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Asym./Biol. Unit (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ABC TRANSPORTER (AQ_297) FROM AQUIFEX AEOLICUS VF5

Authors :   J. Jeyakanthan, S. P. Kanaujia, C. Vasuki Ranjani, K. Sekar, N. Nakaga A. Ebihara, S. Kuramitsu, A. Shinkai, Y. Shiro, S. Yokoyama, Riken St Genomics/Proteomics Initiative (Rsgi)

Date :   30 Mar 07 (Deposition) - 02 Oct 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Abc Transporter, Atp-Binding Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Jeyakanthan, S. P. Kanaujia, C. Vasuki Ranjani, K. Sekar, N. Nakagawa, A. Ebihara, S. Kuramitsu, A. Shinkai, Y. Shiro, S. Yokoyama
Crystal Structure Of Abc Transporter (Aq_297) From Aquifex Aeolicus Vf5
To Be Published
PubMed: search

Molecule 1 - LIPOPROTEIN-RELEASING SYSTEM ATP-BINDING PROTEIN LOLD
	Chains	:	A, B
	EC Number	:	3.6.3.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL-21 CONDON PLUS (DE3)-RIL
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	AQUIFEX AEOLICUS
	Organism Taxid	:	224324
	Strain	:	VF5
	Synonym	:	ABC TRANSPORTER

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 1)

No.	Name	Count	Type	Full Name
1	SO3	1	Ligand/Ion	SULFITE ION

(no "Site" information available for 2PCJ)

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

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

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

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.	LOLD_AQUAE	141-155	2	A:141-155 B:141-155

(no "Exon" information available for 2PCJ)

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:223
 aligned with LOLD_AQUAE | O66646 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:223
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221   
           LOLD_AQUAE     2 AEILRAENIKKVIRGYEILKGISLSVKKGEFVSIIGASGSGKSTLLYILGLLDAPTEGKVFLEGKEVDYTNEKELSLLRNRKLGFVFQFHYLIPELTALENVIVPMLKMGKPKKEAKERGEYLLSELGLGDKLSRKPYELSGGEQQRVAIARALANEPILLFADEPTGNLDSANTKRVMDIFLKINEGGTSIVMVTHERELAELTHRTLEMKDGKVVGEITRV 224
               SCOP domains d2pcja_ A: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains 2pcjA00 A:2-224 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee..eeeeeeeeeeee...eeeeee....hhhhhhhhhh......eeeeee..ee....hhhhhhhhhhhheeee..........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.....eeeee......hhhhhhhhhhhhhhhhhh..eeeee..hhhhhh...eeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER--------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pcj A   2 AEILRAENIKKVIRGYEILKGISLSVKKGEFVSIIGASGSGKSTLLYILGLLDAPTEGKVFLEGKEVDYTNEKELSLLRNRKLGFVFQFHYLIPELTALENVIVPMLKMGKPKKEAKERGEYLLSELGLGDKLSRKPYELSGGEQQRVAIARALANEPILLFADEPTGNLDSANTKRVMDIFLKINEGGTSIVMVTHERELAELTHRTLEMKDGKVVGEITRV 224
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221

Chain B from PDB  Type:PROTEIN  Length:223
 aligned with LOLD_AQUAE | O66646 from UniProtKB/Swiss-Prot  Length:224

    Alignment length:223
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221   
           LOLD_AQUAE     2 AEILRAENIKKVIRGYEILKGISLSVKKGEFVSIIGASGSGKSTLLYILGLLDAPTEGKVFLEGKEVDYTNEKELSLLRNRKLGFVFQFHYLIPELTALENVIVPMLKMGKPKKEAKERGEYLLSELGLGDKLSRKPYELSGGEQQRVAIARALANEPILLFADEPTGNLDSANTKRVMDIFLKINEGGTSIVMVTHERELAELTHRTLEMKDGKVVGEITRV 224
               SCOP domains d2pcjb_ B: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains 2pcjB00 B:2-224 P-loop containing nucleotide triphosphate hydrolases                                                                                                                                                            CATH domains
           Pfam domains (1) ------------------------------------------ABC_tran-2pcjB01 B:44-169                                                                                                     ------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------ABC_tran-2pcjB02 B:44-169                                                                                                     ------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeeeeeeeee..eeeeeeeeeeee...eeeee.....hhhhhhhhhh......eeeeee..ee....hhhhhhhhhhhheeee..........hhhhhhhhhhhhh..hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh....eeeee......hhhhhhhhhhhhhhhhhh..eeeeee.hhhhhh...eeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER--------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pcj B   2 AEILRAENIKKVIRGYEILKGISLSVKKGEFVSIIGASGSGKSTLLYILGLLDAPTEGKVFLEGKEVDYTNEKELSLLRNRKLGFVFQFHYLIPELTALENVIVPMLKMGKPKKEAKERGEYLLSELGLGDKLSRKPYELSGGEQQRVAIARALANEPILLFADEPTGNLDSANTKRVMDIFLKINEGGTSIVMVTHERELAELTHRTLEMKDGKVVGEITRV 224
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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: automated matches (303)

Protein domain: automated matches (303)

Aquifex aeolicus [TaxId: 224324] (4)

1a	d2pcja_	A:
1b	d2pcjb_	B:

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)

Aquifex aeolicus vf5. Organism_taxid: 224324. Strain: vf5. (2)

1a	2pcjA00	A:2-224
1b	2pcjB00	B:2-224

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: ABC_tran (53)

Aquifex aeolicus (1)

1a	ABC_tran-2pcjB01	B:44-169
1b	ABC_tran-2pcjB02	B:44-169

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (LOLD_AQUAE | O66646)

molecular function
	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:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0042954	lipoprotein transporter activity	Enables the directed movement of any conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids, into, out of or within a cell, or between cells.
	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.
biological process
	GO:0042953	lipoprotein transport	The directed movement of any conjugated, water-soluble protein in which the nonprotein group consists of a lipid or lipids, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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:0043190	ATP-binding cassette (ABC) transporter complex	A complex for the transport of metabolites into and out of the cell, typically comprised of four domains; two membrane-associated domains and two ATP-binding domains at the intracellular face of the membrane, that form a central pore through the plasma membrane. Each of the four core domains may be encoded as a separate polypeptide or the domains can be fused in any one of a number of ways into multidomain polypeptides. In Bacteria and Archaebacteria, ABC transporters also include substrate binding proteins to bind substrate external to the cytoplasm and deliver it to the transporter.
	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/Biological Unit
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	LOLD_AQUAE \| O66646	:	2pcl

2pcl	THE SAME PROTEIN RELATED ID: AAE001000297.2 RELATED DB: TARGETDB

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