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(-) Description

Title :  UNIQUE BEHAVIOR OF A HISTIDINE RESPONSIBLE FOR AN ENGINEERED GREEN-TO-RED PHOTOCONVERSION PROCESS
 
Authors :  H. Shimizu, H. Tsutsui, N. Nukina, A. Miyawaki
Date :  27 Jan 06  (Deposition) - 07 Mar 06  (Release) - 15 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Photoconversion, Red State, Luminescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Tsutsui, H. Shimizu, H. Mizuno, N. Nukina, T. Furuta, A. Miyawaki
The E1 Mechanism In Photo-Induced Beta-Elimination Reaction For Green-To-Red Conversion Of Fluorescent Proteins.
Chem. Biol. V. 16 1140 2009
PubMed-ID: 19942137  |  Reference-DOI: 10.1016/J.CHEMBIOL.2009.10.010

(-) Compounds

Molecule 1 - PHOTOCONVERTIBLE FLUORESCENT PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSETB
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: FAVIA FAVUS
    Organism Taxid: 102203

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1CR82Mod. Amino Acid2-[1-AMINO-2-(1H-IMIDAZOL-5-YL)ETHYL]-1-(CARBOXYMETHYL)-4-[(4-OXOCYCLOHEXA-2,5-DIEN-1-YLIDENE)METHYL]-1H-IMIDAZOL-5-OLATE
2MG2Ligand/IonMAGNESIUM ION
3NA2Ligand/IonSODIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:207 , HOH A:1363 , HOH A:1373 , HOH A:1515 , HOH A:1575BINDING SITE FOR RESIDUE MG A 1300
2AC2SOFTWAREVAL A:76 , ASP A:190 , HOH A:1491BINDING SITE FOR RESIDUE NA A 1301
3AC3SOFTWARETYR B:207 , HOH B:2367 , HOH B:2368 , HOH B:2480BINDING SITE FOR RESIDUE MG B 2300
4AC4SOFTWAREVAL B:76 , ASP B:190 , HOH B:2495BINDING SITE FOR RESIDUE NA B 2301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:48 -Pro A:49
2Phe A:83 -Pro A:84
3Gly B:48 -Pro B:49
4Phe B:83 -Pro B:84

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2DDC)

(-) 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:224
 aligned with Q53UG8_FAVFA | Q53UG8 from UniProtKB/TrEMBL  Length:227

    Alignment length:226
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
         Q53UG8_FAVFA     1 MSVITSEMKIELRMEGAVNGHKFVITGKGSGQPFEGIQNVDLTVIEGGPLPFAFDILTTAFHYGNRVFVEYPEEIVDYFKQSFPEGYSWERSMSYEDGGICLATNNITMKKDGSNCFVNEIRFDGVNFPANGPVMQRKTVKWEPSTEKMYVRDGVLKGDVNMALLLQGGGHYRCDFRTTYKAKKVVQLPDYHFVDHQMEITSHDKDYNKVKLYEHAKAHSGLPRLA 226
               SCOP domains d2ddca_ A: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh--.............hhhhhh....eeeeeeeee....eeeeeeeeee......eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ddc A   1 VSVITSEMKIEVRMEGAVNGHKFVITGKGSGQPFEGIQNVDLTVIEGGPLPFAFDILTTAF--hNRVFVKYPEEIVDYFKQSFPEGYSWERSMSYEDGGICLATNNITMKKDGSNCFVNEIRFDGVNFPANGPVMQRKTVKWESSTEKMYVRDGVLKGDVNMALLLQGGGHYRCDFRTTYKAKKVVQLPDYHFVDHLMEITSHDKDYNKVKLYEHAKAHSGLPRLA 226
                                    10        20        30        40        50        60|  |    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220      
                                                                                       61  |                                                                                                                                                                  
                                                                                          64-CR8                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:225
 aligned with Q53UG8_FAVFA | Q53UG8 from UniProtKB/TrEMBL  Length:227

    Alignment length:227
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       
         Q53UG8_FAVFA     1 MSVITSEMKIELRMEGAVNGHKFVITGKGSGQPFEGIQNVDLTVIEGGPLPFAFDILTTAFHYGNRVFVEYPEEIVDYFKQSFPEGYSWERSMSYEDGGICLATNNITMKKDGSNCFVNEIRFDGVNFPANGPVMQRKTVKWEPSTEKMYVRDGVLKGDVNMALLLQGGGHYRCDFRTTYKAKKVVQLPDYHFVDHQMEITSHDKDYNKVKLYEHAKAHSGLPRLAK 227
               SCOP domains d2ddcb_ B: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh--.............hhhhhh....eeeeeeeee....eeeeeeeeee......eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ddc B   1 VSVITSEMKIEVRMEGAVNGHKFVITGKGSGQPFEGIQNVDLTVIEGGPLPFAFDILTTAF--hNRVFVKYPEEIVDYFKQSFPEGYSWERSMSYEDGGICLATNNITMKKDGSNCFVNEIRFDGVNFPANGPVMQRKTVKWESSTEKMYVRDGVLKGDVNMALLLQGGGHYRCDFRTTYKAKKVVQLPDYHFVDHLMEITSHDKDYNKVKLYEHAKAHSGLPRLAK 227
                                    10        20        30        40        50        60|  |    70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       
                                                                                       61  |                                                                                                                                                                   
                                                                                          64-CR8
   Legend:   → Mismatch (orange background)
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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, 2)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q53UG8_FAVFA | Q53UG8)
biological process
    GO:0008218    bioluminescence    The production of light by certain enzyme-catalyzed reactions in cells.

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 Related Entries

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

UniProtKB/TrEMBL
        Q53UG8_FAVFA | Q53UG8: 2ddd 4p76

(-) Related Entries Specified in the PDB File

2ddd GREEN STATE OF THE SAME PROTEIN