1ZGZ - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE RECEIVER DOMAIN OF TMAO RESPIRATORY SYSTEM RESPONSE REGULATOR TORR

Authors :   A. Toro-Roman, T. Wu, A. M. Stock

Date :   22 Apr 05 (Deposition) - 13 Dec 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: C,D  (1x)
Biol. Unit 3: A,B,C,D  (1x)

Keywords :   Two-Component System, Gene Regulation, Transcription Factor, Tmao Respiratory System, Doubly Wound Five-Stranded Beta-Alpha Fold, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Toro-Roman, T. Wu, A. M. Stock
A Common Dimerization Interface In Bacterial Response Regulators Kdpe And Torr.
Protein Sci. V. 14 3077 2005
PubMed-ID: 16322582 | Reference-DOI: 10.1110/PS.051722805

Molecule 1 - TORCAD OPERON TRANSCRIPTIONAL REGULATORY PROTEIN TORR
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PEF26 (PJES307 DERIVATIVE)
	Expression System Strain	:	B834(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	N-TERMINAL RECEIVER DOMAIN (RESIDUES 1-122)
	Gene	:	TORR
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D
Biological Unit 3 (1x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 15)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 7)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	MSE	6	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 3 (3, 15)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MSE	12	Mod. Amino Acid	SELENOMETHIONINE
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG C:85 , LEU D:104 , GLU D:105 , LEU D:106 , ARG D:107 , HOH D:407 , HOH D:450 , HOH D:451	BINDING SITE FOR RESIDUE SO4 D 401
2	AC2	SOFTWARE	LEU A:104 , LEU A:106 , ARG A:107	BINDING SITE FOR RESIDUE SO4 A 402
3	AC3	SOFTWARE	ARG B:66 , GLU B:70 , ARG D:66 , ARG D:69 , HOH D:430	BINDING SITE FOR RESIDUE GOL B 301

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

Asymmetric Unit

No.	Residues
1	Lys A:102	-	Pro A:103
2	Lys B:102	-	Pro B:103
3	Lys C:102	-	Pro C:103
4	Lys D:102	-	Pro D:103

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

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RESPONSE_REGULATORY	PS50110	Response regulatory domain profile.	TORR_ECOLI	4-117	4	A:4-117 B:4-117 C:4-117 D:4-117

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RESPONSE_REGULATORY	PS50110	Response regulatory domain profile.	TORR_ECOLI	4-117	2	A:4-117 B:4-117 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RESPONSE_REGULATORY	PS50110	Response regulatory domain profile.	TORR_ECOLI	4-117	2	- - C:4-117 D:4-117

Biological Unit 3 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RESPONSE_REGULATORY	PS50110	Response regulatory domain profile.	TORR_ECOLI	4-117	4	A:4-117 B:4-117 C:4-117 D:4-117

(no "Exon" information available for 1ZGZ)

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:121
 aligned with TORR_ECOLI | P38684 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:121
                                    11        21        31        41        51        61        71        81        91       101       111       121 
           TORR_ECOLI     2 PHHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIMQNQSVDLILLDINLPDENGLMLTRALRERSTVGIILVTGRSDRIDRIVGLEMGADDYVTKPLELRELVVRVKNLLWRIDL 122
               SCOP domains d1zgza1 A:2-121 TorCAD operon transcriptional regulator TorD, N-terminal domain                                         - SCOP domains
               CATH domains 1zgzA00 A:2-122  [code=3.40.50.2300, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh...eeeee......hhhhhhhhhhh....eeeeee...hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RESPONSE_REGULATORY  PDB: A:4-117 UniProt: 4-117                                                                  ----- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zgz A   2 PHHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREImQNQSVDLILLDINLPDENGLmLTRALRERSTVGIILVTGRSDRIDRIVGLEmGADDYVTKPLELRELVVRVKNLLWRIDQ 122
                                    11        21        31        41|       51        61 |      71        81        91  |    101       111       121 
                                                                   42-MSE               63-MSE                         94-MSE

Chain B from PDB  Type:PROTEIN  Length:120
 aligned with TORR_ECOLI | P38684 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:120
                                    11        21        31        41        51        61        71        81        91       101       111       121
           TORR_ECOLI     2 PHHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIMQNQSVDLILLDINLPDENGLMLTRALRERSTVGIILVTGRSDRIDRIVGLEMGADDYVTKPLELRELVVRVKNLLWRID 121
               SCOP domains d1zgzb_ B: automated matches                                                                                             SCOP domains
               CATH domains 1zgzB00 B:2-121  [code=3.40.50.2300, no name defined]                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh...eeeee......hhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --RESPONSE_REGULATORY  PDB: B:4-117 UniProt: 4-117                                                                  ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1zgz B   2 PHHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREImQNQSVDLILLDINLPDENGLmLTRALRERSTVGIILVTGRSDRIDRIVGLEmGADDYVTKPLELRELVVRVKNLLWRID 121
                                    11        21        31        41|       51        61 |      71        81        91  |    101       111       121
                                                                   42-MSE               63-MSE                         94-MSE

Chain C from PDB  Type:PROTEIN  Length:120
 aligned with TORR_ECOLI | P38684 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:120
                                    11        21        31        41        51        61        71        81        91       101       111       121
           TORR_ECOLI     2 PHHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIMQNQSVDLILLDINLPDENGLMLTRALRERSTVGIILVTGRSDRIDRIVGLEMGADDYVTKPLELRELVVRVKNLLWRID 121
               SCOP domains d1zgzc_ C: automated matches                                                                                             SCOP domains
               CATH domains 1zgzC00 C:2-121  [code=3.40.50.2300, no name defined]                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhh...eeeee......hhhhhhhhhhhhh..eeeeeee..hhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --RESPONSE_REGULATORY  PDB: C:4-117 UniProt: 4-117                                                                  ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1zgz C   2 PHHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREImQNQSVDLILLDINLPDENGLmLTRALRERSTVGIILVTGRSDRIDRIVGLEmGADDYVTKPLELRELVVRVKNLLWRID 121
                                    11        21        31        41|       51        61 |      71        81        91  |    101       111       121
                                                                   42-MSE               63-MSE                         94-MSE

Chain D from PDB  Type:PROTEIN  Length:120
 aligned with TORR_ECOLI | P38684 from UniProtKB/Swiss-Prot  Length:230

    Alignment length:120
                                    11        21        31        41        51        61        71        81        91       101       111       121
           TORR_ECOLI     2 PHHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREIMQNQSVDLILLDINLPDENGLMLTRALRERSTVGIILVTGRSDRIDRIVGLEMGADDYVTKPLELRELVVRVKNLLWRID 121
               SCOP domains d1zgzd_ D: automated matches                                                                                             SCOP domains
               CATH domains 1zgzD00 D:2-121  [code=3.40.50.2300, no name defined]                                                                    CATH domains
           Pfam domains (1) ---Response_reg-1zgzD01 D:5-114                                                                                  ------- Pfam domains (1)
           Pfam domains (2) ---Response_reg-1zgzD02 D:5-114                                                                                  ------- Pfam domains (2)
           Pfam domains (3) ---Response_reg-1zgzD03 D:5-114                                                                                  ------- Pfam domains (3)
           Pfam domains (4) ---Response_reg-1zgzD04 D:5-114                                                                                  ------- Pfam domains (4)
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhh...eeeee......hhhhhhhhhhhhh..eeeeee...hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE --RESPONSE_REGULATORY  PDB: D:4-117 UniProt: 4-117                                                                  ---- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1zgz D   2 PHHIVIVEDEPVTQARLQSYFTQEGYTVSVTASGAGLREImQNQSVDLILLDINLPDENGLmLTRALRERSTVGIILVTGRSDRIDRIVGLEmGADDYVTKPLELRELVVRVKNLLWRID 121
                                    11        21        31        41|       51        61 |      71        81        91  |    101       111       121
                                                                   42-MSE               63-MSE                         94-MSE

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Flavodoxin-like (1057)

Superfamily: CheY-like (258)

Family: automated matches (82)

Protein domain: automated matches (82)

Escherichia coli [TaxId: 562] (6)

1a	d1zgzb_	B:
1b	d1zgzc_	C:
1c	d1zgzd_	D:

Family: CheY-related (166)

Protein domain: TorCAD operon transcriptional regulator TorD, N-terminal domain (1)

Escherichia coli [TaxId: 562] (1)

d1zgza1

A:2-121

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.2300, no name defined] (308)

Escherichia coli. Organism_taxid: 562. (30)

1a	1zgzA00	A:2-122
1b	1zgzB00	B:2-121
1c	1zgzC00	C:2-121
1d	1zgzD00	D:2-121

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CheY (97)

Family: Response_reg (94)

Escherichia coli (strain K12) (13)

1a	Response_reg-1zgzD01	D:5-114
1b	Response_reg-1zgzD02	D:5-114
1c	Response_reg-1zgzD03	D:5-114
1d	Response_reg-1zgzD04	D:5-114

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (TORR_ECOLI | P38684)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0000156	phosphorelay response regulator activity	Responds to a phosphorelay sensor to initiate a change in cell state or activity. The activity of the response regulator is regulated by transfer of a phosphate from a histidine residue in the sensor, to an aspartate residue in the response regulator. Many but not all response regulators act as transcriptional regulators to elicit a response.
biological process
	GO:0000160	phosphorelay signal transduction system	A conserved series of molecular signals found in prokaryotes and eukaryotes; involves autophosphorylation of a histidine kinase and the transfer of the phosphate group to an aspartate that then acts as a phospho-donor to response regulator proteins.
	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 Unit
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	Cis Peptide Bonds
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		Lys B:102 - Pro B:103	[ RasMol ]
		Lys C:102 - Pro C:103	[ RasMol ]
		Lys D:102 - Pro D:103	[ RasMol ]

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	1zgz
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 15)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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