An Asymmetric Abc Transporter.
Mol. Cell V. 24 51 2001
PubMed-ID: 17018292 | Reference-DOI: 10.1016/J.MOLCEL.2006.07.034

Molecule 1 - ANTIGEN PEPTIDE TRANSPORTER 1
	Chains	:	A, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	ATPASE DOMAIN, RESIDUES 465-725
	Mutation	:	YES
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Other Details	:	TRANSPORTER ASSOCIATED WITH ANTIGEN PROCESSING 1 (TAP1)
	Synonym	:	TAP1, APT1, PEPTIDE TRANSPORTER TAP1, ATP-BINDING CASSETTE SUB-FAMILY B MEMBER 2

		1	2
Asymmetric/Biological Unit	:	A	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 5)

No.	Name	Count	Type	Full Name
1	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION
3	PO4	1	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ATP A:1 , SER A:522 , HOH A:2003 , HOH A:2036 , HOH A:2114	BINDING SITE FOR RESIDUE MG A 2
2	AC2	SOFTWARE	LYS A:481 , HOH A:2005 , HOH A:2008	BINDING SITE FOR RESIDUE PO4 A 3
3	AC3	SOFTWARE	ATP D:1 , SER D:522 , HOH D:2001 , HOH D:2002 , HOH D:2007	BINDING SITE FOR RESIDUE MG D 2
4	AC4	SOFTWARE	MG A:2 , TYR A:489 , VAL A:497 , ASN A:517 , GLY A:518 , SER A:519 , GLY A:520 , LYS A:521 , SER A:522 , THR A:523 , GLN A:678 , HOH A:2001 , HOH A:2002 , HOH A:2003 , HOH A:2004 , HOH A:2114 , GLN D:619 , SER D:621 , GLY D:622 , GLY D:623 , GLN D:624 , HOH D:2118	BINDING SITE FOR RESIDUE ATP A 1
5	AC5	SOFTWARE	GLN A:619 , SER A:621 , GLY A:622 , GLY A:623 , GLN A:624 , HOH A:2104 , MG D:2 , TYR D:489 , HIS D:492 , VAL D:497 , ASN D:517 , GLY D:518 , SER D:519 , GLY D:520 , LYS D:521 , SER D:522 , THR D:523 , GLN D:678 , HOH D:2001 , HOH D:2002 , HOH D:2003 , HOH D:2004 , HOH D:2005 , HOH D:2006 , HOH D:2007 , HOH D:2008 , HOH D:2009	BINDING SITE FOR RESIDUE ATP D 1

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

(no "Cis Peptide Bond" information available for 2IXE)

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

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ABC_TRANSPORTER_1	PS00211	ABC transporters family signature.	TAP1_RAT	620-634	2	A:620-634 D:620-634

(no "Exon" information available for 2IXE)

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:251
 aligned with TAP1_RAT | P36370 from UniProtKB/Swiss-Prot  Length:725

    Alignment length:251
                                   478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718 
             TAP1_RAT   469 GSLAPLNMKGLVKFQDVSFAYPNHPNVQVLQGLTFTLYPGKVTALVGPNGSGKSTVAALLQNLYQPTGGKVLLDGEPLVQYDHHYLHTQVAAVGQEPLLFGRSFRENIAYGLTRTPTMEEITAVAMESGAHDFISGFPQGYDTEVGETGNQLSGGQRQAVALARALIRKPRLLILDDATSALDAGNQLRVQRLLYESPEWASRTVLLITQQLSLAERAHHILFLKEGSVCEQGTHLQLMERGGCYRSMVEA 719
               SCOP domains d2ixea_ A: automated matches                                                                                                                                                                                                                                SCOP domains
               CATH domains --------2ixeA01 A:477-717 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                           -- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...........eeeeeeee..........eeeeeeee....eeeee.....hhhhhhhhhh......eeeeee..ee....hhhhhhhheeee.........hhhhhhhh......hhhhhhhhhhhh.hhhhhhhh.hhhhh..hhhhh..hhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhh......eeeee..hhhhhh...eeeeee..eeeeeehhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ixe A 469 GSLAPLNMKGLVKFQDVSFAYPNHPNVQVLQGLTFTLYPGKVTALVGPNGSGKSTVAALLQNLYQPTGGKVLLDGEPLVQYDHHYLHTQVAAVGQEPLLFGRSFRENIAYGLTRTPTMEEITAVAMESGAHDFISGFPQGYDTEVGETGNQLSGGQRQAVALARALIRKPRLLILDNATSALDAGNQLRVQRLLYESPEWASRTVLLITQQLSLAERAHHILFLKEGSVCEQGTHLQLMERGGCYRSMVEA 719
                                   478       488       498       508       518       528       538       548       558       568       578       588       598       608       618       628       638       648       658       668       678       688       698       708       718

Chain D from PDB  Type:PROTEIN  Length:248
 aligned with TAP1_RAT | P36370 from UniProtKB/Swiss-Prot  Length:725

    Alignment length:255
                                   476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706       716     
             TAP1_RAT   467 LSGSLAPLNMKGLVKFQDVSFAYPNHPNVQVLQGLTFTLYPGKVTALVGPNGSGKSTVAALLQNLYQPTGGKVLLDGEPLVQYDHHYLHTQVAAVGQEPLLFGRSFRENIAYGLTRTPTMEEITAVAMESGAHDFISGFPQGYDTEVGETGNQLSGGQRQAVALARALIRKPRLLILDDATSALDAGNQLRVQRLLYESPEWASRTVLLITQQLSLAERAHHILFLKEGSVCEQGTHLQLMERGGCYRSMVEALA 721
               SCOP domains d2ixed_ D: automated matches                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------2ixeD01 D:477-717 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                                           ---- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeeeeee..........eeeeeeee...eeeeee.....hhhhhhhhhh......eeeeee..ee....hhhhhhhheeee.--......hhhhhhhh......hhhhhhhhhhhhhhhhhhhhh.hhhhh..-----..hhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhh.hhhh.eeeee..hhhhhhh..eeeeee..eeeeeehhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER--------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ixe D 467 LSGSLAPLNMKGLVKFQDVSFAYPNHPNVQVLQGLTFTLYPGKVTALVGPNGSGKSTVAALLQNLYQPTGGKVLLDGEPLVQYDHHYLHTQVAAVG--PLLFGRSFRENIAYGLTRTPTMEEITAVAMESGAHDFISGFPQGYDTEV-----QLSGGQRQAVALARALIRKPRLLILDNATSALDAGNQLRVQRLLYESPEWASRTVLLITQQLSLAERAHHILFLKEGSVCEQGTHLQLMERGGCYRSMVEALA 721
                                   476       486       496       506       516       526       536       546       556     | 566       576       586       596       606      |  -  |    626       636       646       656       666       676       686       696       706       716     
                                                                                                                         562  |                                             613   619                                                                                                      
                                                                                                                            565

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/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: P-loop containing nucleoside triphosphate hydrolases (2083)

Superfamily: P-loop containing nucleoside triphosphate hydrolases (2083)

Family: ABC transporter ATPase domain-like (94)

Protein domain: automated matches (8)

Norway rat (Rattus norvegicus) [TaxId: 10116] (3)

1a	d2ixea_	A:
1b	d2ixed_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: P-loop containing nucleotide triphosphate hydrolases (1378)

Rat (Rattus norvegicus) (9)

1a	2ixeD01	D:477-717
1b	2ixeA01	A:477-717

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,D (TAP1_RAT | P36370)

molecular function
	GO:0043531	ADP binding	Interacting selectively and non-covalently with ADP, adenosine 5'-diphosphate.
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016887	ATPase activity	Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
	GO:0042626	ATPase activity, coupled to transmembrane movement of substances	Catalysis of the reaction: ATP + H2O = ADP + phosphate, to directly drive the active transport of a substance across a membrane.
	GO:0042288	MHC class I protein binding	Interacting selectively and non-covalently with major histocompatibility complex class I molecules; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation.
	GO:0042287	MHC protein binding	Interacting selectively and non-covalently with major histocompatibility complex molecules; a set of molecules displayed on cell surfaces that are responsible for lymphocyte recognition and antigen presentation.
	GO:0046978	TAP1 binding	Interacting selectively and non-covalently with the TAP1 subunit of TAP (transporter associated with antigen processing) protein.
	GO:0046979	TAP2 binding	Interacting selectively and non-covalently with the TAP2 subunit of TAP (transporter associated with antigen processing) protein.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0042605	peptide antigen binding	Interacting selectively and non-covalently with an antigen peptide.
	GO:0015433	peptide antigen-transporting ATPase activity	Catalysis of the reaction: peptide antigen(in) + ATP = peptide antigen(out) + ADP + phosphate.
	GO:0015197	peptide transporter activity	Enables the directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells.
	GO:0015440	peptide-transporting ATPase activity	Catalysis of the reaction: ATP + H2O + peptide(in) = ADP + phosphate + peptide(out). Peptides exported include alpha-hemolysin, cyclolysin, colicin V and siderophores from Gram-negative bacteria, and bacteriocin, subtilin, competence factor and pediocin from Gram-positive bacteria.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
	GO:0042803	protein homodimerization activity	Interacting selectively and non-covalently with an identical protein to form a homodimer.
	GO:0046980	tapasin binding	Interacting selectively and non-covalently with tapasin, a member of the MHC class I loading complex which bridges the TAP peptide transporter to class I molecules.
biological process
	GO:0002250	adaptive immune response	An immune response mediated by cells expressing specific receptors for antigen produced through a somatic diversification process, and allowing for an enhanced secondary response to subsequent exposures to the same antigen (immunological memory).
	GO:0019885	antigen processing and presentation of endogenous peptide antigen via MHC class I	The process in which an antigen-presenting cell expresses a peptide antigen of endogenous origin on its cell surface in association with an MHC class I protein complex. The peptide antigen is typically, but not always, processed from a whole protein. Class I here refers to classical class I molecules.
	GO:0002485	antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-dependent	The process in which an antigen-presenting cell expresses a peptide antigen of endogenous origin on its cell surface in association with an MHC class I protein complex following intracellular transport via a TAP-dependent ER pathway. The peptide is typically a fragment of a larger endogenous protein which has been degraded within the cell and becomes associated with the MHC class I molecule in the ER following TAP-dependent transport from the cytosol. Class I here refers to classical class I molecules.
	GO:0002489	antigen processing and presentation of endogenous peptide antigen via MHC class Ib via ER pathway, TAP-dependent	The process in which an antigen-presenting cell expresses a peptide antigen of endogenous origin on its cell surface in association with an MHC class Ib protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger endogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class Ib molecule. Class Ib here refers to non-classical class I molecules, such as those of the HLA-E gene family.
	GO:0002481	antigen processing and presentation of exogenous protein antigen via MHC class Ib, TAP-dependent	The process in which an antigen-presenting cell expresses a peptide antigen of exogenous origin on its cell surface in association with an MHC class Ib protein complex following intracellular transport via a TAP (transporter associated with antigen processing) pathway. The peptide is typically a fragment of a larger exogenous protein which has been degraded within the cell and is dependent on TAP transport from the cytosol to ER for association with the MHC class Ib molecule. Class Ib here refers to non-classical class I molecules, such as those of the HLA-E gene family.
	GO:0002376	immune system process	Any process involved in the development or functioning of the immune system, an organismal system for calibrated responses to potential internal or invasive threats.
	GO:0046968	peptide antigen transport	The directed movement of a peptide antigen into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. The peptide antigen is typically, but not always, processed from an endogenous or exogenous protein.
	GO:0015833	peptide transport	The directed movement of peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0002591	positive regulation of antigen processing and presentation of peptide antigen via MHC class I	Any process that activates or increases the frequency, rate, or extent of antigen processing and presentation of peptide antigen via MHC class I.
	GO:0042270	protection from natural killer cell mediated cytotoxicity	The process of protecting a cell from natural killer cell mediated cytotoxicity.
	GO:0015031	protein transport	The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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
	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:0042825	TAP complex	A heterodimer composed of the subunits TAP1 and TAP2 (transporter associated with antigen presentation). Functions in the transport of antigenic peptides from the cytosol to the lumen of the endoplasmic reticulum.
	GO:0005783	endoplasmic reticulum	The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
	GO:0005789	endoplasmic reticulum membrane	The lipid bilayer surrounding the endoplasmic reticulum.
	GO:0030176	integral component of endoplasmic reticulum membrane	The component of the endoplasmic reticulum 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: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:0043231	intracellular membrane-bounded organelle	Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

Asymmetric/Biological Unit
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	TAP1_RAT \| P36370	:	2ixf 2ixg 4k8o

2ixf	CRYSTAL STRUCTURE OF THE ATPASE DOMAIN OF TAP1 WITH ATP (D645Q, Q678H MUTANT)
2ixg	CRYSTAL STRUCTURE OF THE ATPASE DOMAIN OF TAP1 WITH ATP (S621A, G622V, D645N MUTANT)

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