2JB9 - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   PHOB RESPONSE REGULATOR RECEIVER DOMAIN CONSTITUTIVELY-ACTIVE DOUBLE MUTANT D10A AND D53E.

Authors :   C. Ferrer-Orta, R. Arribas-Bosacoma, S. -K. Kim, A. G. Blanco, P. J. B. P F. X. Gomis-Ruth, B. L. Wanner, M. Coll, M. Sola

Date :   05 Dec 06 (Deposition) - 04 Jan 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Sensory Transduction, Dna-Binding, Two-Component Regulatory System, Gene Regulation, Phosphate Transport, Activation Of The Pho Regulon, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Arribas-Bosacoma, S. -K. Kim, C. Ferrer-Orta, A. G. Blanco, P. J. B. Pereira, F. X. Gomis-Ruth, B. L. Wanner, M. Coll, M. Sola
The X-Ray Crystal Structures Of Two Constitutively Active Mutants Of The E. Coli Phob Receiver Domain Give Insights Into Activation
J. Mol. Biol. V. 366 626 2007
PubMed-ID: 17182055 | Reference-DOI: 10.1016/J.JMB.2006.11.038
(for further references see the PDB file header)

Molecule 1 - PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBAT-4
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Fragment	:	RECEIVER DOMAIN, RESIDUES 1-127
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	PHOB RESPONSE REGULATOR D10A-D53E

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2JB9)

(no "Site" information available for 2JB9)

(no "SS Bond" information available for 2JB9)

Asymmetric Unit

No.	Residues
1	Glu A:44	-	Pro A:45
2	Lys A:105	-	Pro A:106
3	Met B:73	-	Thr B:74
4	Lys B:105	-	Pro B:106

(no "SAP(SNP)/Variant" information available for 2JB9)

Asymmetric Unit (1, 2)

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

Biological Unit 1 (1, 1)

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

Biological Unit 2 (1, 1)

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

(no "Exon" information available for 2JB9)

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
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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 d2jb9a_ A: automated matches                                                                                              SCOP domains
               CATH domains 2jb9A00 A:3-123  [code=3.40.50.2300, no name defined]                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhh........eeeee......hhhhhhhhhh.hhhhhh..eeeeeehhhhhhhhhhh.....eeeee..hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -RESPONSE_REGULATORY  PDB: A:4-120 UniProt: 4-120                                                                     --- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jb9 A   3 RRILVVEAEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLEWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRRI 123
                                    12        22        32        42        52        62        72        82        92       102       112       122

Chain B from PDB  Type:PROTEIN  Length:122
 aligned with PHOB_ECOLI | P0AFJ5 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:122
                                    11        21        31        41        51        61        71        81        91       101       111       121  
           PHOB_ECOLI     2 ARRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRRI 123
               SCOP domains d2jb9b_ B: automated matches                                                                                               SCOP domains
               CATH domains 2jb9B00 B:2-123  [code=3.40.50.2300, no name defined]                                                                      CATH domains
           Pfam domains (1) ---Response_reg-2jb9B01 B:5-117                                                                                     ------ Pfam domains (1)
           Pfam domains (2) ---Response_reg-2jb9B02 B:5-117                                                                                     ------ Pfam domains (2)
         Sec.struct. author ..eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhhh.......eeeee......hhhhhhhhhh.........eeeee.hhhhhhhhh.......eeee...hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --RESPONSE_REGULATORY  PDB: B:4-120 UniProt: 4-120                                                                     --- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 2jb9 B   2 ARRILVVEAEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLEWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRRI 123
                                    11        21        31        41        51        61        71        81        91       101       111       121

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	d2jb9a_	A:
1b	d2jb9b_	B:

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. (24)

1a	2jb9B00	B:2-123
1b	2jb9A00	A:3-123

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: CheY (97)

Family: Response_reg (94)

Escherichia coli (strain K12) (13)

1a	Response_reg-2jb9B01	B:5-117
1b	Response_reg-2jb9B02	B:5-117

Asymmetric Unit(hide GO term definitions)

Chain A,B (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.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Sites
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	Cis Peptide Bonds
		Glu A:44 - Pro A:45	[ RasMol ]
		Lys A:105 - Pro A:106	[ RasMol ]
		Lys B:105 - Pro B:106	[ RasMol ]
		Met B:73 - Thr B:74	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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Access by PDB/NDB ID
	2jb9
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
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Access by UniProt ID/Accession number
	PHOB_ECOLI \| P0AFJ5
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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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UniProtKB/Swiss-Prot
	PHOB_ECOLI \| P0AFJ5	:	1b00 1gxp 1gxq 1qqi 1zes 2iyn 2jba 2z33 3t72

1b00	PHOB RECEIVER DOMAIN FROM ESCHERICHIA COLI
1gxp	PHOB EFFECTOR DOMAIN IN COMPLEX WITH PHO BOX DNA.
1gxq	CRYSTAL STRUCTURE OF THE PHOB EFFECTOR DOMAIN
1qqi	SOLUTION STRUCTURE OF THE DEOXYRIBONUCLEIC ACID-BINDING AND TRANSACTIVATION DOMAIN OF PHOB FROM ESCHERICHIA COLI
1zes	BEF3- ACTIVATED PHOB RECEIVER DOMAIN
2iyn	THE CO-FACTOR-INDUCED PRE-ACTIVE CONFORMATION IN PHOB
2jba	PHOB RESPONSE REGULATOR RECEIVER DOMAIN CONSTITUTIVELY-ACTIVE DOUBLE MUTANT D53A AND Y102C.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (11, 11)

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