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(-) Description

Title :  CRYSTAL STRUCTURE OF FAR-RED FLUORESCENT PROTEIN KATUSHKA CRYSTALLIZED AT PH 5.0
 
Authors :  S. Pletnev, N. V. Pletneva, V. Z. Pletnev
Date :  08 Nov 10  (Deposition) - 25 May 11  (Release) - 22 Feb 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Katushka, Far-Red Fluorescent Protein, Beta-Barrel, Biomarker, Mutant Variant Of Eqfp578, Met-Tyr-Gly Chromophore, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. V. Pletneva, V. Z. Pletnev, I. I. Shemiakina, D. M. Chudakov, I. Artemyev, A. Wlodawer, Z. Dauter, S. Pletnev
Crystallographic Study Of Red Fluorescent Protein Eqfp578 And Its Far-Red Variant Katushka Reveals Opposite Ph-Induce Isomerization Of Chromophore.
Protein Sci. V. 20 1265 2011
PubMed-ID: 21563226  |  Reference-DOI: 10.1002/PRO.654

(-) Compounds

Molecule 1 - RED FLUORESCENT PROTEIN EQFP578
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: SEA ANEMONES
    Organism Scientific: ENTACMAEA QUADRICOLOR
    Organism Taxid: 6118

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1NRQ2Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
1NRQ2Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1NRQ4Mod. Amino Acid{(4Z)-4-(4-HYDROXYBENZYLIDENE)-2-[3-(METHYLTHIO)PROPANIMIDOYL]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
2SO46Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:127 , SER A:128 , HOH A:274 , ALA B:150 , ASP B:151 , ARG B:155 , HOH B:317BINDING SITE FOR RESIDUE SO4 A 226
2AC2SOFTWAREALA A:150 , ASP A:151 , ARG A:155 , HOH A:306 , HOH A:344 , PRO B:127 , SER B:128BINDING SITE FOR RESIDUE SO4 A 227
3AC3SOFTWAREGLY A:139 , LYS A:163 , LYS A:198 , LEU A:199 , GLU A:200 , ARG A:201 , LYS B:203 , HOH B:304BINDING SITE FOR RESIDUE SO4 B 226

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3PJ5)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:49 -Pro A:50
2Phe A:84 -Pro A:85
3Gly B:49 -Pro B:50
4Phe B:84 -Pro B:85

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3PJ5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3PJ5)

(-) Exons   (0, 0)

(no "Exon" information available for 3PJ5)

(-) Sequences/Alignments

Asymmetric 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 H3JQU5_ENTQU | H3JQU5 from UniProtKB/TrEMBL  Length:226

    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      
         H3JQU5_ENTQU     1 EDSELISENMHMKLYMEGTVNDHHFKCTSEGEGKPYEGTQTMKIKVVEGGPLPFAFDILATSFMYGSKTFINHTQGIPDFFKQSFPEGFTWERITTYEDGGVLTATQDTSLQNGCLIYNVKINGVNFPSNGPVMQKKTLGWEASTEMLYPADSGLRGHSQMALKLVGGGYLHCSLKTTYRSKKPAKNLKMPGFYFVDRKLERIKEADKETYVEQHEMAVARYCDLP 226
               SCOP domains d3pj5a_ A: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--.....ee.....hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeee....eeeeeeeeeee....eeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pj5 A   0 EDSELISENMHMKLYMEGTVNDHHFKCTSEGEGKPYEGTQTMKIKVVEGGPLPFAFDILATSFm--SKTFINHTQGIPDFFKQSFPEGFTWERITTYEDGGVLTATQDTSLQNGCLIYNVKINGVNFPSNGPVMQKKTLGWEASTEMLYPADSGLRGHSQMALKLVGGGYLHCSLKTTYRSKKPAKNLKMPGFYFVDRKLERIKEADKETYVEQHEMAVARYCDLP 225
                                     9        19        29        39        49        59   |  | 69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219      
                                                                                          63-NRQ                                                                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:224
 aligned with H3JQU5_ENTQU | H3JQU5 from UniProtKB/TrEMBL  Length:226

    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      
         H3JQU5_ENTQU     1 EDSELISENMHMKLYMEGTVNDHHFKCTSEGEGKPYEGTQTMKIKVVEGGPLPFAFDILATSFMYGSKTFINHTQGIPDFFKQSFPEGFTWERITTYEDGGVLTATQDTSLQNGCLIYNVKINGVNFPSNGPVMQKKTLGWEASTEMLYPADSGLRGHSQMALKLVGGGYLHCSLKTTYRSKKPAKNLKMPGFYFVDRKLERIKEADKETYVEQHEMAVARYCDLP 226
               SCOP domains d3pj5b_ B: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--hhhhhee.....hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeee....eeeeeeeeeee....eeeeeeeeeeee..hhhhh.....eeeeeeeeeeeee....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pj5 B   0 EDSELISENMHMKLYMEGTVNDHHFKCTSEGEGKPYEGTQTMKIKVVEGGPLPFAFDILATSFm--SKTFINHTQGIPDFFKQSFPEGFTWERITTYEDGGVLTATQDTSLQNGCLIYNVKINGVNFPSNGPVMQKKTLGWEASTEMLYPADSGLRGHSQMALKLVGGGYLHCSLKTTYRSKKPAKNLKMPGFYFVDRKLERIKEADKETYVEQHEMAVARYCDLP 225
                                     9        19        29        39        49        59   |  | 69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219      
                                                                                          63-NRQ
   Legend:   → Mismatch (orange background)
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  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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3PJ5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3PJ5)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (H3JQU5_ENTQU | H3JQU5)
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.

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

3bx9 MONOMERIC FAR-RED FLUORESCENT PROTEIN MKATE CRYSTALLIZED AT PH 2.0
3bxa MONOMERIC FAR-RED FLUORESCENT PROTEIN MKATE CRYSTALLIZED AT PH 4.2
3bxb MONOMERIC FAR-RED FLUORESCENT PROTEIN MKATE CRYSTALLIZED AT PH 7.0
3bxc MONOMERIC FAR-RED FLUORESCENT PROTEIN MKATE CRYSTALLIZED AT PH 9.0
3pib FAR-RED FLUORESCENT PROTEIN EQFP578 CRYSTALLIZED AT PH 5.5
3pj7 FAR-RED FLUORESCENT PROTEIN KATUSHKA CRYSTALLIZED AT PH 8.5
3pjb FAR-RED FLUORESCENT PROTEIN EQFP578 CRYSTALLIZED AT PH 4.0