2XRL - JenaLib

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Title :   TET-REPRESSOR CLASS D T103A WITH DOXYCYCLINE

Authors :   G. J. Palm, P. Waack, W. Hinrichs

Date :   16 Sep 10 (Deposition) - 05 Oct 11 (Release) - 05 Oct 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Transcription, Antibiotic Resistance, Dna-Binding, Helix-Turn-Helix (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Hinrichs
T103A Mutant Of Tetrd With Doxycycline
To Be Published
PubMed: search

Molecule 1 - TETRACYCLINE REPRESSOR PROTEIN CLASS D
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PWH610
	Expression System Strain	:	K-12
	Expression System Taxid	:	83333
	Expression System Variant	:	RB791
	Expression System Vector Type	:	PLASMID
	Fragment	:	RESIDUES 2-208
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	DXT	1	Ligand/Ion	(4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE
3	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	DXT	2	Ligand/Ion	(4S,4AR,5S,5AR,6R,12AS)-4-(DIMETHYLAMINO)-3,5,10,12,12A-PENTAHYDROXY-6-METHYL-1,11-DIOXO-1,4,4A,5,5A,6,11,12A-OCTAHYDROTETRACENE-2-CARBOXAMIDE
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:3 , LEU A:4 , GLN A:76 , ARG A:80 , HOH A:2095	BINDING SITE FOR RESIDUE CL A1209
2	AC2	SOFTWARE	ARG A:3 , SER A:74 , SER A:77	BINDING SITE FOR RESIDUE CL A1210
3	AC3	SOFTWARE	HIS A:64 , SER A:67 , ASN A:82 , PHE A:86 , HIS A:100 , ARG A:104 , PRO A:105 , VAL A:113 , GLN A:116 , ILE A:134 , SER A:138 , LEU A:174 , MG A:1212 , HOH A:1214 , HOH A:1215 , HOH A:2105	BINDING SITE FOR RESIDUE DXT A1211
4	AC4	SOFTWARE	HIS A:100 , DXT A:1211 , HOH A:1213 , HOH A:1214 , HOH A:1215	BINDING SITE FOR RESIDUE MG A1212

(no "SS Bond" information available for 2XRL)

(no "Cis Peptide Bond" information available for 2XRL)

(no "SAP(SNP)/Variant" information available for 2XRL)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_TETR_2	PS50977	TetR-type HTH domain profile.	TETR4_ECOLX	3-63	1	A:3-63
2	HTH_TETR_1	PS01081	TetR-type HTH domain signature.	TETR4_ECOLX	21-52	1	A:21-52

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_TETR_2	PS50977	TetR-type HTH domain profile.	TETR4_ECOLX	3-63	2	A:3-63
2	HTH_TETR_1	PS01081	TetR-type HTH domain signature.	TETR4_ECOLX	21-52	2	A:21-52

(no "Exon" information available for 2XRL)

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:207
 aligned with TETR4_ECOLX | P0ACT4 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:207
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       
          TETR4_ECOLX     2 ARLNRESVIDAALELLNETGIDGLTTRKLAQKLGIEQPTLYWHVKNKRALLDALAVEILARHHDYSLPAAGESWQSFLRNNAMSFRRALLRYRDGAKVHLGTRPDEKQYDTVETQLRFMTENGFSLRDGLYAISAVSHFTLGAVLEQQEHTAALTDRPAAPDENLPPLLREALQIMDSDDGEQAFLHGLESLIRGFEVQLTALLQIV 208
               SCOP domains d2xrla1 A:2-67 automated matches                                  d2xrla2 A:68-208 automated matches                                                                                                            SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -HTH_TETR_2  PDB: A:3-63 UniProt: 3-63                        ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------HTH_TETR_1  PDB: A:21-52        ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xrl A   2 SRLNRESVIDAALELLNETGIDGLTTRKLAQKLGIEQPTLYWHVKNKRALLDALAVEILARHHDYSLPAAGESWQSFLRNNAMSFRRALLRYRDGAKVHLGARPDEKQYDTVETQLRFMTENGFSLRDGLYAISAVSHFTLGAVLEQQEHTAALTDRPAAPDENLPPLLREALQIMDSDDGEQAFLHGLESLIRGFEVQLTALLQIV 208
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201

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 2XRL)

(no "Pfam Domain" information available for 2XRL)

Asymmetric Unit(hide GO term definitions)

Chain A (TETR4_ECOLX | P0ACT4)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
biological process
	GO:0045892	negative regulation of transcription, DNA-templated	Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	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:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.

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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2xrl)

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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	2xrl
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1a6i	TET REPRESSOR, CLASS D VARIANT
1bj0	TETRACYCLINE CHELATED MG2+ -ION INITIATES HELIX UNWINDING FOR TET REPRESSOR INDUCTION
1bjy	TETRACYCLINE CHELATED MG2+ -ION INITIATES HELIX UNWINDING FOR TET REPRESSOR INDUCTION
1bjz	TETRACYCLINE CHELATED MG2+ -ION INITIATES HELIX UNWINDING FOR TET REPRESSOR INDUCTION
1du7	CRYSTAL STRUCTURE OF TET REPRESSOR CLASS D WITH 4- EPI- TETRACYCLINE
1ork	TET REPRESSOR, CLASS D IN COMPLEX WITH 9-(N,N- DIMETHYLGLYCYLAMIDO)-6-DEMETHYL-6-DEOXY-TETRACYCLINE
1qpi	CRYSTAL STRUCTURE OF TETRACYCLINE REPRESSOR/OPERATOR COMPLEX
2tct	MOL_ID: 1; MOLECULE: TETRACYCLINE REPRESSOR; CHAIN: NULL ; SYNONYM: TET REPRESSOR, CLASS D; ENGINEERED: YES
2trt	TETRACYCLINE REPRESSOR CLASS D
2vke	TET REPRESSOR CLASS D COMPLEXED WITH COBALT AND TETRACYCLINE
2vkv	TETR (BD) VARIANT L17G WITH REVERSE PHENOTYPE
2x6o	TET REPRESSOR CLASS D IN COMPLEX WITH 7-CHLOR-2- CYANO-ISO-TETRACYCLINE
2x9d	TET REPRESSOR (CLASS D) IN COMPLEX WITH ISO-7- CHLORTETRACYCLINE
2xb5	TET REPRESSOR (CLASS D) IN COMPLEX WITH 7- IODOTETRACYCLINE
2xgc	CRYSTAL STRUCTURE OF A DESIGNED HETERODIMERIC VARIANT T -A(I)B OF THE TETRACYCLINE REPRESSOR
2xgd	CRYSTAL STRUCTURE OF A DESIGNED HOMODIMERIC VARIANT T- A(L)A(L) OF THE TETRACYCLINE REPRESSOR
2xge	CRYSTAL STRUCTURE OF A DESIGNED HETERODIMERIC VARIANT T -A(A)B OF THE TETRACYCLINE REPRESSOR
2xps	TETR(D) IN COMPLEX WITH ANHYDROTETRACYCLINE AND MAGNESIUM
2xpt	TETR(D) IN COMPLEX WITH MINOCYCLINE AND MAGNESIUM.
2xpu	TETR(D) IN COMPLEX WITH ANHYDROTETRACYCLINE.
2xpv	TETR(D) IN COMPLEX WITH MINOCYCLINE AND MG.
2xpw	TETR(D) IN COMPLEX WITH OXYTETRACYCLINE AND MAGNESIUM.
3zqf	STRUCTURE OF TETRACYCLINE REPRESSOR IN COMPLEX WITH ANTIINDUCER PEPTIDE-TAP1
3zqg	STRUCTURE OF TETRACYCLINE REPRESSOR IN COMPLEX WITH ANTIINDUCER PEPTIDE-TAP2
3zqh	STRUCTURE OF TETRACYCLINE REPRESSOR IN COMPLEX WITH INDUCER PEPTIDE-TIP3
3zqi	STRUCTURE OF TETRACYCLINE REPRESSOR IN COMPLEX WITH INDUCER PEPTIDE-TIP2

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (2, 2)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

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