1R8D | PD0482 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF MTAN BOUND TO DNA

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

Date :   23 Oct 03 (Deposition) - 17 Aug 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Protein-Dna Complex, Transcription/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. J. Newberry, R. G. Brennan
The Structural Mechanism For Transcription Activation By Merr Family Member Multidrug Transporter Activation, N Terminus.
J. Biol. Chem. V. 279 20356 2004
PubMed-ID: 14985361 | Reference-DOI: 10.1074/JBC.M400960200
(for further references see the PDB file header)

Molecule 1 - 26-MER
	Chains	:	C
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - 26-MER
	Chains	:	D
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - TRANSCRIPTION ACTIVATOR MTAN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBAD
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL TRUNCATION MUTANT OF MTA
	Gene	:	MTA
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 2)

No.	Name	Count	Type	Full Name
1	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:17 , HIS A:21 , ASN A:24 , DC D:3	BINDING SITE FOR RESIDUE SO4 A 300
2	AC2	SOFTWARE	ARG B:17 , HIS B:21 , ASN B:24 , DC C:3	BINDING SITE FOR RESIDUE SO4 B 301

(no "SS Bond" information available for 1R8D)

(no "Cis Peptide Bond" information available for 1R8D)

(no "SAP(SNP)/Variant" information available for 1R8D)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_MERR_2	PS50937	MerR-type HTH domain profile.	MTA_BACSU	2-71	2	A:2-71 B:2-71

(no "Exon" information available for 1R8D)

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:109
 aligned with MTA_BACSU | P71039 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:109
                                    10        20        30        40        50        60        70        80        90       100         
            MTA_BACSU     1 MKYQVKQVAEISGVSIRTLHHYDNIELLNPSALTDAGYRLYSDADLERLQQILFFKEIGFRLDEIKEMLDHPNFDRKAALQSQKEILMKKKQRMDEMIQTIDRTLLSVD 109
               SCOP domains d1r8da_ A: Multidrug transporter activator MtaN                                                               SCOP domains
               CATH domains 1r8dA00 A:1-109  [code=1.10.1660.10, no name defined]                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh.hhhhhhhhhhh......ee.....ee.hhhhhhhhhhhhhhhhh..hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -HTH_MERR_2  PDB: A:2-71 UniProt: 2-71                                 -------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------- Transcript
                 1r8d A   1 MKYQVKQVAEISGVSIRTLHHYDNIELLNPSALTDAGYRLYSDADLERLQQILFFKEIGFRLDEIKEMLDHPNFDRKAALQSQKEILMKKKQRMDEMIQTIDRTLLSVD 109
                                    10        20        30        40        50        60        70        80        90       100

Chain B from PDB  Type:PROTEIN  Length:107
 aligned with MTA_BACSU | P71039 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:107
                                    10        20        30        40        50        60        70        80        90       100       
            MTA_BACSU     1 MKYQVKQVAEISGVSIRTLHHYDNIELLNPSALTDAGYRLYSDADLERLQQILFFKEIGFRLDEIKEMLDHPNFDRKAALQSQKEILMKKKQRMDEMIQTIDRTLLS 107
               SCOP domains d1r8db_ B: Multidrug transporter activator MtaN                                                             SCOP domains
               CATH domains 1r8dB00 B:1-107  [code=1.10.1660.10, no name defined]                                                       CATH domains
           Pfam domains (1) ---MerR-1r8dB01 B:4-41                   ----MerR-DNA-bind-1r8dB03 B:46-107                                 Pfam domains (1)
           Pfam domains (2) ---MerR-1r8dB02 B:4-41                   ----MerR-DNA-bind-1r8dB04 B:46-107                                 Pfam domains (2)
         Sec.struct. author ...hhhhhhhhhh.hhhhhhhhhhh......ee.....ee.hhhhhhhhhhhhhhhhh..hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -HTH_MERR_2  PDB: B:2-71 UniProt: 2-71                                 ------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------- Transcript
                 1r8d B   1 MKYQVKQVAEISGVSIRTLHHYDNIELLNPSALTDAGYRLYSDADLERLQQILFFKEIGFRLDEIKEMLDHPNFDRKAALQSQKEILMKKKQRMDEMIQTIDRTLLS 107
                                    10        20        30        40        50        60        70        80        90       100

Chain C from PDB  Type:DNA  Length:26
                                                          
                 1r8d C -14 TTGACCCTAACGTTGCGTGATTGTTT  13
                                    -5  ||     7      
                                       -2|            
                                         1

Chain D from PDB  Type:DNA  Length:26
                                                          
                 1r8d D -14 AAAACAATCACGCAACGTTAGGGTCA  13
                                    -5  ||     7      
                                       -2|            
                                         1

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: Putative DNA-binding domain (45)

Superfamily: Putative DNA-binding domain (45)

Family: DNA-binding N-terminal domain of transcription activators (16)

Protein domain: Multidrug transporter activator MtaN (2)

Bacillus subtilis [TaxId: 1423] (2)

1a	d1r8da_	A:
1b	d1r8db_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Multidrug-efflux Transporter Regulator; Chain: A; Domain 2 (22)

Homologous Superfamily: [code=1.10.1660.10, no name defined] (17)

[unclassified] (5)

1a	1r8dB00	B:1-107
1b	1r8dA00	A:1-109

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: MerR (15)

Bacillus subtilis (8)

1a	MerR-1r8dB01	B:4-41
1b	MerR-1r8dB02	B:4-41

Family: MerR-DNA-bind (12)

Bacillus subtilis (2)

2a	MerR-DNA-bind-1r8dB03	B:46-107
2b	MerR-DNA-bind-1r8dB04	B:46-107

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (MTA_BACSU | P71039)

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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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