2XGE - JenaLib

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Title :   CRYSTAL STRUCTURE OF A DESIGNED HETERODIMERIC VARIANT T-A(A) B OF THE TETRACYCLINE REPRESSOR

Authors :   M. T. Stiebritz, S. Wengrzik, J. P. Richter, Y. A. Muller

Date :   03 Jun 10 (Deposition) - 22 Sep 10 (Release) - 20 Oct 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.14

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

Keywords :   Chimera, Transcription, Transcription Regulation, Antibiotic Resistance (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. T. Stiebritz, S. Wengrzik, D. L. Klein, J. P. Richter, A. Srebrzynski, S. Weiler, Y. A. Muller
Computational Design Of A Chain-Specific Tetracycline Repressor Heterodimer.
J. Mol. Biol. V. 403 371 2010
PubMed-ID: 20816982 | Reference-DOI: 10.1016/J.JMB.2010.07.055

Molecule 1 - TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 1-50,51-208
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

Molecule 2 - TETRACYCLINE REPRESSOR PROTEIN CLASS B FROM TRANSPOSON TN10, TETRACYCLINE REPRESSOR PROTEIN CLASS D
	Chains	:	B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	RESIDUES 1-50,51-208
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	EDO	-1	Ligand/Ion	1,2-ETHANEDIOL
3	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:131 , LEU A:174 , MET A:177 , ASP A:178 , LEU B:131 , LEU B:174 , MET B:177 , ASP B:178	BINDING SITE FOR RESIDUE EDO A 592
2	AC2	SOFTWARE	HIS A:100 , THR A:103 , HIS B:100 , THR B:103	BINDING SITE FOR RESIDUE NA A 593
3	AC3	SOFTWARE	ARG A:3 , SER A:74 , ARG B:3 , SER B:74	BINDING SITE FOR RESIDUE CL A 594

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

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

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

Asymmetric Unit (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 B:3-63
2	HTH_TETR_1	PS01081	TetR-type HTH domain signature.	TETR4_ECOLX	21-52	2	A:21-52 B: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 -

Biological Unit 2 (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	- B:3-63
2	HTH_TETR_1	PS01081	TetR-type HTH domain signature.	TETR4_ECOLX	21-52	2	- B:21-52

(no "Exon" information available for 2XGE)

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:193
 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 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2xgeA01 A:2-66 Homeodomain-like                                  2xgeA02 A:67-208 Tetracycline Repressor, domain 2                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhheeeeeeehhhhhheeeehhhhheeeeehhhhhhhhhhhhhhhheeee..eeeeehhhhhhhhhhhhhhhheeeeehhhhhhee..ehhhhhhhhhhhhhhheeeeehhhhhhhhhhhhhhhhhhhhhhhe.--------------.hhhhheeeeeeeeeeehhhhhhhheeeehhhhhhhheeeee. 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
                 2xge A   2 SRLDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAVEILARHHDYSLPAAGESWQSFLRNNAMSFRRALLRYRDGAKVHLGTRPDEKQYDTVETQLRFMTENGFSLRDGLYAISWVSHFTLGAVLEQQEH--------------LPPLLREALQIMDSDDGEQAFLHGLESAIRGIEVQLTALLQIV 208
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151         -    |  171       181       191       201       
                                                                                                                                                                               151            166

Chain B from PDB  Type:PROTEIN  Length:193
 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 --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2xgeB01 B:2-66 Homeodomain-like                                  2xgeB02 B:67-208 Tetracycline Repressor, domain 2                                                                                              CATH domains
           Pfam domains (1) -------------------------------------------------TetR_------------TetR_C-2xgeB03 B:68-201                                                                                                               ------- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------TetR_------------TetR_C-2xgeB04 B:68-201                                                                                                               ------- Pfam domains (2)
         Sec.struct. author .eeehhhhhhhhhhhhhhheeeeeeehhhhhheeee..eeeeeeeehhhhhhhhhhhhhhhheeee..eeeeehhhhhhhhhhhhhhhheeeeehhhhhhee..ehhhhhhhhhhhhhhheeeeehhhhhhhhhhhhhhhhhhhhhhhe.--------------...eeeeeeeeeeeeeehhhhhhhheeeehhhhhhhheeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -HTH_TETR_2  PDB: B:3-63 UniProt: 3-63                        ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------HTH_TETR_1  PDB: B:21-52        ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2xge B   2 SRLDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAVEILARHHDYSLPAAGESWQSFLRNNAMSFRRALLRYRDGAKVHLGTRPDEKQYDTVETQLRFMTENGFSLRDGLYAISAVSHATLGAVLEQQEH--------------LPPLLREALQIMDSDDGEQAFLHGLEWLIRGFEVQLTALLQIV 208
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151         -    |  171       181       191       201       
                                                                                                                                                                               151            166

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 2XGE)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Arc Repressor Mutant, subunit A (1030)

Homologous Superfamily: Homeodomain-like (288)

Escherichia coli. Organism_taxid: 562. (17)

1a	2xgeA01	A:2-66
1b	2xgeB01	B:2-66

Topology: Tetracycline Repressor; domain 2 (126)

Homologous Superfamily: Tetracycline Repressor, domain 2 (124)

Escherichia coli. Organism_taxid: 562. (10)

2a	2xgeA02	A:67-208
2b	2xgeB02	B:67-208

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HTH (544)

Family: TetR_N (84)

Escherichia coli (12)

1a	TetR_N-2xgeB01	B:51-55
1b	TetR_N-2xgeB02	B:51-55

Clan: TetR_C (33)

Family: TetR_C (16)

Escherichia coli (12)

2a	TetR_C-2xgeB03	B:68-201
2b	TetR_C-2xgeB04	B:68-201

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2xge)

Biological Units
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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

Description

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Ligands, Modified Residues, Ions (3, 3)

Sites (3, 3)

SS Bonds (0, 0)

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Exons (0, 0)

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CATH Domains (2, 4)

Pfam Domains (2, 4)

Gene Ontology (6, 12)

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