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Asym./Biol. Unit (Jmol Viewer)

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Title :   GREEN FLUORESCENT PROTEIN: CYCLIZED-ONLY INTERMEDIATE OF CHROMOPHORE MATURATION IN THE Q183E VARIANT

Authors :   T. I. Wood, D. P. Barondeau, C. Hitomi, J. A. Tainer, E. D. Getzoff

Date :   28 Jul 07 (Deposition) - 21 Apr 09 (Release) - 21 Apr 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.50

Chains :   Asym./Biol. Unit : A

Keywords :   Cyclized Intermediate, Chromophore, Gfp, Luminescence, Photoprotein, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. I. Wood, D. P. Barondeau, C. Hitomi, J. A. Tainer, E. D. Getzoff
Green Fluorescent Protein Chromophore - Cyclized Intermediate
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - GREEN FLUORESCENT PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PTIW188
	Expression System Strain	:	BL21/ DE3 PRIL
	Expression System Taxid	:	562
	Expression System Vector	:	PET11
	Expression System Vector Type	:	PLASMID
	Gene	:	GFP
	Mutation	:	YES
	Organism Common	:	JELLYFISH
	Organism Scientific	:	AEQUOREA VICTORIA
	Organism Taxid	:	6100
	Synonym	:	GREEN FLUORESCENT PROTEIN (GFP)

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 4)

No.	Name	Count	Type	Full Name
1	CZO	1	Mod. Amino Acid	[(2R,4S)-2-[(1S,2R)-1-AMINO-2-HYDROXYPROPYL]-2-HYDROXY-4-(4-HYDROXYBENZYL)-5-OXOIMIDAZOLIDIN-1-YL]ACETIC ACID
2	EDO	2	Ligand/Ion	1,2-ETHANEDIOL
3	MG	1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:301 , HOH A:302 , HOH A:303 , HOH A:304 , HOH A:305 , HOH A:306	BINDING SITE FOR RESIDUE MG A 300
2	AC2	SOFTWARE	ARG A:109 , ARG A:122 , GLU A:124 , HOH A:1282	BINDING SITE FOR RESIDUE EDO A 400
3	AC3	SOFTWARE	LYS A:107 , GLU A:124 , LYS A:214	BINDING SITE FOR RESIDUE EDO A 401

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

Asymmetric/Biological Unit

No.	Residues
1	Met A:88	-	Pro A:89

Asymmetric/Biological Unit (4, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_GFP_AEQVI_001 *	F	100	Y	GFP_AEQVI	---	---	A	F	100	Y
2	UniProt	VAR_GFP_AEQVI_002 *	T	108	S	GFP_AEQVI	---	---	A	T	108	S
3	UniProt	VAR_GFP_AEQVI_003 *	L	141	M	GFP_AEQVI	---	---	A	L	141	M
4	UniProt	VAR_GFP_AEQVI_004 *	V	219	I	GFP_AEQVI	---	---	A	V	219	I
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 2QRF)

(no "Exon" information available for 2QRF)

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 A from PDB  Type:PROTEIN  Length:226
 aligned with GFP_AEQVI | P42212 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:228
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222        
            GFP_AEQVI     3 KGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGIT 230
               SCOP domains d2qrfa_ A: Green fluorescent protein, GFP                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains --GFP-2qrfA01 A:5-229                                                                                                                                                                                                              - Pfam domains
         Sec.struct. author hhhhhhh..eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeee.......hhhhhh...--.hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------Y-------S--------------------------------M-----------------------------------------------------------------------------I----------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qrf A   3 KGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTL--gVQCFSRYPDHMKQHDFFKSAMPEGYVQERTISFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYEQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGIT 230
                                    12        22        32        42        52        62 |  ||  72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222        
                                                                                        64  ||                                                                                                                                                                  
                                                                                           66-CZO                                                                                                                                                               
                                                                                            68

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: GFP-like (339)

Superfamily: GFP-like (339)

Family: Fluorescent proteins (271)

Protein domain: Green fluorescent protein, GFP (161)

Jellyfish (Aequorea victoria) [TaxId: 6100] (158)

d2qrfa_

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GFP (101)

Family: GFP (101)

Aequorea victoria (Jellyfish) (53)

GFP-2qrfA01

A:5-229

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (GFP_AEQVI | P42212)

molecular function
	GO:0003674	molecular_function	Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
biological process
	GO:0008218	bioluminescence	The production of light by certain enzyme-catalyzed reactions in cells.
	GO:0006091	generation of precursor metabolites and energy	The chemical reactions and pathways resulting in the formation of precursor metabolites, substances from which energy is derived, and any process involved in the liberation of energy from these substances.
	GO:0018298	protein-chromophore linkage	The covalent or noncovalent attachment of a chromophore to a protein.
cellular component
	GO:0005575	cellular_component	The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Met A:88 - Pro A:89	[ RasMol ]

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	2qrf
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1ema	GFP MOLECULAR REPLACEMENT MODEL
2awj	GFP R96M VARIANT, PRECYCLIZED INTERMEDIATE
2awl	GFP R96K VARIANT
2awm	GFP R96A Q183R RECOVERY VARIANT
2qt2
2qz0

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 4)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (4, 4)

PROSITE Motifs (0, 0)

Exons (0, 0)

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