2PR5 - JenaLib

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Title :   STRUCTURAL BASIS FOR LIGHT-DEPENDENT SIGNALING IN THE DIMERIC LOV PHOTOSENSOR YTVA (DARK STRUCTURE)

Authors :   A. Moglich, K. Moffat

Date :   03 May 07 (Deposition) - 07 Aug 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.45

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

Keywords :   Light-Oxygen-Voltage, Lov, Per-Arnt-Sim, Pas, Flavoprotein, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Moglich, K. Moffat
Structural Basis For Light-Dependent Signaling In The Dimeric Lov Domain Of The Photosensor Ytva.
J. Mol. Biol. V. 373 112 2007
PubMed-ID: 17764689 | Reference-DOI: 10.1016/J.JMB.2007.07.039

Molecule 1 - BLUE-LIGHT PHOTORECEPTOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PAM001
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PET28
	Fragment	:	RESIDUES 20-147
	Gene	:	PFYP
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 5)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
3	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	FMN	2	Ligand/Ion	FLAVIN MONONUCLEOTIDE
3	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (2, 8)

No.	Name	Count	Type	Full Name
1	ACY	4	Ligand/Ion	ACETIC ACID
2	FMN	4	Ligand/Ion	FLAVIN MONONUCLEOTIDE
3	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:706 , HOH A:724 , HOH A:728 , HOH B:728	BINDING SITE FOR RESIDUE NA A 701
2	AC2	SOFTWARE	VAL A:28 , THR A:30 , ASN A:37 , ASN A:61 , CYS A:62 , ARG A:63 , LEU A:65 , GLN A:66 , VAL A:75 , ILE A:78 , ARG A:79 , LEU A:82 , ASN A:94 , ASN A:104 , LEU A:106 , ILE A:108 , GLY A:121 , GLN A:123 , HOH A:703 , HOH A:706 , HOH A:724 , HOH A:727 , HOH A:737 , HOH A:840	BINDING SITE FOR RESIDUE FMN A 500
3	AC3	SOFTWARE	THR B:30 , ASN B:37 , ASN B:61 , CYS B:62 , ARG B:63 , LEU B:65 , GLN B:66 , VAL B:75 , ARG B:79 , LEU B:82 , ASN B:94 , ASN B:104 , LEU B:106 , PHE B:119 , GLY B:121 , GLN B:123 , HOH B:604 , HOH B:610 , HOH B:620 , HOH B:621 , HOH B:638 , HOH B:720	BINDING SITE FOR RESIDUE FMN B 501
4	AC4	SOFTWARE	ARG A:24 , VAL A:25 , HOH A:722 , HOH A:833 , HOH A:875 , ILE B:122 , ASN B:124 , HOH B:696	BINDING SITE FOR RESIDUE ACY A 601
5	AC5	SOFTWARE	LYS A:97 , HIS B:69 , GLN B:93	BINDING SITE FOR RESIDUE ACY B 602

(no "SS Bond" information available for 2PR5)

(no "Cis Peptide Bond" information available for 2PR5)

(no "SAP(SNP)/Variant" information available for 2PR5)

Asymmetric Unit (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PAC	PS50113	PAC domain profile.	PHOT_BACSU	88-138	2	A:88-138 B:88-138
2	STAS	PS50801	STAS domain profile.	PHOT_BACSU	147-258	1	A:147-147

Biological Unit 1 (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PAC	PS50113	PAC domain profile.	PHOT_BACSU	88-138	2	A:88-138 B:88-138
2	STAS	PS50801	STAS domain profile.	PHOT_BACSU	147-258	1	A:147-147

Biological Unit 2 (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PAC	PS50113	PAC domain profile.	PHOT_BACSU	88-138	4	A:88-138 B:88-138
2	STAS	PS50801	STAS domain profile.	PHOT_BACSU	147-258	2	A:147-147

(no "Exon" information available for 2PR5)

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:127
 aligned with PHOT_BACSU | O34627 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:127
                                    30        40        50        60        70        80        90       100       110       120       130       140       
           PHOT_BACSU    21 DHVRVGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGKNCRFLQGKHTDPAEVDNIRTALQNKEPVTVQIQNYKKDGTMFWNELNIDPMEIEDKTYFVGIQNDITKQKEYEKLLEDSLTEITALS 147
               SCOP domains d2pr5a_ A: automated matches                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee........eeeehhhhhhhhh.hhhhhh..hhhhhh....hhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeeeeeee..eeeeeeeeeehhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------PAC  PDB: A:88-138 UniProt: 88-138                 --------S PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pr5 A  21 DHVRVGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGKNCRFLQGKHTDPAEVDNIRTALQNKEPVTVQIQNYKKDGTMFWNELNIDPMEIEDKTYFVGIQNDITKQKEYEKLLEDSLTEITALS 147
                                    30        40        50        60        70        80        90       100       110       120       130       140

Chain B from PDB  Type:PROTEIN  Length:126
 aligned with PHOT_BACSU | O34627 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:126
                                    30        40        50        60        70        80        90       100       110       120       130       140      
           PHOT_BACSU    21 DHVRVGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGKNCRFLQGKHTDPAEVDNIRTALQNKEPVTVQIQNYKKDGTMFWNELNIDPMEIEDKTYFVGIQNDITKQKEYEKLLEDSLTEITAL 146
               SCOP domains d2pr5b_ B: automated matches                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---PAS_9-2pr5B01 B:24-128                                                                                   ------------------ Pfam domains (1)
           Pfam domains (2) ---PAS_9-2pr5B02 B:24-128                                                                                   ------------------ Pfam domains (2)
         Sec.struct. author .....eeeee........eeeehhhhhhhhh.hhhhh...hhhhhh....hhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeeeeeee..eeeeeeeeeehhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------PAC  PDB: B:88-138 UniProt: 88-138                 -------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pr5 B  21 DHVRVGVVITDPALEDNPIVYVNQGFVQMTGYETEEILGKNCRFLQGKHTDPAEVDNIRTALQNKEPVTVQIQNYKKDGTMFWNELNIDPMEIEDKTYFVGIQNDITKQKEYEKLLEDSLTEITAL 146
                                    30        40        50        60        70        80        90       100       110       120       130       140

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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) (23004)

Fold: Profilin-like (304)

Superfamily: PYP-like sensor domain (PAS domain) (163)

Family: automated matches (33)

Protein domain: automated matches (33)

Bacillus subtilis [TaxId: 1423] (2)

1a	d2pr5a_	A:
1b	d2pr5b_	B:

(no "CATH Domain" information available for 2PR5)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PAS_Fold (84)

Family: PAS_9 (29)

Bacillus subtilis (2)

1a	PAS_9-2pr5B01	B:24-128
1b	PAS_9-2pr5B02	B:24-128

Asymmetric Unit(hide GO term definitions)

Chain A,B (PHOT_BACSU | O34627)

molecular function
	GO:0000155	phosphorelay sensor kinase activity	Catalysis of the phosphorylation of a histidine residue in response to detection of an extracellular signal such as a chemical ligand or change in environment, to initiate a change in cell state or activity. The two-component sensor is a histidine kinase that autophosphorylates a histidine residue in its active site. The phosphate is then transferred to an aspartate residue in a downstream response regulator, to trigger a response.
	GO:0009881	photoreceptor activity	The function of absorbing and responding to incidental electromagnetic radiation, particularly visible light. The response may involve a change in conformation.
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:0018298	protein-chromophore linkage	The covalent or noncovalent attachment of a chromophore to a protein.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0050896	response to stimulus	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 a stimulus. The process begins with detection of the stimulus and ends with a change in state or activity or the cell or organism.
	GO:0023014	signal transduction by protein phosphorylation	A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
cellular component
	GO:0005622	intracellular	The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.

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	PHOT_BACSU \| O34627	:	1ium 2mwg 2pr6 4gcz

2pr6	LIGHT STRUCTURE OF YTVA-LOV

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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