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Title :   CRYSTAL STRUCTURE OF THE ATP/MG2+ BOUND COMPOSITE DIMER OF HLYB-NBD

Authors :   J. Zaitseva, S. Jenewein, I. B. Holland, L. Schmitt

Date :   10 Sep 04 (Deposition) - 07 Jun 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)

Keywords :   Abc-Transporter, Atpase, Haemolysin B, Atp-Dependent Transport Protein, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Zaitseva, S. Jenewein, T. Jumpertz, I. B. Holland, L. Schmitt
H662 Is The Linchpin Of Atp Hydrolysis In The Nucleotide-Binding Domain Of The Abc Transporter Hlyb
Embo J. V. 24 1901 2005
PubMed-ID: 15889153 | Reference-DOI: 10.1038/SJ.EMBOJ.7600657

Molecule 1 - ALPHA-HEMOLYSIN TRANSLOCATION ATP-BINDING PROTEIN HLYB
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PPSG116
	Expression System Strain	:	DH5ALPHA
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	HLYB-NBD(RESIDUES 467-707)
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	HLYB

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 8)

No.	Name	Count	Type	Full Name
1	ATP	4	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MG	4	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 2)

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

Biological Unit 2 (1, 2)

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

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:160 , HOH A:165 , HOH A:171 , SER A:509 , ATP A:800	BINDING SITE FOR RESIDUE MG A 801
2	AC2	SOFTWARE	HOH B:36 , HOH B:162 , HOH B:169 , SER B:509 , ATP B:1800	BINDING SITE FOR RESIDUE MG B 1801
3	AC3	SOFTWARE	HOH C:137 , HOH C:148 , HOH C:166 , SER C:509 , ATP C:2800	BINDING SITE FOR RESIDUE MG C 2801
4	AC4	SOFTWARE	HOH D:8 , HOH D:147 , HOH D:150 , SER D:509 , ATP D:3800	BINDING SITE FOR RESIDUE MG D 3801
5	AC5	SOFTWARE	HOH A:22 , HOH A:160 , HOH A:165 , HOH A:171 , TYR A:477 , ILE A:484 , SER A:504 , GLY A:505 , SER A:506 , GLY A:507 , LYS A:508 , SER A:509 , THR A:510 , MG A:801 , GLY B:605 , SER B:607 , GLY B:609 , GLN B:610	BINDING SITE FOR RESIDUE ATP A 800
6	AC6	SOFTWARE	ALA A:604 , GLY A:605 , LEU A:606 , SER A:607 , GLY A:608 , GLY A:609 , GLN A:610 , HOH B:37 , HOH B:90 , HOH B:109 , HOH B:162 , HOH B:169 , TYR B:477 , ILE B:484 , SER B:504 , GLY B:505 , SER B:506 , GLY B:507 , LYS B:508 , SER B:509 , THR B:510 , MG B:1801	BINDING SITE FOR RESIDUE ATP B 1800
7	AC7	SOFTWARE	HOH C:51 , HOH C:137 , HOH C:148 , HOH C:166 , TYR C:477 , ILE C:484 , SER C:504 , GLY C:505 , SER C:506 , GLY C:507 , LYS C:508 , SER C:509 , THR C:510 , MG C:2801 , HOH D:118 , GLY D:605 , SER D:607 , GLY D:608 , GLY D:609 , GLN D:610	BINDING SITE FOR RESIDUE ATP C 2800
8	AC8	SOFTWARE	GLY C:605 , LEU C:606 , SER C:607 , GLY C:608 , GLY C:609 , GLN C:610 , HOH D:8 , HOH D:147 , HOH D:150 , HOH D:172 , TYR D:477 , ILE D:484 , SER D:504 , GLY D:505 , SER D:506 , GLY D:507 , LYS D:508 , SER D:509 , THR D:510 , LYS D:513 , MG D:3801	BINDING SITE FOR RESIDUE ATP D 3800

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

(no "Cis Peptide Bond" information available for 1XEF)

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ABC_TRANSPORTER_1	PS00211	ABC transporters family signature.	HLYBP_ECOLX	606-620	4	A:606-620 B:606-620 C:606-620 D:606-620

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ABC_TRANSPORTER_1	PS00211	ABC transporters family signature.	HLYBP_ECOLX	606-620	2	A:606-620 B:606-620 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ABC_TRANSPORTER_1	PS00211	ABC transporters family signature.	HLYBP_ECOLX	606-620	2	- - C:606-620 D:606-620

(no "Exon" information available for 1XEF)

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:241
 aligned with HLYBP_ECOLX | P08716 from UniProtKB/Swiss-Prot  Length:707

    Alignment length:241
                                   476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706 
          HLYBP_ECOLX   467 DITFRNIRFRYKPDSPVILDNINLSIKQGEVIGIVGRSGSGKSTLTKLIQRFYIPENGQVLIDGHDLALADPNWLRRQVGVVLQDNVLLNRSIIDNISLANPGMSVEKVIYAAKLAGAHDFISELREGYNTIVGEQGAGLSGGQRQRIAIARALVNNPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIIIAHRLSTVKNADRIIVMEKGKIVEQGKHKELLSEPESLYSYLYQLQSD 707
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.........eeeeeeee....eeeeee....hhhhhhhhhh......eeeeee..ee.hhhhhhhhhhheeee.........hhhhhhh......hhhhhhhhhhhh.hhhhhhh..hhhhh.........hhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhh...eeeee..hhhhhh...eeeeee..eeeeeehhhhhhh...hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER--------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xef A 467 DITFRNIRFRYKPDSPVILDNINLSIKQGEVIGIVGRSGSGKSTLTKLIQRFYIPENGQVLIDGHDLALADPNWLRRQVGVVLQDNVLLNRSIIDNISLANPGMSVEKVIYAAKLAGAHDFISELREGYNTIVGEQGAGLSGGQRQRIAIARALVNNPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIIIAARLSTVKNADRIIVMEKGKIVEQGKHKELLSEPESLYSYLYQLQSD 707
                                   476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706

Chain B from PDB  Type:PROTEIN  Length:241
 aligned with HLYBP_ECOLX | P08716 from UniProtKB/Swiss-Prot  Length:707

    Alignment length:241
                                   476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706 
          HLYBP_ECOLX   467 DITFRNIRFRYKPDSPVILDNINLSIKQGEVIGIVGRSGSGKSTLTKLIQRFYIPENGQVLIDGHDLALADPNWLRRQVGVVLQDNVLLNRSIIDNISLANPGMSVEKVIYAAKLAGAHDFISELREGYNTIVGEQGAGLSGGQRQRIAIARALVNNPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIIIAHRLSTVKNADRIIVMEKGKIVEQGKHKELLSEPESLYSYLYQLQSD 707
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.........eeeeeeee....eeeee.....hhhhhhhh........eeeeee..ee....hhhhhhhheeee.........hhhhhhhh.....hhhhhhhhhhhh.hhhhhhhh.hhhhh.........hhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhh...eeeee...........eeeeee..eeeeeehhhhhhh...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER--------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xef B 467 DITFRNIRFRYKPDSPVILDNINLSIKQGEVIGIVGRSGSGKSTLTKLIQRFYIPENGQVLIDGHDLALADPNWLRRQVGVVLQDNVLLNRSIIDNISLANPGMSVEKVIYAAKLAGAHDFISELREGYNTIVGEQGAGLSGGQRQRIAIARALVNNPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIIIAARLSTVKNADRIIVMEKGKIVEQGKHKELLSEPESLYSYLYQLQSD 707
                                   476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706

Chain C from PDB  Type:PROTEIN  Length:241
 aligned with HLYBP_ECOLX | P08716 from UniProtKB/Swiss-Prot  Length:707

    Alignment length:241
                                   476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706 
          HLYBP_ECOLX   467 DITFRNIRFRYKPDSPVILDNINLSIKQGEVIGIVGRSGSGKSTLTKLIQRFYIPENGQVLIDGHDLALADPNWLRRQVGVVLQDNVLLNRSIIDNISLANPGMSVEKVIYAAKLAGAHDFISELREGYNTIVGEQGAGLSGGQRQRIAIARALVNNPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIIIAHRLSTVKNADRIIVMEKGKIVEQGKHKELLSEPESLYSYLYQLQSD 707
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.........eeeeeeee....eeeeee....hhhhhhhh........eeeeee..ee....hhhhhhhheeee.........hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhh.hhhhh.........hhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhh...eeeee..hhhhhh...eeeeee..eeeeeehhhhhhh...hhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER--------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xef C 467 DITFRNIRFRYKPDSPVILDNINLSIKQGEVIGIVGRSGSGKSTLTKLIQRFYIPENGQVLIDGHDLALADPNWLRRQVGVVLQDNVLLNRSIIDNISLANPGMSVEKVIYAAKLAGAHDFISELREGYNTIVGEQGAGLSGGQRQRIAIARALVNNPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIIIAARLSTVKNADRIIVMEKGKIVEQGKHKELLSEPESLYSYLYQLQSD 707
                                   476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706

Chain D from PDB  Type:PROTEIN  Length:241
 aligned with HLYBP_ECOLX | P08716 from UniProtKB/Swiss-Prot  Length:707

    Alignment length:241
                                   476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706 
          HLYBP_ECOLX   467 DITFRNIRFRYKPDSPVILDNINLSIKQGEVIGIVGRSGSGKSTLTKLIQRFYIPENGQVLIDGHDLALADPNWLRRQVGVVLQDNVLLNRSIIDNISLANPGMSVEKVIYAAKLAGAHDFISELREGYNTIVGEQGAGLSGGQRQRIAIARALVNNPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIIIAHRLSTVKNADRIIVMEKGKIVEQGKHKELLSEPESLYSYLYQLQSD 707
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ------------------------------------------ABC_tran-1xefD01 D:509-634                                                                                                    ------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------------------------ABC_tran-1xefD02 D:509-634                                                                                                    ------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ------------------------------------------ABC_tran-1xefD03 D:509-634                                                                                                    ------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) ------------------------------------------ABC_tran-1xefD04 D:509-634                                                                                                    ------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .eeeeeeee.........eeeeeeee....eeeeee....hhhhhhhh........eeeeee..ee.hhhhhhhhhhheeee.........hhhhhhhh.....hhhhhhhhhhhh.hhhhhhh..hhhhh.........hhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhh...eeeee...........eeeeee..eeeeeehhhhhhh...hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER--------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1xef D 467 DITFRNIRFRYKPDSPVILDNINLSIKQGEVIGIVGRSGSGKSTLTKLIQRFYIPENGQVLIDGHDLALADPNWLRRQVGVVLQDNVLLNRSIIDNISLANPGMSVEKVIYAAKLAGAHDFISELREGYNTIVGEQGAGLSGGQRQRIAIARALVNNPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIIIAARLSTVKNADRIIVMEKGKIVEQGKHKELLSEPESLYSYLYQLQSD 707
                                   476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696       706

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 '\|'

(no "SCOP Domain" information available for 1XEF)

(no "CATH Domain" information available for 1XEF)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: ABC_tran (53)

Escherichia coli (3)

1a	ABC_tran-1xefD01	D:509-634
1b	ABC_tran-1xefD02	D:509-634
1c	ABC_tran-1xefD03	D:509-634
1d	ABC_tran-1xefD04	D:509-634

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (HLYBP_ECOLX | P08716)

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: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: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: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:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
	GO:0008565	protein transporter activity	Enables the directed movement of proteins into, out of or within a cell, or between cells.
biological process
	GO:0030253	protein secretion by the type I secretion system	The process in which proteins are secreted into the extracellular milieu via the type I secretion system; secretion occurs in a continuous process without the distinct presence of periplasmic intermediates and does not involve proteolytic processing of secreted proteins.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	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: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: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.
	GO:0030256	type I protein secretion system complex	A complex of three secretory proteins that carry out secretion in the type I secretion system: an inner membrane transport ATPase (termed ABC protein for ATP-binding cassette), which provides the energy for protein secretion; an outer membrane protein, which is exported via the sec pathway; and a membrane fusion protein, which is anchored in the inner membrane and spans the periplasmic space.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1xef)

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	1xef
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	HLYBP_ECOLX \| P08716
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	HLYBP_ECOLX \| P08716	:	1mt0 2ff7 2ffa 2ffb 2fgj 2fgk 2pmk 3b5j

(no "Related Entries Specified in the PDB File" available for 1XEF)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Related Entries Specified in the PDB File