3D71 - JenaLib

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Title :   CRYSTAL STRUCTURE OF E253Q BMRR BOUND TO 22 BASE PAIR PROMOTER SITE

Authors :   K. J. Newberry, J. L. Huffman, R. G. Brennan

Date :   20 May 08 (Deposition) - 26 Aug 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.80

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

Keywords :   Transcription Regulator, Protein-Dna Complex, Multidrug Binding Protein, Merr Family, Winged-Helix, Activator, Dna- Binding, Transcription Regulation, Transcription Regulator/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. J. Newberry, J. L. Huffman, M. C. Miller, N. Vazquez-Laslop, A. A. Neyfakh, R. G. Brennan
Structures Of Bmrr-Drug Complexes Reveal A Rigid Multidrug Binding Pocket And Transcription Activation Through Tyrosine Expulsion
J. Biol. Chem. V. 283 26795 2008
PubMed-ID: 18658145 | Reference-DOI: 10.1074/JBC.M804191200
(for further references see the PDB file header)

Molecule 1 - MULTIDRUG-EFFLUX TRANSPORTER 1 REGULATOR
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBAD
	Expression System Strain	:	TOP10
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 1-278
	Gene	:	BMRR, BMR1R
	Mutation	:	YES
	Organism Scientific	:	BACILLUS SUBTILIS

Molecule 2 - BMR PROMOTER DNA
	Chains	:	M
	Engineered	:	YES
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 11)

No.	Name	Count	Type	Full Name
1	ETF	1	Ligand/Ion	TRIFLUOROETHANOL
2	FLC	1	Ligand/Ion	CITRATE ANION
3	IMD	5	Ligand/Ion	IMIDAZOLE
4	PGO	3	Ligand/Ion	S-1,2-PROPANEDIOL
5	ZN	1	Ligand/Ion	ZINC ION

Biological Unit 1 (4, 20)

No.	Name	Count	Type	Full Name
1	ETF	2	Ligand/Ion	TRIFLUOROETHANOL
2	FLC	2	Ligand/Ion	CITRATE ANION
3	IMD	10	Ligand/Ion	IMIDAZOLE
4	PGO	6	Ligand/Ion	S-1,2-PROPANEDIOL
5	ZN	-1	Ligand/Ion	ZINC ION

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:189	BINDING SITE FOR RESIDUE ZN A 501
02	AC2	SOFTWARE	PRO A:144 , TYR A:187 , ILE A:255	BINDING SITE FOR RESIDUE FLC A 756
03	AC3	SOFTWARE	ARG A:111 , ARG A:133 , ASN A:197	BINDING SITE FOR RESIDUE PGO A 600
04	AC4	SOFTWARE	SER A:175 , PHE A:176 , MET A:207 , ILE A:209 , SER A:249 , ASP A:250	BINDING SITE FOR RESIDUE PGO A 602
05	AC5	SOFTWARE	TYR A:5 , TYR A:35 , GLN A:234 , LYS A:235 , LYS A:238	BINDING SITE FOR RESIDUE PGO A 604
06	AC6	SOFTWARE	TYR A:5 , ALA A:34 , ASN A:232 , LYS A:235	BINDING SITE FOR RESIDUE ETF A 901
07	AC7	SOFTWARE	ILE A:51 , ASN A:149 , ILE A:255	BINDING SITE FOR RESIDUE IMD A 302
08	AC8	SOFTWARE	PRO A:144 , ILE A:182 , PRO A:226	BINDING SITE FOR RESIDUE IMD A 303
09	AC9	SOFTWARE	GLU A:129 , ILE A:132 , LEU A:254 , GLU A:271 , LYS A:273	BINDING SITE FOR RESIDUE IMD A 304
10	BC1	SOFTWARE	TYR A:35 , LYS A:238	BINDING SITE FOR RESIDUE IMD A 305
11	BC2	SOFTWARE	ARG A:133 , THR A:196 , LYS A:198 , ILE A:200	BINDING SITE FOR RESIDUE IMD A 306

(no "SS Bond" information available for 3D71)

(no "Cis Peptide Bond" information available for 3D71)

(no "SAP(SNP)/Variant" information available for 3D71)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_MERR_2	PS50937	MerR-type HTH domain profile.	BMRR_BACSU	5-75	1	A:5-75
2	HTH_MERR_1	PS00552	MerR-type HTH domain signature.	BMRR_BACSU	9-31	1	A:9-31

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_MERR_2	PS50937	MerR-type HTH domain profile.	BMRR_BACSU	5-75	2	A:5-75
2	HTH_MERR_1	PS00552	MerR-type HTH domain signature.	BMRR_BACSU	9-31	2	A:9-31

(no "Exon" information available for 3D71)

Asymmetric Unit

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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
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Chain A from PDB  Type:PROTEIN  Length:277
 aligned with BMRR_BACSU | P39075 from UniProtKB/Swiss-Prot  Length:278

    Alignment length:277
                                    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       
           BMRR_BACSU     2 KESYYSIGEVSKLANVSIKALRYYDKIDLFKPAYVDPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKAQDLEMEELFAFYTEQERQIREKLDFLSALEQTISLVKKRMKRQMEYPALGEVFVLDEEEIRIIQTEAEGIGPENVLNASYSKLKKFIESADGFTNNSYGATFSFQPYTSIDEMTYRHIFTPVLTNKQISSITPDMEITTIPKGRYACIAYNFSPEHYFLNLQKLIKYIADRQLTVVSDVYELIIPIHYSPKKQEEYRVEMKIRIAE 278
               SCOP domains d3d71a1 A:2-120 automated matches                                                                                      d3d71a2 A:121-278 automated matches                                                                                                                            SCOP domains
               CATH domains 3d71A01 A:2-75  [code=1.10.1660.10, no name defined]                      3d71A02 A:76-119 Single helix bin           3d71A03 A:120-278 Multidrug-efflux Transporter 1 Regulator Bmrr; Chain                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eehhhhhhhhh.hhhhhhhhhhh......ee......eee..hhhhhhhhhhhhhhh..hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeee..eeeeeee.........hhhhhhhhhhhhhhhhh.....eeeee......hhhhh...eeeee..............eeeee..eeeeeeeee.hhhhhhhhhhhhhhhhhhh...eeeeeeeeeee..........eeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---HTH_MERR_2  PDB: A:5-75 UniProt: 5-75                                  ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------HTH_MERR_1  PDB: A:9-31------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3d71 A   2 KESYYSIGEVSKLANVSIKALRYYDKIDLFKPAYVDPDTSYRYYTDSQLIHLDLIKSLKYIGTPLEEMKKAQDLEMEELFAFYTEQERQIREKLDFLSALEQTISLVKKRMKRQMEYPALGEVFVLDEEEIRIIQTEAEGIGPENVLNASYSKLKKFIESADGFTNNSYGATFSFQPYTSIDEMTYRHIFTPVLTNKQISSITPDMEITTIPKGRYACIAYNFSPEHYFLNLQKLIKYIADRQLTVVSDVYQLIIPIHYSPKKQEEYRVEMKIRILD 278
                                    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

Chain M from PDB  Type:DNA  Length:23
                                                       
                 3d71 M -12 GACCCTCCCCTTAGGGGAGGGTC  12
                                    -3||       9   
                                     -2|           
                                       1

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	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 "Pfam Domain" information available for 3D71)

Asymmetric Unit(hide GO term definitions)

Chain A (BMRR_BACSU | P39075)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
biological process
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

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	3d71
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1bow	C-TERMINAL FRAGMENT OF BMRR
1exj	WTBMRR BOUND TO DNA AND TPP
1r8e	WTBMRR BOUND TO DNA TO 2.4 A RESOLUTION
2bow	C-TERMINAL FRAGMENT OF BMRR BOUND TO TPP
3d6y	R275E BMRR BOUND TO DNA AND BERBERINE
3d6z	R275E BMRR BOUND TO DNA AND RHODAMINE 6G
3d70	E253A BMRR BOUND TO DNA

Description

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Ligands, Modified Residues, Ions (5, 11)

Sites (11, 11)

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