2IYN - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   THE CO-FACTOR-INDUCED PRE-ACTIVE CONFORMATION IN PHOB

Authors :   M. Sola, D. L. Drew, A. G. Blanco, F. X. Gomis-Ruth, M. Coll

Date :   19 Jul 06 (Deposition) - 30 Aug 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.08

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: A,B  (1x)
Biol. Unit 5: C  (2x)

Keywords :   Transcription, Transcription Factor, Phosphate Transport, Activator, Sensory Transduction, Phosphate Regulation, Two-Component Regulatory System, Alpha/Beta Doubly-Wound Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Sola, D. L. Drew, A. G. Blanco, F. X. Gomis-Ruth, M. Coll
The Cofactor-Induced Pre-Active Conformation In Phob.
Acta Crystallogr. , Sect. D V. 62 1046 2006
PubMed-ID: 16929106 | Reference-DOI: 10.1107/S0907444906024541

Molecule 1 - PHOSPHATE REGULON TRANSCRIPTIONAL REGULATORY PROTEIN PHOB
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBAT4
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Fragment	:	RECEIVER DOMAIN, RESIDUES 1-127
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:	A	B
Biological Unit 5 (2x)	:			C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 3)

No.	Name	Count	Type	Full Name
1	MG	3	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 5 (0, 0)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:10 , ASP A:53 , MET A:55 , HOH A:2019 , HOH A:2020	BINDING SITE FOR RESIDUE MG A1122
2	AC2	SOFTWARE	ASP B:10 , ASP B:53 , MET B:55 , HOH B:2002 , HOH B:2016	BINDING SITE FOR RESIDUE MG B1125
3	AC3	SOFTWARE	ASP C:10 , ASP C:53 , MET C:55 , HOH C:2002 , HOH C:2003 , HOH C:2016	BINDING SITE FOR RESIDUE MG C1123

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

Asymmetric Unit

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

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

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
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, 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 -

Biological Unit 3 (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	- - C:4-120

Biological Unit 4 (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 5 (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	- - C:4-120

(no "Exon" information available for 2IYN)

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:110
 aligned with PHOB_ECOLI | P0AFJ5 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:119
                                    12        22        32        42        52        62        72        82        92       102       112         
           PHOB_ECOLI     3 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMR 121
               SCOP domains d2iyna_ A: automated matches                                                                                            SCOP domains
               CATH domains 2iynA00 A:3-121  [code=3.40.50.2300, no name defined]                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhh........eeeee.ee..eehhhhhhhhhh........eeeeee..---------.....eeeee..hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -RESPONSE_REGULATORY  PDB: A:4-120 UniProt: 4-120                                                                     - PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 2iyn A   3 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARG---------ETGADDYITKPFSPKELVARIKAVMR 121
                                    12        22        32        42        52        62        72        82   |     -   |   102       112         
                                                                                                              86        96

Chain B from PDB  Type:PROTEIN  Length:124
 aligned with PHOB_ECOLI | P0AFJ5 from UniProtKB/Swiss-Prot  Length:229

    Alignment length:124
                                    10        20        30        40        50        60        70        80        90       100       110       120    
           PHOB_ECOLI     1 MARRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRRIS 124
               SCOP domains d2iynb_ B: automated matches                                                                                                 SCOP domains
               CATH domains 2iynB00 B:1-124  [code=3.40.50.2300, no name defined]                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee..hhhhhhhhhhhhhhh..eeeee.hhhhhhh........eeeee......hhhhhhhhhhh........eeeee..hhhhhhhh.......eeee...hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---RESPONSE_REGULATORY  PDB: B:4-120 UniProt: 4-120                                                                     ---- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 2iyn B   1 MARRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTARGEEEDRVRGLETGADDYITKPFSPKELVARIKAVMRRIS 124
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain C from PDB  Type:PROTEIN  Length:108
 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 d2iync_ C: automated matches                                                                                             SCOP domains
               CATH domains 2iynC00 C:3-122  [code=3.40.50.2300, no name defined]                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhh...eeeee.hhhhhhh........eeeee......hhhhhhhhhhh........eeeee.------------....eeee...hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -RESPONSE_REGULATORY  PDB: C:4-120 UniProt: 4-120                                                                     -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 2iyn C   3 RRILVVEDEAPIREMVCFVLEQNGFQPVEAEDYDSAVNQLNEPWPDLILLDWMLPGGSGIQFIKHLKRESMTRDIPVVMLTA------------TGADDYITKPFSPKELVARIKAVMRR 122
                                    12        22        32        42        52        62        72        82 |       -    |  102       112       122
                                                                                                            84           97

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	d2iyna_	A:
1b	d2iynb_	B:
1c	d2iync_	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. (24)

1a	2iynB00	B:1-124
1b	2iynA00	A:3-121
1c	2iynC00	C:3-122

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

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.

Asymmetric Unit
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	Cis Peptide Bonds
		Glu A:44 - Pro A:45	[ RasMol ]
		Glu B:44 - Pro B:45	[ RasMol ]
		Glu C:44 - Pro C:45	[ RasMol ]
		Lys A:105 - Pro A:106	[ RasMol ]
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		Lys C:105 - Pro C:106	[ RasMol ]

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Access by PDB/NDB ID
	2iyn
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	PHOB_ECOLI \| P0AFJ5
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UniProtKB/Swiss-Prot
	PHOB_ECOLI \| P0AFJ5	:	1b00 1gxp 1gxq 1qqi 1zes 2jb9 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

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 3)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 3)

Exons (0, 0)

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SCOP Domains (1, 3)

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Gene Ontology (11, 11)

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