2NS8 - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   HOW AN IN VITRO SELECTED PEPTIDE MIMICS THE ANTIBIOTIC TETRACYCLINE TO INDUCE TET REPRESSOR

Authors :   S. R. Luckner, M. Klotzsche, C. Berens, W. Hillen, Y. A. Muller

Date :   03 Nov 06 (Deposition) - 24 Jul 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.55

Chains :   Asym. Unit : A,B,C,D,E,F,G,H,Z
Biol. Unit 1: A,B,E,H,Z  (1x)
Biol. Unit 2: C,D,F,G  (1x)
Biol. Unit 3: A (1x),B (1x),C (1x),D (1x),E (1x),F (1x),G (1x),H (1x),Z (1x)

Keywords :   Transcription Regulator, Helix-Turn-Helix, Bound Repressor-Inducing Peptide, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. R. Luckner, M. Klotzsche, C. Berens, W. Hillen, Y. A. Muller
How An Agonist Peptide Mimics The Antibiotic Tetracycline T Induce Tet-Repressor
J. Mol. Biol. V. 368 780 2007
PubMed-ID: 17374541 | Reference-DOI: 10.1016/J.JMB.2007.02.030

Molecule 1 - TETRACYCLINE REPRESSOR PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PWH610
	Expression System Strain	:	RB791
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TETR
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Other Details	:	RESIDUES 1-187 ARE FROM VARIANT B, RESIDUES 188-208 ARE FROM VARIANT D
	Strain	:	K12

Molecule 2 - 16 RESIDUE PEPTIDE TIP (TRANSCRIPTION INDUCING PEPTIDE)
	Chains	:	H, E, F, G, Z
	Engineered	:	YES
	Other Details	:	PEPTIDE HAS BEEN SYNTHESIZED
	Synthetic	:	YES

		1	2	3	4	5	6	7	8	9
Asymmetric Unit	:	A	B	C	D	E	F	G	H	Z
Biological Unit 1 (1x)	:	A	B			E			H	Z
Biological Unit 2 (1x)	:			C	D		F	G
Biological Unit 3 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)	E (1x)	F (1x)	G (1x)	H (1x)	Z (1x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	ACE	4	Mod. Amino Acid	ACETYL GROUP

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	ACE	2	Mod. Amino Acid	ACETYL GROUP

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	ACE	-1	Mod. Amino Acid	ACETYL GROUP

(no "Site" information available for 2NS8)

(no "SS Bond" information available for 2NS8)

(no "Cis Peptide Bond" information available for 2NS8)

(no "SAP(SNP)/Variant" information available for 2NS8)

Asymmetric Unit (2, 7)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_TETR_2	PS50977	TetR-type HTH domain profile.	TETR2_ECOLX	3-63	3	A:3-63 C:3-63 D:3-63
2	HTH_TETR_1	PS01081	TetR-type HTH domain signature.	TETR2_ECOLX	21-52	4	A:21-52 B:21-52 C:21-52 D:21-52

Biological Unit 1 (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_TETR_2	PS50977	TetR-type HTH domain profile.	TETR2_ECOLX	3-63	1	A:3-63 - -
2	HTH_TETR_1	PS01081	TetR-type HTH domain signature.	TETR2_ECOLX	21-52	2	A:21-52 B: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.	TETR2_ECOLX	3-63	2	- C:3-63 D:3-63
2	HTH_TETR_1	PS01081	TetR-type HTH domain signature.	TETR2_ECOLX	21-52	2	- - C:21-52 D:21-52

Biological Unit 3 (2, 7)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	HTH_TETR_2	PS50977	TetR-type HTH domain profile.	TETR2_ECOLX	3-63	3	A:3-63 C:3-63 D:3-63
2	HTH_TETR_1	PS01081	TetR-type HTH domain signature.	TETR2_ECOLX	21-52	4	A:21-52 B:21-52 C:21-52 D:21-52

(no "Exon" information available for 2NS8)

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:200
 aligned with TETR2_ECOLX | P04483 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:200
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202
          TETR2_ECOLX     3 RLDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAIEMLDRHHTHFCPLEGESWQDFLRNNAKSFRCALLSHRDGAKVHLGTRPTEKQYETLENQLAFLCQQGFSLENALYALSAVGHFTLGCVLEDQEHQVAKEERETPTTDSMPPLLRQAIELFDHQGAEPAFLFGLELIICGLEKQLK 202
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ns8A01 A:3-66 Homeodomain-like                                 2ns8A02 A:67-202 Tetracycline Repressor, domain 2                                                                                        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhhhhh....hhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh 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
                 2ns8 A   3 RLDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAIEMLDRHHTHFSPLEGESWQDFLRNNAKSFRNALLSHRDGAKVHLGTRPTEKQYETLENQLAFLTQQGFSLENALYALSAVGHFTLGSVLEDQEHQVAKEERETPTTDSMPPLLRQAIELFDHQGAEPAFLHGLESLIRGFEVQLT 202
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202

Chain B from PDB  Type:PROTEIN  Length:204
 aligned with TETR2_ECOLX | P04483 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:204
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203    
          TETR2_ECOLX     4 LDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAIEMLDRHHTHFCPLEGESWQDFLRNNAKSFRCALLSHRDGAKVHLGTRPTEKQYETLENQLAFLCQQGFSLENALYALSAVGHFTLGCVLEDQEHQVAKEERETPTTDSMPPLLRQAIELFDHQGAEPAFLFGLELIICGLEKQLKCESGS 207
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2ns8B01 B:4-66 Homeodomain-like                                2ns8B02 B:67-207 Tetracycline Repressor, domain 2                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh...hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) HTH_TETR_2  PDB: - UniProt: 3-63                            ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) -----------------HTH_TETR_1  PDB: B:21-52        ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2ns8 B   4 LDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAIEMLDRHHTHFSPLEGESWQDFLRNNAKSFRNALLSHRDGAKVHLGTRPTEKQYETLENQLAFLTQQGFSLENALYALSAVGHFTLGSVLEDQEHQVAKEERETPTTDSMPPLLRQAIELFDHQGAEPAFLHGLESLIRGFEVQLTALLQI 207
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203

Chain C from PDB  Type:PROTEIN  Length:206
 aligned with TETR2_ECOLX | P04483 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:206
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201      
          TETR2_ECOLX     2 SRLDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAIEMLDRHHTHFCPLEGESWQDFLRNNAKSFRCALLSHRDGAKVHLGTRPTEKQYETLENQLAFLCQQGFSLENALYALSAVGHFTLGCVLEDQEHQVAKEERETPTTDSMPPLLRQAIELFDHQGAEPAFLFGLELIICGLEKQLKCESGS 207
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ns8C01 C:2-66 Homeodomain-like                                  2ns8C02 C:67-207 Tetracycline Repressor, domain 2                                                                                             CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhhhh...hhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -HTH_TETR_2  PDB: C:3-63 UniProt: 3-63                        ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE (1)
                PROSITE (2) -------------------HTH_TETR_1  PDB: C:21-52        ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ns8 C   2 SRLDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAIEMLDRHHTHFSPLEGESWQDFLRNNAKSFRNALLSHRDGAKVHLGTRPTEKQYETLENQLAFLTQQGFSLENALYALSAVGHFTLGSVLEDQEHQVAKEERETPTTDSMPPLLRQAIELFDHQGAEPAFLHGLESLIRGFEVQLTALLQI 207
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201

Chain D from PDB  Type:PROTEIN  Length:198
 aligned with TETR2_ECOLX | P04483 from UniProtKB/Swiss-Prot  Length:207

    Alignment length:201
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202 
          TETR2_ECOLX     3 RLDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAIEMLDRHHTHFCPLEGESWQDFLRNNAKSFRCALLSHRDGAKVHLGTRPTEKQYETLENQLAFLCQQGFSLENALYALSAVGHFTLGCVLEDQEHQVAKEERETPTTDSMPPLLRQAIELFDHQGAEPAFLFGLELIICGLEKQLKC 203
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2ns8D01 D:3-66 Homeodomain-like                                 2ns8D02 D:67-203 Tetracycline Repressor, domain 2                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh..hhhhhhh....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..---...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) HTH_TETR_2  PDB: D:3-63 UniProt: 3-63                        -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------HTH_TETR_1  PDB: D:21-52        ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ns8 D   3 RLDKSKVINSALELLNEVGIEGLTTRKLAQKLGVEQPTLYWHVKNKRALLDALAIEMLDRHHTHFSPLEGESWQDFLRNNAKSFRNALLSHRDGAKVHLGTRPTEKQYETLENQLAFLTQQGFSLENALYALSAVGHFTLGSVLEDQEHQVAKEERET---DSMPPLLRQAIELFDHQGAEPAFLHGLESLIRGFEVQLTA 203
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       | - |     172       182       192       202 
                                                                                                                                                                                       160 164

Chain E from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ....hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 2ns8 E   0 xWTWNAYAFAAP  11
                            |        9  
                            0-ACE

Chain F from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 2ns8 F   0 xWTWNAYAFAAPS  12
                            |        9   
                            0-ACE

Chain G from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ............ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 2ns8 G   0 xWTWNAYAFAAP  11
                            |        9  
                            0-ACE

Chain H from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author ............. Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 2ns8 H   0 xWTWNAYAFAAPS  12
                            |        9   
                            0-ACE

Chain Z from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 2ns8 Z   1 WTWN   4

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 2NS8)

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 k12. Organism_taxid: 83333. Strain: k12. (2)

1a	2ns8B01	B:4-66
1b	2ns8A01	A:3-66
1c	2ns8D01	D:3-66
1d	2ns8C01	C:2-66

Topology: Tetracycline Repressor; domain 2 (126)

Homologous Superfamily: Tetracycline Repressor, domain 2 (124)

Escherichia coli k12. Organism_taxid: 83333. Strain: k12. (2)

2a	2ns8B02	B:67-207
2b	2ns8C02	C:67-207
2c	2ns8A02	A:67-202
2d	2ns8D02	D:67-203

(no "Pfam Domain" information available for 2NS8)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (TETR2_ECOLX | P04483)

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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(no "Sites" information available for 2ns8)

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	2ns8
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1qpi	CRYSTAL STRUCTURE OF TETRACYCLINE REPRESSOR/OPERATOR COMPLEX
2ns7
2tct	THE COMPLEX FORMED BETWEEN TET REPRESSOR AND TETRACYCLINE- MG2+ REVEALS MECHANISM OF ANTIBIOTIC RESISTANCE

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 4)

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