2FZU - JenaLib

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Title :   REDUCED ENOLATE CHROMOPHORE INTERMEDIATE FOR GFP VARIANT

Authors :   D. P. Barondeau, J. A. Tainer, E. D. Getzoff

Date :   10 Feb 06 (Deposition) - 14 Mar 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.25

Chains :   Asym./Biol. Unit : A

Keywords :   Chromophore, Intermediate, Biosynthesis, Post-Translational Modification, High Resolution, Luminescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. P. Barondeau, J. A. Tainer, E. D. Getzoff
Structural Evidence For An Enolate Intermediate In Gfp Fluorophore Biosynthesis.
J. Am. Chem. Soc. V. 128 3166 2006
PubMed-ID: 16522096 | Reference-DOI: 10.1021/JA0552693
(for further references see the PDB file header)

Molecule 1 - GREEN FLUORESCENT PROTEIN
	Chains	:	A
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	GFP
	Mutation	:	YES
	Organism Scientific	:	AEQUOREA VICTORIA
	Organism Taxid	:	6100

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 3)

No.	Name	Count	Type	Full Name
1	C12	1	Mod. Amino Acid	2-(1-AMINO-2-HYDROXYPROPYL)-4-(4-HYDROXYBENZYL)-1-(2-OXOETHYL)-1H-IMIDAZOL-5-OLATE
2	EDO	1	Ligand/Ion	1,2-ETHANEDIOL
3	MG	1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:1351 , HOH A:1352 , HOH A:1353 , HOH A:1354 , HOH A:1355 , HOH A:1356	BINDING SITE FOR RESIDUE MG A 301
2	AC2	SOFTWARE	VAL A:11 , GLU A:34 , ASP A:36 , LYS A:41 , THR A:43 , HOH A:1109 , HOH A:1127 , HOH A:1299 , HOH A:1313	BINDING SITE FOR RESIDUE EDO A 303

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

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 2FZU)

(no "Exon" information available for 2FZU)

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:234
 aligned with GFP_AEQVI | P42212 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:236
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232      
            GFP_AEQVI     3 KGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK 238
               SCOP domains d2fzua_ A: Green fluorescent protein, GFP                                                                                                                                                                                                    SCOP domains
               CATH domains 2fzuA00 A:3-238 Green Fluorescent Protein                                                                                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh..eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeee.......hhhhhh...-.-hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee....hhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------Y-------S--------------------------------M-----------------------------------------------------------------------------I------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2fzu A   3 KGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTL-t-VQCFSRYPDHMKQHDFFKSAMPEGYVQERTISFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYITADKQKNGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK 238
                                    12        22        32        42        52        62 | | |  72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232      
                                                                                        64 | |                                                                                                                                                                          
                                                                                          66-C12                                                                                                                                                                        
                                                                                            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)

d2fzua_

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Green Fluorescent Protein (102)

Homologous Superfamily: Green Fluorescent Protein (102)

Aequorea victoria. Organism_taxid: 6100. (30)

2fzuA00

A:3-238

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

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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	Cis Peptide Bonds
		Met A:88 - Pro A:89	[ RasMol ]

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2fwq	REDUCED ENOLATE CHROMOPHORE INTERMEDIATE FOR Y66H GFP VARIANT

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 3)

Sites (2, 2)

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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SCOP Domains (1, 1)

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Gene Ontology (5, 5)

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