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(-) Description

Title :  MONOMERIC RED FLUORESCENT PROTEIN, DSRED.M1
 
Authors :  D. E. Strongin, B. Bevis, N. Khuong, M. E. Downing, R. L. Strack, K. Sundaram, B. S. Glick, R. J. Keenan
Date :  30 Aug 07  (Deposition) - 06 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.59
Chains :  Asym./Biol. Unit :  A
Keywords :  Dsred, Gfp-Like, Monomeric, Chromophore, Luminescence, Photoprotein, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. E. Strongin, B. Bevis, N. Khuong, M. E. Downing, R. L. Strack, K. Sundaram, B. S. Glick, R. J. Keenan
Structural Rearrangements Near The Chromophore Influence The Maturation Speed And Brightness Of Dsred Variants.
Protein Eng. Des. Sel. V. 20 525 2007
PubMed-ID: 17962222  |  Reference-DOI: 10.1093/PROTEIN/GZM046

(-) Compounds

Molecule 1 - RED FLUORESCENT PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE31
    Expression System Strain: DH10B/PREP4
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: SEA ANEMONE
    Organism Scientific: DISCOSOMA SP.
    Organism Taxid: 86600
    Synonym: DSRED.M1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 9)

Asymmetric/Biological Unit (4, 9)
No.NameCountTypeFull Name
1CL3Ligand/IonCHLORIDE ION
2CRQ1Mod. Amino Acid[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETIC ACID
3EDO2Ligand/Ion1,2-ETHANEDIOL
4ZN3Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:75 , HIS A:193 , CL A:1227 , CL A:1228BINDING SITE FOR RESIDUE ZN A1224
2AC2SOFTWAREASP A:78 , HIS A:204 , HIS A:221 , CL A:1229BINDING SITE FOR RESIDUE ZN A1225
3AC3SOFTWAREGLU A:144 , HIS A:172BINDING SITE FOR RESIDUE ZN A1226
4AC4SOFTWAREHIS A:75 , PRO A:80 , TYR A:82 , LEU A:157 , HIS A:193 , ZN A:1224 , HOH A:2058BINDING SITE FOR RESIDUE CL A1227
5AC5SOFTWAREHIS A:75 , MET A:83 , VAL A:195 , ZN A:1224BINDING SITE FOR RESIDUE CL A1228
6AC6SOFTWAREASP A:78 , HIS A:204 , HIS A:221 , ZN A:1225BINDING SITE FOR RESIDUE CL A1229
7AC7SOFTWAREASN A:98 , PHE A:99 , GLU A:100 , THR A:174 , ASP A:176BINDING SITE FOR RESIDUE EDO A1230
8AC8SOFTWAREGLU A:94 , SER A:96 , LYS A:178 , VAL A:180BINDING SITE FOR RESIDUE EDO A1231

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:52 -Pro A:53
2Phe A:87 -Pro A:88

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2VAD)

(-) 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 A from PDB  Type:PROTEIN  Length:218
 aligned with RFP_DISSP | Q9U6Y8 from UniProtKB/Swiss-Prot  Length:225

    Alignment length:220
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223
            RFP_DISSP     4 SKNVIKEFMRFKVRMEGTVNGHEFEIEGEGEGRPYEGHNTVKLKVTKGGPLPFAWDILSPQFQYGSKVYVKHPADIPDYKKLSFPEGFKWERVMNFEDGGVVTVTQDSSLQDGCFIYKVKFIGVNFPSDGPVMQKKTMGWEASTERLYPRDGVLKGEIHKALKLKDGGHYLVEFKSIYMAKKPVQLPGYYYVDSKLDITSHNEDYTIVEQYERTEGRHHL 223
               SCOP domains d2vada_ A: automated matches                                                                                                                                                                                                 SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--hhhhh.......hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2vad A   4 TEDVIKEFMQFKVRMEGSVNGHYFEIEGEGEGKPYEGTQTAKLQVTKGGPLPFAWDILSPQFq--SKAYVKHPADIPDYMKLSFPEGFTWERSMNFEDGGVVEVQQDSSLQDGTFIYKVKFKGVNFPADGPVMQKKTAGWEPSTEKLYPQDGVLKGEISHALKLKDGGHYTCDFKTVYKAKKPVQLPGNHYVDSKLDITNHNEDYTVVEQYEHAEARHSG 223
                                    13        23        33        43        53        63  |  |  73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223
                                                                                         66-CRQ
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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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RFP_DISSP | Q9U6Y8)
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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        RFP_DISSP | Q9U6Y8: 1g7k 1ggx 1zgo 1zgp 1zgq 2h5o 2h5r 2h8q 2v4e 2vae 4i2y 4kf4 4kf5

(-) Related Entries Specified in the PDB File

2vae FAST MATURING RED FLUORESCENT PROTEIN, DSRED. T4