1UWP - JenaLib

Title :   INITIAL EVENTS IN THE PHOTOCYCLE OF PHOTOACTIVE YELLOW PROTEIN

Authors :   R. Kort, K. J. Hellingwerf, R. B. G. Ravelli

Date :   11 Feb 04 (Deposition) - 10 May 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.20

Chains :   Asym./Biol. Unit : X

Keywords :   Signaling Protein, Pas, Lov, Gaf, Domains, Fold Photocycle, Photoactive, Photoreceptor, Yellow (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Kort, K. J. Hellingwerf, R. B. G. Ravelli
Initial Events In The Photocycle Of Photoactive Yellow Protein
J. Biol. Chem. V. 279 26417 2004
PubMed-ID: 15026418 | Reference-DOI: 10.1074/JBC.M311961200
(for further references see the PDB file header)

Compounds

Molecule 1 - PHOTOACTIVE YELLOW PROTEIN
	Chains	:	X
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PQE30
	Expression System Strain	:	M15/ PREP4 PHISP
	Expression System Taxid	:	562
	Organism Scientific	:	HALORHODOSPIRA HALOPHILA
	Organism Taxid	:	1053
	Other Details	:	LIGHT STATE
	Other Details - Source	:	HALORHODOSPIRA HALOPHILA PREVIOUSLY KNOWN AS ECTOTHIORHODOSPIRA HALOPHILA
	Strain	:	BN9626
	Synonym	:	PYP

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

Sequences/Alignments

Asymmetric/Biological 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 X from PDB  Type:PROTEIN  Length:125
 aligned with PYP_HALHA | P16113 from UniProtKB/Swiss-Prot  Length:125

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
            PYP_HALHA     1 MEHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFKEGVASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV 125
               SCOP domains d1uwpx_ X: Photoactive yellow protein, PYP                                                                                    SCOP domains
               CATH domains -1uwpX00 X:2-125  [code=3.30.450.20, no name defined]                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhhh..hhhhhh....eeeeee....eeeehhhhhhhhh.hhhhhh...hhhhhhhhhh...hhhhhhhhhhhh..eeeeeeee......eeeeeeeee.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------PAS  PDB: X:23-86 UniProt: 23-86                                --------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 1uwp X   1 mEHVAFGSEDIENTLAKmDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFKEGVASGNLNTmFEYTFDYQmTPTKVKVHmKKALSGDSYWVFVKRV 125
                            |       10       |20        30        40        50        60        70        80        90|      100       110       120     
                            |               18-MSE                                                                   91-MSE  100-MSE  109-MSE            
                            1-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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

Chain X (PYP_HALHA | P16113)

molecular function
	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:0007602	phototransduction	The sequence of reactions within a cell required to convert absorbed photons into a molecular signal.
	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.

Visualization

Interactive Views

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		HC4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1uwp)

Still Images

Databases and Analysis Tools

Databases

Access by PDB/NDB ID
	1uwp
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	PYP_HALHA \| P16113
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Analysis Tools

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	PYP_HALHA \| P16113
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File

1d7e	CRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVEYELLOW PROTEIN
1f98	CRYSTAL STRUCTURE OF THE PHOTOACTIVE YELLOW PROTEIN MUTANTT50V
1f9i	CRYSTAL STRUCTURE OF THE PHOTOACTIVE YELLOW PROTEIN MUTANTY42F
1gsv	CRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVE YELLOW PROTEIN
1gsw	CRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVE YELLOW PROTEIN G51S MUTANT
1gsx	CRYSTAL STRUCTURE OF THE P65 CRYSTAL FORM OF PHOTOACTIVE YELLOW PROTEIN G47S/G51S MUTANT
1kou	CRYSTAL STRUCTURE OF THE PHOTOACTIVE YELLOW PROTEINRECONSTITUTED WITH CAFFEIC ACID AT 1. 16 A RESOLUTION
1nwz	PYP ULTRA-HIGH RESOLUTION STRUCTURE OF A BACTERIALPHOTORECEPTOR
1odv	PHOTOACTIVE YELLOW PROTEIN 1-25 DELETION MUTANT
1uwn	THE INITIAL EVENTS IN THE PHOTOCYCLE OF PHOTOACTIVE YELLOW PROTEIN: A COMMON MECHANISM ON LIGHT ACTIVATION IN PHOTORECEPTOR PROTEINS
2phy	PHOTOACTIVE YELLOW PROTEIN, DARK STATE (UNBLEACHED) 2PHY 3
2pyp	PHOTOACTIVE YELLOW PROTEIN, PHOTOSTATIONARY STATE, 50%GROUND STATE, 50% BLEACHED
2pyr	PHOTOACTIVE YELLOW PROTEIN, 1 NANOSECOND INTERMEDIATE (287K)
3phy	PHOTOACTIVE YELLOW PROTEIN, DARK STATE (UNBLEACHED),SOLUTION STRUCTURE, NMR, 26 STRUCTURES
3pyp	PHOTOACTIVE YELLOW PROTEIN, CRYOTRAPPED EARLY LIGHT CYCLEINTERMEDIATE

Description