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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF LMRA ATP-BINDING DOMAIN

Authors :   Y. Yuan, H. Chen, D. Patel

Date :   24 Sep 02 (Deposition) - 02 Dec 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

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

Keywords :   Abc Transporter, Asymmetric Dimer, Tetramer, P-Glycoprotein, Two-Site Alternating Mechanism, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Yuan, H. Chen, D. Patel
Crystal Structure Of Lmra Atp-Binding Domain Reveals The Two-Site Alternating Mechanism At Molecular Level
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - MULTIDRUG RESISTANCE ABC TRANSPORTER ATP-BINDING AND PERMEASE PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	ATP-BINDING DOMAIN
	Organism Scientific	:	LACTOCOCCUS LACTIS
	Organism Taxid	:	1358
	Synonym	:	LMRA

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 6)

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

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ADP B:1600 , ASP C:2353	BINDING SITE FOR RESIDUE MG C 1601
2	AC2	SOFTWARE	SER D:3383 , ADP D:3600 , HOH D:4046 , HOH D:4078	BINDING SITE FOR RESIDUE MG D 3601
3	AC3	SOFTWARE	TYR A:352 , ASP A:353 , GLU A:356 , ILE A:358 , GLY A:379 , GLY A:380 , GLY A:381 , LYS A:382 , SER A:383 , THR A:384 , HOH A:4074 , SER D:3355 , GLU D:3356 , ADP D:3600	BINDING SITE FOR RESIDUE ATP A 601
4	AC4	SOFTWARE	TYR B:1352 , GLU B:1356 , ILE B:1358 , SER B:1378 , GLY B:1379 , GLY B:1380 , GLY B:1381 , LYS B:1382 , SER B:1383 , THR B:1384 , MG C:1601 , ASP C:2353 , SER C:2355 , ATP C:2601 , HOH C:4029	BINDING SITE FOR RESIDUE ADP B 1600
5	AC5	SOFTWARE	ASP B:1353 , SER B:1355 , GLU B:1356 , ADP B:1600 , TYR C:2352 , SER C:2378 , GLY C:2379 , GLY C:2380 , GLY C:2381 , LYS C:2382 , SER C:2383 , THR C:2384 , HOH C:4032	BINDING SITE FOR RESIDUE ATP C 2601
6	AC6	SOFTWARE	ASP A:353 , SER A:355 , ATP A:601 , TYR D:3352 , GLU D:3356 , ILE D:3358 , PRO D:3377 , SER D:3378 , GLY D:3379 , GLY D:3380 , GLY D:3381 , LYS D:3382 , SER D:3383 , THR D:3384 , MG D:3601 , HOH D:4039	BINDING SITE FOR RESIDUE ADP D 3600

(no "SS Bond" information available for 1MV5)

(no "Cis Peptide Bond" information available for 1MV5)

(no "SAP(SNP)/Variant" information available for 1MV5)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ABC_TRANSPORTER_1	PS00211	ABC transporters family signature.	LMRA_LACLA	487-501	4	A:481-495 B:1481-1495 C:2481-2495 D:3481-3495

(no "Exon" information available for 1MV5)

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:242
 aligned with LMRA_LACLA | Q9CHL8 from UniProtKB/Swiss-Prot  Length:590

    Alignment length:242
                                   357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587  
          LMRA_LACLA    348 TLSARHVDFAYDDSEQILRDISFEAQPNSIIAFAGPSGGGKSTIFSLLERFYQPTAGEITIDGQPIDNISLENWRSQIGFVSQDSAIMAGTIRENLTYGLEGDYTDEDLWQVLDLAFARSFVENMPDQLNTEVGERGVKISGGQRQRLAIARAFLRNPKILMLDEATASLDSESESMVQKALDSLMKGRTTLVIAHRLSTIVDADKIYFIEKGQITGSGKHNELVATHPLYAKYVSEQLTVG  589
               SCOP domains d1mv5a_ A: Multidrug resistance ABC transporter LmrA, C-terminal domain                                                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee........eeeeeeee...eeeeee.....hhhhhhhhhh.........eee..ee..............ee........eehhhhh........hhhhhhhhhhhhh.........hhhh.ee.......hhhhhhhhhhhhhhhhh..eeeee...........hhhhhhhhhhhh..eeeee..hhhhhhhh..eeeee..ee....hhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER---------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1mv5 A  342 MLSARHVDFAYDDSEQILRDISFEAQPNSIIAFAGPSGGGKSTIFSLLERFYQPTAGEITIDGQPIDNISLENWRSQIGFVSQDSAIMAGTIRENLTYGLEGDYTDEDLWQVLDLAFARSFVENMPDQLNTEVGERGVKISGGQRQRLAIARAFLRNPKILMLDEATASLDSESESMVQKALDSLMKGRTTLVIAHRLSTIVDADKIYFIEKGQITGSGKHNELVATHPLYAKYVSEQLTVG  583
                                   351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581

Chain B from PDB  Type:PROTEIN  Length:242
 aligned with LMRA_LACLA | Q9CHL8 from UniProtKB/Swiss-Prot  Length:590

    Alignment length:242
                                   357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587  
          LMRA_LACLA    348 TLSARHVDFAYDDSEQILRDISFEAQPNSIIAFAGPSGGGKSTIFSLLERFYQPTAGEITIDGQPIDNISLENWRSQIGFVSQDSAIMAGTIRENLTYGLEGDYTDEDLWQVLDLAFARSFVENMPDQLNTEVGERGVKISGGQRQRLAIARAFLRNPKILMLDEATASLDSESESMVQKALDSLMKGRTTLVIAHRLSTIVDADKIYFIEKGQITGSGKHNELVATHPLYAKYVSEQLTVG  589
               SCOP domains d1mv5b_ B: Multidrug resistance ABC transporter LmrA, C-terminal domain                                                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee........eeeeeeee....eeeee.....hhhhhhhhhh......eeeeee...hhhhh....................eehhhhhhh......hhhhhhhhhhhh.hhhhhh........ee.........hhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhh..eee....hhhhhhhh.eeeeee..eeeeeehhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER---------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1mv5 B 1342 MLSARHVDFAYDDSEQILRDISFEAQPNSIIAFAGPSGGGKSTIFSLLERFYQPTAGEITIDGQPIDNISLENWRSQIGFVSQDSAIMAGTIRENLTYGLEGDYTDEDLWQVLDLAFARSFVENMPDQLNTEVGERGVKISGGQRQRLAIARAFLRNPKILMLDEATASLDSESESMVQKALDSLMKGRTTLVIAHRLSTIVDADKIYFIEKGQITGSGKHNELVATHPLYAKYVSEQLTVG 1583
                                  1351      1361      1371      1381      1391      1401      1411      1421      1431      1441      1451      1461      1471      1481      1491      1501      1511      1521      1531      1541      1551      1561      1571      1581

Chain C from PDB  Type:PROTEIN  Length:242
 aligned with LMRA_LACLA | Q9CHL8 from UniProtKB/Swiss-Prot  Length:590

    Alignment length:242
                                   357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587  
          LMRA_LACLA    348 TLSARHVDFAYDDSEQILRDISFEAQPNSIIAFAGPSGGGKSTIFSLLERFYQPTAGEITIDGQPIDNISLENWRSQIGFVSQDSAIMAGTIRENLTYGLEGDYTDEDLWQVLDLAFARSFVENMPDQLNTEVGERGVKISGGQRQRLAIARAFLRNPKILMLDEATASLDSESESMVQKALDSLMKGRTTLVIAHRLSTIVDADKIYFIEKGQITGSGKHNELVATHPLYAKYVSEQLTVG  589
               SCOP domains d1mv5c_ C: Multidrug resistance ABC transporter LmrA, C-terminal domain                                                                                                                                                                            SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee........eeeeeeee....eeeee.....hhhhhhhhhh........eeee..ee....hhhhhhhheeeee.......ee.hhhhhh.....hhhhhhhhhhhhh.hhhhhhh.......ee.......hhhhhhhhhhhhhhhhh..eeeee.............hhhhhhhhh...eeeee..hhhhhhhh.eeeeee..eeeeeehhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER---------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1mv5 C 2342 MLSARHVDFAYDDSEQILRDISFEAQPNSIIAFAGPSGGGKSTIFSLLERFYQPTAGEITIDGQPIDNISLENWRSQIGFVSQDSAIMAGTIRENLTYGLEGDYTDEDLWQVLDLAFARSFVENMPDQLNTEVGERGVKISGGQRQRLAIARAFLRNPKILMLDEATASLDSESESMVQKALDSLMKGRTTLVIAHRLSTIVDADKIYFIEKGQITGSGKHNELVATHPLYAKYVSEQLTVG 2583
                                  2351      2361      2371      2381      2391      2401      2411      2421      2431      2441      2451      2461      2471      2481      2491      2501      2511      2521      2531      2541      2551      2561      2571      2581

Chain D from PDB  Type:PROTEIN  Length:241
 aligned with LMRA_LACLA | Q9CHL8 from UniProtKB/Swiss-Prot  Length:590

    Alignment length:241
                                   357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587 
          LMRA_LACLA    348 TLSARHVDFAYDDSEQILRDISFEAQPNSIIAFAGPSGGGKSTIFSLLERFYQPTAGEITIDGQPIDNISLENWRSQIGFVSQDSAIMAGTIRENLTYGLEGDYTDEDLWQVLDLAFARSFVENMPDQLNTEVGERGVKISGGQRQRLAIARAFLRNPKILMLDEATASLDSESESMVQKALDSLMKGRTTLVIAHRLSTIVDADKIYFIEKGQITGSGKHNELVATHPLYAKYVSEQLTV  588
               SCOP domains d1mv5d_ D: Multidrug resistance ABC transporter LmrA, C-terminal domain                                                                                                                                                                           SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------------------------------------ABC_tran-1mv5D01 D:3383-3509                                                                                                   ------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -----------------------------------------ABC_tran-1mv5D02 D:3383-3509                                                                                                   ------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) -----------------------------------------ABC_tran-1mv5D03 D:3383-3509                                                                                                   ------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) -----------------------------------------ABC_tran-1mv5D04 D:3383-3509                                                                                                   ------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author .eee..eee........eeee..........eee.....hhhhhhhhhh.........eee.......hhhhhhhhh.............hhhhhhh.......hhhhhhhhhh...hhhhhhh..hhhhh..........hhhhhhhhhhhhh.....eee.............hhhhhhhhhhhh..eee....hhhhhhh...eeeee..eeee..hhhhhhhhh.hhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------ABC_TRANSPORTER--------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1mv5 D 3342 MLSARHVDFAYDDSEQILRDISFEAQPNSIIAFAGPSGGGKSTIFSLLERFYQPTAGEITIDGQPIDNISLENWRSQIGFVSQDSAIMAGTIRENLTYGLEGDYTDEDLWQVLDLAFARSFVENMPDQLNTEVGERGVKISGGQRQRLAIARAFLRNPKILMLDEATASLDSESESMVQKALDSLMKGRTTLVIAHRLSTIVDADKIYFIEKGQITGSGKHNELVATHPLYAKYVSEQLTV 3582
                                  3351      3361      3371      3381      3391      3401      3411      3421      3431      3441      3451      3461      3471      3481      3491      3501      3511      3521      3531      3541      3551      3561      3571      3581

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 "CATH Domain" information available for 1MV5)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: P-loop_NTPase (1112)

Family: ABC_tran (53)

Lactococcus lactis subsp. lactis (Streptococcus lactis) (1)

1a	ABC_tran-1mv5D01	D:3383-3509
1b	ABC_tran-1mv5D02	D:3383-3509
1c	ABC_tran-1mv5D03	D:3383-3509
1d	ABC_tran-1mv5D04	D:3383-3509

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (LMRA_LACLA | Q9CHL8)

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:0008559	xenobiotic-transporting ATPase activity	Catalysis of the reaction: ATP + H2O + xenobiotic(in) = ADP + phosphate + xenobiotic(out).
biological process
	GO:0006855	drug transmembrane transport	The process in which a drug is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
	GO:0046677	response to antibiotic	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
	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.
	GO:0042908	xenobiotic transport	The directed movement of a xenobiotic, a compound foreign to living organisms, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1mv5)

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	1mv5
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Description

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Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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