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Title :   STRUCTURES OF MDT PROTEINS

Authors :   M. A. Schumacher

Date :   02 Jul 08 (Deposition) - 27 Jan 09 (Release) - 27 Jan 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.66

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

Keywords :   Mdt, Persistence, Multidrug Resistance, Tolerance, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. A. Schumacher, K. M. Piro, W. Xu, S. Hansen, K. Lewis, R. G. Brennan
Molecular Mechanisms Of Hipa-Mediated Multidrug Tolerance And Its Neutralization By Hipb.
Science V. 323 396 2009
PubMed-ID: 19150849 | Reference-DOI: 10.1126/SCIENCE.1163806
(for further references see the PDB file header)

Molecule 1 - PROTEIN HIPA
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBAD22
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	HIPA, B1507, JW1500
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 28)

No.	Name	Count	Type	Full Name
1	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MG	4	Ligand/Ion	MAGNESIUM ION
3	MSE	20	Mod. Amino Acid	SELENOMETHIONINE
4	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
4	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 12)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	MG	-1	Ligand/Ion	MAGNESIUM ION
3	MSE	10	Mod. Amino Acid	SELENOMETHIONINE
4	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:98 , ALA A:152 , GLY A:153 , ALA A:154 , GLN A:155 , LYS A:157 , ILE A:179 , LYS A:181 , PRO A:218 , VAL A:233 , GLU A:234 , ARG A:235 , PHE A:236 , ASP A:237 , GLN A:252 , HIS A:311 , LYS A:313 , ASN A:314 , TYR A:331 , ASP A:332 , MG A:441 , MG A:442 , HOH A:860 , HOH A:861 , HOH A:867 , HOH A:932 , HOH A:1063	BINDING SITE FOR RESIDUE ATP A 500
2	AC2	SOFTWARE	ASN A:314 , ASP A:332 , ATP A:500 , HOH A:860	BINDING SITE FOR RESIDUE MG A 441
3	AC3	SOFTWARE	GLN A:309 , ASP A:332 , ATP A:500	BINDING SITE FOR RESIDUE MG A 442
4	AC4	SOFTWARE	ALA A:358 , SER A:359 , LYS A:363 , ARG A:372 , HIS A:373 , HOH A:1014 , HOH A:1201	BINDING SITE FOR RESIDUE SO4 A 833
5	AC5	SOFTWARE	ASP B:67 , VAL B:98 , ALA B:152 , GLY B:153 , ALA B:154 , GLN B:155 , LYS B:157 , ILE B:179 , LYS B:181 , VAL B:233 , GLU B:234 , ARG B:235 , PHE B:236 , ASP B:237 , GLN B:252 , HIS B:311 , LYS B:313 , ASN B:314 , TYR B:331 , ASP B:332 , MG B:441 , MG B:442 , HOH B:835 , HOH B:837 , HOH B:842 , HOH B:858 , HOH B:861 , HOH B:1011 , HOH B:1145	BINDING SITE FOR RESIDUE ATP B 501
6	AC6	SOFTWARE	ASP B:332 , ATP B:501 , HOH B:1058 , HOH B:1165	BINDING SITE FOR RESIDUE MG B 441
7	AC7	SOFTWARE	ASN B:314 , ASP B:332 , ATP B:501 , HOH B:835	BINDING SITE FOR RESIDUE MG B 442
8	AC8	SOFTWARE	ALA B:358 , SER B:359 , LYS B:363 , ARG B:372 , HIS B:373	BINDING SITE FOR RESIDUE SO4 B 834

(no "SS Bond" information available for 3DNT)

(no "Cis Peptide Bond" information available for 3DNT)

(no "SAP(SNP)/Variant" information available for 3DNT)

(no "PROSITE Motif" information available for 3DNT)

(no "Exon" information available for 3DNT)

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:415
 aligned with HIPA_ECOLI | P23874 from UniProtKB/Swiss-Prot  Length:440

    Alignment length:436
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431      
           HIPA_ECOLI     2 PKLVTWMNNQRVGELTKLANGAHTFKYAPEWLASRYARPLSLSLPLQRGNITSDAVFNFFDNLLPDSPIVRDRIVKRYHAKSRQPFDLLSEIGRDSVGAVTLIPEDETVTHPIMAWEKLTEARLEEVLTAYKADIPLGMIREENDFRISVAGAQEKTALLRIGNDWCIPKGITPTTHIIKLPIGEIRQPNATLDLSQSVDNEYYCLLLAKELGLNVPDAEIIKAGNVRALAVERFDRRWNAERTVLLRLPQEDMCQTFGLPSSVKYESDGGPGIARIMAFLMGSSEALKDRYDFMKFQVFQWLIGATDGHAKNFSVFIQAGGSYRLTPFYDIISAFPVLGGTGIHISDLKLAMGLNASKGKKTAIDKIYPRHFLATAKVLRFPEVQMHEILSDFARMIPAALDNVKTSLPTDFPENVVTAVESNVLRLHGRLSREY 437
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee..eeeeeeee.....eeeeehhhhhhh...............ee.hhhhhhhhhh....hhhhhhhhhhhhh....hhhhhhhhhh.......eee.--------...eee.hhhhhhhhhhhhhhhhhhhh................eeeeeee..eeeee.......eeee...-------------hhhhhhhhhhhhhhhh......eeeeee..eeeeeee...eee......eee..eeehhhhh..hhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhh.eeee.hhh.eee........hhhhh.....hhhh.eeeeeee....eeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dnt A   2 PKLVTWmNNQRVGELTKLANGAHTFKYAPEWLASRYARPLSLSLPLQRGNITSDAVFNFFDNLLPDSPIVRDRIVKRYHAKSRQPFDLLSEIGRDSVGAVTLIP--------ImAWEKLTEARLEEVLTAYKADIPLGmIREENDFRISVAGAQEKTALLRIGNDWCIPKGITPTTHIIKLPI-------------QSVDNEYYCLLLAKELGLNVPDAEIIKAGNVRALAVERFDRRWNAERTVLLRLPQEDmCQTFGLPSSVKYESDGGPGIARImAFLmGSSEALKDRYDFmKFQVFQWLIGATQGHAKNFSVFIQAGGSYRLTPFYDIISAFPVLGGTGIHISDLKLAmGLNASKGKKTAIDKIYPRHFLATAKVLRFPEVQmHEILSDFARmIPAALDNVKTSLPTDFPENVVTAVESNVLRLHGRLSREY 437
                                  | 11        21        31        41        51        61        71        81        91       101   |     -  ||   121       131       141       151       161       171       181  |      -      |201       211       221       231       241       251   |   261       271       281 |     291    |  301       311       321       331       341       351  |    361       371       381      |391      |401       411       421       431      
                                  8-MSE                                                                                          105      114|                      140-MSE                                     184           198                                                      255-MSE                 279-MSE          296-MSE                                                   354-MSE                           388-MSE   398-MSE                                   
                                                                                                                                           115-MSE                                                                                                                                                                 283-MSE

Chain B from PDB  Type:PROTEIN  Length:419
 aligned with HIPA_ECOLI | P23874 from UniProtKB/Swiss-Prot  Length:440

    Alignment length:433
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432   
           HIPA_ECOLI     3 KLVTWMNNQRVGELTKLANGAHTFKYAPEWLASRYARPLSLSLPLQRGNITSDAVFNFFDNLLPDSPIVRDRIVKRYHAKSRQPFDLLSEIGRDSVGAVTLIPEDETVTHPIMAWEKLTEARLEEVLTAYKADIPLGMIREENDFRISVAGAQEKTALLRIGNDWCIPKGITPTTHIIKLPIGEIRQPNATLDLSQSVDNEYYCLLLAKELGLNVPDAEIIKAGNVRALAVERFDRRWNAERTVLLRLPQEDMCQTFGLPSSVKYESDGGPGIARIMAFLMGSSEALKDRYDFMKFQVFQWLIGATDGHAKNFSVFIQAGGSYRLTPFYDIISAFPVLGGTGIHISDLKLAMGLNASKGKKTAIDKIYPRHFLATAKVLRFPEVQMHEILSDFARMIPAALDNVKTSLPTDFPENVVTAVESNVLRLHGRLSR 435
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeeeeee.....eeeeehhhhhh................ee.hhhhhhhhhh....hhhhhhhhhhhhh....hhhhhhhhhh......eeeee...........eee.hhhhhhhhhhhhhhh.....................eeeeeee..eeeee.......eeee..--------------hhhhhhhhhhhhhhhh......eeeeee..eeeeeee...eee......eee..eeehhhhh..hhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhhhhhhhhhh.....hhhh.eeee.hhh.eee........hhhhh.....hhhh.eeeeeee....eeee.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dnt B   3 KLVTWmNNQRVGELTKLANGAHTFKYAPEWLASRYARPLSLSLPLQRGNITSDAVFNFFDNLLPDSPIVRDRIVKRYHAKSRQPFDLLSEIGRDSVGAVTLIPEDETVTHPImAWEKLTEARLEEVLTAYKADIPLGmIREENDFRISVAGAQEKTALLRIGNDWCIPKGITPTTHIIKLP--------------QSVDNEYYCLLLAKELGLNVPDAEIIKAGNVRALAVERFDRRWNAERTVLLRLPQEDmCQTFGLPSSVKYESDGGPGIARImAFLmGSSEALKDRYDFmKFQVFQWLIGATQGHAKNFSVFIQAGGSYRLTPFYDIISAFPVLGGTGIHISDLKLAmGLNASKGKKTAIDKIYPRHFLATAKVLRFPEVQmHEILSDFARmIPAALDNVKTSLPTDFPENVVTAVESNVLRLHGRLSR 435
                                 |  12        22        32        42        52        62        72        82        92       102       112  |    122       132       142       152       162       172       182|        -     | 202       212       222       232       242       252  |    262       272      |282|      292   |   302       312       322       332       342       352 |     362       372       382     | 392     | 402       412       422       432   
                                 8-MSE                                                                                                    115-MSE                  140-MSE                                    183            198                                                      255-MSE                 279-MSE          296-MSE                                                   354-MSE                           388-MSE   398-MSE                                 
                                                                                                                                                                                                                                                                                                                  283-MSE

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 3DNT)

(no "CATH Domain" information available for 3DNT)

(no "Pfam Domain" information available for 3DNT)

Asymmetric Unit(hide GO term definitions)

Chain A,B (HIPA_ECOLI | P23874)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	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: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:0004674	protein serine/threonine kinase activity	Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0022611	dormancy process	A developmental process in which dormancy (sometimes called a dormant state) is induced, maintained or broken. Dormancy is a suspension of most physiological activity and growth that can be reactivated.
	GO:0043086	negative regulation of catalytic activity	Any process that stops or reduces the activity of an enzyme.
	GO:0036289	peptidyl-serine autophosphorylation	The phosphorylation by a protein of one or more of its own serine amino acid residues, or a serine residue on an identical protein.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	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:0044010	single-species biofilm formation	A process in which planktonically growing microorganisms of the same species grow at a liquid-air interface or on a solid substrate under the flow of a liquid and produce extracellular polymers that facilitate matrix formation, resulting in a change in the organisms' growth rate and gene transcription.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3dnt)

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	3dnt
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	HIPA_ECOLI \| P23874
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	HIPA_ECOLI \| P23874	:	2wiu 3dnu 3dnv 3fbr 3hzi 3tpb 3tpd 3tpe 3tpt 3tpv 4yg7 5k98

Description

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Chains, Units

Ligands, Modified Residues, Ions (4, 28)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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