2PMK - JenaLib

Title :   CRYSTAL STRUCTURES OF AN ISOLATED ABC-ATPASE IN COMPLEX WITH TNP-ADP

Authors :   C. Oswald, S. Jenewein, I. B. Holland, L. Schmitt

Date :   23 Apr 07 (Deposition) - 05 Feb 08 (Release) - 23 Sep 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym./Biol. Unit : A

Keywords :   Abc-Transporter, Atpase, Nbd, Tnp-Nucleotide, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. Oswald, S. Jenewein, S. H. Smits, I. B. Holland, L. Schmitt
Water-Mediated Protein-Fluorophore Interactions Modulate Th Affinity Of An Abc-Atpase/Tnp-Adp Complex
J. Struct. Biol. V. 162 85 2008
PubMed-ID: 18155559 | Reference-DOI: 10.1016/J.JSB.2007.11.006

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR A:477 , PRO A:482 , ILE A:484 , GLY A:505 , SER A:506 , GLY A:507 , LYS A:508 , SER A:509 , THR A:510 , LYS A:513 , TYR A:519 , TRP A:540 , ARG A:543 , GLU A:689 , SER A:692 , GLU A:693 , PRO A:694 , HOH A:713 , HOH A:721 , HOH A:742 , HOH A:759 , HOH A:782 , HOH A:799 , HOH A:832 , HOH A:852	BINDING SITE FOR RESIDUE 128 A 301
2	AC2	SOFTWARE	TYR A:477 , ILE A:484 , ARG A:503 , SER A:504 , GLY A:505 , SER A:506 , GLY A:507 , LYS A:508 , SER A:509 , THR A:510 , LYS A:513 , TYR A:519 , GLU A:689 , PRO A:694 , HOH A:713 , HOH A:721 , HOH A:742 , HOH A:759 , HOH A:782 , HOH A:801 , HOH A:832 , HOH A:852 , HOH A:898	BINDING SITE FOR RESIDUE ADP A 401

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

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:243
 aligned with HLYBP_ECOLX | P08716 from UniProtKB/Swiss-Prot  Length:707

    Alignment length:253
                                   464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704   
          HLYBP_ECOLX   455 YHGKLTLPEINGDITFRNIRFRYKPDSPVILDNINLSIKQGEVIGIVGRSGSGKSTLTKLIQRFYIPENGQVLIDGHDLALADPNWLRRQVGVVLQDNVLLNRSIIDNISLANPGMSVEKVIYAAKLAGAHDFISELREGYNTIVGEQGAGLSGGQRQRIAIARALVNNPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIIIAHRLSTVKNADRIIVMEKGKIVEQGKHKELLSEPESLYSYLYQLQSD 707
               SCOP domains d2          pmka_ A: Haemolysin B ATP-binding protein                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------ABC_tran-2pmkA01 A:509-634                                                                                                    ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .e----------eeeeeeeeee......eeeeeeeeeee...eeeee.....hhhhhhhhhh......eeeeee..ee....hhhhhhhheeee.........hhhhhhh......hhhhhhhhhhhh.hhhhhh...hhhhh.........hhhhhhhhhhhhhhh....eeee.......hhhhhhhhhhhhhhhhh..eeeee..hhhhhh...eeeeee..eeeeeehhhhhhhh..hhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER--------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pmk A 465 HH----------DITFRNIRFRYKPDSPVILDNINLSIKQGEVIGIVGRSGSGKSTLTKLIQRFYIPENGQVLIDGHDLALADPNWLRRQVGVVLQDNVLLNRSIIDNISLANPGMSVEKVIYAAKLAGAHDFISELREGYNTIVGEQGAGLSGGQRQRIAIARALVNNPKILIFDEATSALDYESEHVIMRNMHKICKGRTVIIIAHRLSTVKNADRIIVMEKGKIVEQGKHKELLSEPESLYSYLYQLQSD 707
                             |       -  |    474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704   
                             |        467                                                                                                                                                                                                                                                
                           466

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)

CATH Domains (0, 0)

Pfam Domains (1, 1)

Gene Ontology (15, 15)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (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.

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