1ZES - JenaLib

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Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   BEF3- ACTIVATED PHOB RECEIVER DOMAIN

Authors :   P. Bachhawat, G. T. Montelione, A. M. Stock

Date :   19 Apr 05 (Deposition) - 20 Sep 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

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

Keywords :   Chey-Like Fold, Response Regulator, Transcription Factor, Phob, Activated, Transcription Activator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   P. Bachhawat, G. V. Swapna, G. T. Montelione, A. M. Stock
Mechanism Of Activation For Transcription Factor Phob Suggested By Different Modes Of Dimerization In The Inactive And Active States.
Structure V. 13 1353 2005
PubMed-ID: 16154092 | Reference-DOI: 10.1016/J.STR.2005.06.006
(for further references see the PDB file header)

Molecule 1 - PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PEF28
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PJES307
	Fragment	:	N-TERMINAL DOMAIN (RESIDUES 1-125)
	Gene	:	PHOB
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Other Details	:	RESTRICTION SITES NDE1, BAMH1

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	BEF	3	Ligand/Ion	BERYLLIUM TRIFLUORIDE ION
2	MG	3	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	BEF	2	Ligand/Ion	BERYLLIUM TRIFLUORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	BEF	2	Ligand/Ion	BERYLLIUM TRIFLUORIDE ION
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP C:10 , ASP C:53 , MET C:55 , BEF C:203 , HOH C:309 , HOH C:315	BINDING SITE FOR RESIDUE MG C 301
2	AC2	SOFTWARE	ASP A:10 , ASP A:53 , MET A:55 , BEF A:201 , HOH A:303 , HOH A:304	BINDING SITE FOR RESIDUE MG A 302
3	AC3	SOFTWARE	ASP B:10 , ASP B:53 , MET B:55 , BEF B:202 , HOH B:304 , HOH B:307	BINDING SITE FOR RESIDUE MG B 303
4	AC4	SOFTWARE	ASP A:53 , TRP A:54 , MET A:55 , THR A:83 , ALA A:84 , LYS A:105 , MG A:302 , HOH A:303 , HOH A:304 , HOH A:332	BINDING SITE FOR RESIDUE BEF A 201
5	AC5	SOFTWARE	ASP B:53 , TRP B:54 , MET B:55 , THR B:83 , ALA B:84 , LYS B:105 , MG B:303 , HOH B:304 , HOH B:307	BINDING SITE FOR RESIDUE BEF B 202
6	AC6	SOFTWARE	ASP C:53 , TRP C:54 , MET C:55 , THR C:83 , ALA C:84 , LYS C:105 , MG C:301 , HOH C:309	BINDING SITE FOR RESIDUE BEF C 203

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

Asymmetric Unit

No.	Residues
1	Glu A:44	-	Pro A:45
2	Lys A:105	-	Pro A:106
3	Lys B:105	-	Pro B:106
4	Glu C:44	-	Pro C:45
5	Lys C:105	-	Pro C:106

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

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RESPONSE_REGULATORY	PS50110	Response regulatory domain profile.	PHOB_ECO57	4-120	3	A:4-120 B:4-120 C:4-120
1	RESPONSE_REGULATORY	PS50110	Response regulatory domain profile.	PHOB_ECOLI	4-120	3	A:4-120 B:4-120 C:4-120

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RESPONSE_REGULATORY	PS50110	Response regulatory domain profile.	PHOB_ECO57	4-120	2	A:4-120 - -
1	RESPONSE_REGULATORY	PS50110	Response regulatory domain profile.	PHOB_ECOLI	4-120	2	A:4-120 - -

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RESPONSE_REGULATORY	PS50110	Response regulatory domain profile.	PHOB_ECO57	4-120	2	- B:4-120 C:4-120
1	RESPONSE_REGULATORY	PS50110	Response regulatory domain profile.	PHOB_ECOLI	4-120	2	- B:4-120 C:4-120

(no "Exon" information available for 1ZES)

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 PHOB_ECO57 | P0AFJ6 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:121
                                    12        22        32        42        52        62        72        82        92       102       112       122 
           PHOB_ECO57     3 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRRI 123
               SCOP domains d1zesa_ A: automated matches                                                                                              SCOP domains
               CATH domains 1zesA00 A:3-123  [code=3.40.50.2300, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhhh......eeee.......hhhhhhhhhhhh.......eeeee...hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -RESPONSE_REGULATORY  PDB: A:4-120 UniProt: 4-120                                                                     --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zes A   3 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRRI 123
                                    12        22        32        42        52        62        72        82        92       102       112       122

Chain A from PDB  Type:PROTEIN  Length:121
 aligned with PHOB_ECOLI | P0AFJ5 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:121
                                    12        22        32        42        52        62        72        82        92       102       112       122 
           PHOB_ECOLI     3 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRRI 123
               SCOP domains d1zesa_ A: automated matches                                                                                              SCOP domains
               CATH domains 1zesA00 A:3-123  [code=3.40.50.2300, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhhh......eeee.......hhhhhhhhhhhh.......eeeee...hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -RESPONSE_REGULATORY  PDB: A:4-120 UniProt: 4-120                                                                     --- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zes A   3 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRRI 123
                                    12        22        32        42        52        62        72        82        92       102       112       122

Chain B from PDB  Type:PROTEIN  Length:118
 aligned with PHOB_ECO57 | P0AFJ6 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:120
                                    12        22        32        42        52        62        72        82        92       102       112       122
           PHOB_ECO57     3 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRR 122
               SCOP domains d1zesb_ B: automated matches                                                                                             SCOP domains
               CATH domains 1zesB00 B:3-122  [code=3.40.50.2300, no n  ame defined]                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhhh.--...eeee.......hhhhhhhhhhhh.......eeeee...hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -RESPONSE_REGULATORY  PDB: B:4-120 UniProt: 4-120                                                                     -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1zes B   3 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLN--WPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRR 122
                                    12        22        32        42|  |    52        62        72        82        92       102       112       122
                                                                   43 46

Chain B from PDB  Type:PROTEIN  Length:118
 aligned with PHOB_ECOLI | P0AFJ5 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:120
                                    12        22        32        42        52        62        72        82        92       102       112       122
           PHOB_ECOLI     3 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRR 122
               SCOP domains d1zesb_ B: automated matches                                                                                             SCOP domains
               CATH domains 1zesB00 B:3-122  [code=3.40.50.2300, no n  ame defined]                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhhh.--...eeee.......hhhhhhhhhhhh.......eeeee...hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) -RESPONSE_REGULATORY  PDB: B:4-120 UniProt: 4-120                                                                     -- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1zes B   3 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLN--WPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRR 122
                                    12        22        32        42|  |    52        62        72        82        92       102       112       122
                                                                   43 46

Chain C from PDB  Type:PROTEIN  Length:120
 aligned with PHOB_ECO57 | P0AFJ6 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:120
                                    12        22        32        42        52        62        72        82        92       102       112       122
           PHOB_ECO57     3 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRR 122
               SCOP domains d1zesc_ C: automated matches                                                                                             SCOP domains
               CATH domains 1zesC00 C:3-122  [code=3.40.50.2300, no name defined]                                                                    CATH domains
           Pfam domains (1) --Response_reg-1zesC01 C:5-117                                                                                     ----- Pfam domains (1)
           Pfam domains (2) --Response_reg-1zesC02 C:5-117                                                                                     ----- Pfam domains (2)
           Pfam domains (3) --Response_reg-1zesC03 C:5-117                                                                                     ----- Pfam domains (3)
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhh........eeee.......hhhhhhhhhhhh.......eeeee...hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -RESPONSE_REGULATORY  PDB: C:4-120 UniProt: 4-120                                                                     -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1zes C   3 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRR 122
                                    12        22        32        42        52        62        72        82        92       102       112       122

Chain C from PDB  Type:PROTEIN  Length:120
 aligned with PHOB_ECOLI | P0AFJ5 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:120
                                    12        22        32        42        52        62        72        82        92       102       112       122
           PHOB_ECOLI     3 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRR 122
               SCOP domains d1zesc_ C: automated matches                                                                                             SCOP domains
               CATH domains 1zesC00 C:3-122  [code=3.40.50.2300, no name defined]                                                                    CATH domains
           Pfam domains (1) --Response_reg-1zesC01 C:5-117                                                                                     ----- Pfam domains (1)
           Pfam domains (2) --Response_reg-1zesC02 C:5-117                                                                                     ----- Pfam domains (2)
           Pfam domains (3) --Response_reg-1zesC03 C:5-117                                                                                     ----- Pfam domains (3)
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhh........eeee.......hhhhhhhhhhhh.......eeeee...hhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (2) -RESPONSE_REGULATORY  PDB: C:4-120 UniProt: 4-120                                                                     -- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 1zes C   3 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRR 122
                                    12        22        32        42        52        62        72        82        92       102       112       122

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: CheY-related (166)

Protein domain: automated matches (29)

Escherichia coli [TaxId: 562] (4)

1a	d1zesa_	A:
1b	d1zesb_	B:
1c	d1zesc_	C:

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	1zesA00	A:3-123
1b	1zesC00	C:3-122
1c	1zesB00	B:3-122

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CheY (97)

Family: Response_reg (94)

Escherichia coli O157:H7 (7)

1a	Response_reg-1zesC01	C:5-117
1b	Response_reg-1zesC02	C:5-117
1c	Response_reg-1zesC03	C:5-117

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (PHOB_ECOLI | P0AFJ5)

molecular function
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0001108	bacterial-type RNA polymerase holo enzyme binding	Interacting selectively and non-covalently with the basal transcription machinery which is composed of a bacterial-type RNA polymerase core enzyme and a sigma factor, the minimal set of factors required for formation of the preinitiation complex (PIC) by a bacterial-type RNA polymerase.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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:0006817	phosphate ion transport	The directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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:2000142	regulation of DNA-templated transcription, initiation	Any process that modulates the frequency, rate or extent of DNA-templated transcription initiation.
	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.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain A,B,C (PHOB_ECO57 | P0AFJ6)

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:0006817	phosphate ion transport	The directed movement of phosphate into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	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.
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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(no "Related Entries Specified in the PDB File" available for 1ZES)

Description

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Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

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Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File