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(-) Description

Title :  CRYSTAL STRUCTURE OF MONOMERIC KUSABIRA-ORANGE (MKO), ORANGE-EMITTING GFP-LIKE PROTEIN, AT PH 6.0
 
Authors :  A. Kikuchi, E. Fukumura, S. Karasawa, H. Mizuno, A. Miyawaki, Y. Shiro, Structural Genomics/Proteomics Initiative (Rsgi)
Date :  21 Apr 08  (Deposition) - 21 Oct 08  (Release) - 02 May 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Gfp-Like Protein, Luminescent Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kikuchi, E. Fukumura, S. Karasawa, H. Mizuno, A. Miyawaki, Y. Shiro
Structural Characterization Of A Thiazoline-Containing Chromophore In An Orange Fluorescent Protein, Monomeric Kusabira Orange
Biochemistry V. 47 11573 2008
PubMed-ID: 18844376  |  Reference-DOI: 10.1021/BI800727V

(-) Compounds

Molecule 1 - FLUORESCENT PROTEIN
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSET
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MKO
    Organism Common: MUSHROOM CORAL
    Organism Scientific: FUNGIA CONCINNA
    Organism Taxid: 496660
    Synonym: ORANGE-EMITTING GFP-LIKE PROTEIN, MKO

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1CFY4Mod. Amino Acid[(4Z)-2-{(2R)-2-[(1S)-1-AMINO-2-PHENYLETHYL]-2-HYDROXY-2,5-DIHYDRO-1,3-THIAZOL-4-YL}-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CFY1Mod. Amino Acid[(4Z)-2-{(2R)-2-[(1S)-1-AMINO-2-PHENYLETHYL]-2-HYDROXY-2,5-DIHYDRO-1,3-THIAZOL-4-YL}-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CFY1Mod. Amino Acid[(4Z)-2-{(2R)-2-[(1S)-1-AMINO-2-PHENYLETHYL]-2-HYDROXY-2,5-DIHYDRO-1,3-THIAZOL-4-YL}-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CFY1Mod. Amino Acid[(4Z)-2-{(2R)-2-[(1S)-1-AMINO-2-PHENYLETHYL]-2-HYDROXY-2,5-DIHYDRO-1,3-THIAZOL-4-YL}-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1CFY1Mod. Amino Acid[(4Z)-2-{(2R)-2-[(1S)-1-AMINO-2-PHENYLETHYL]-2-HYDROXY-2,5-DIHYDRO-1,3-THIAZOL-4-YL}-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 2ZMW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe A:86 -Pro A:87
2Phe B:86 -Pro B:87
3Phe C:86 -Pro C:87
4Phe D:86 -Pro D:87

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ZMW)

(-) 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:214
 aligned with Q6I7B2_FUNCO | Q6I7B2 from UniProtKB/TrEMBL  Length:218

    Alignment length:217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
         Q6I7B2_FUNCO     2 VSVIKPEMKMRYYMDGSVNGHEFTIEGEGTGRPYEGHQEMTLRVTMAKGGPMPFAFDLVSHVFCYGHRPFTKYPEEIPDYFKQAFPEGLSWERSLEFEDGGSASVSAHISLRGNTFYHKSKFTGVNFPADGPIMQNQSVDWEPSTEKITASDGVLKGDVTMYLKLEGGGNHKCQFKTTYKAAKKILKMPGSHYISHRLVRKTEGNITELVEDAVAHS 218
               SCOP domains d2zmwa_ A: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeeeee.........hhhhhh.--.-............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zmw A   2 VSVIKPEMKMRYYMDGSVNGHEFTIEGEGTGRPYEGHQEMTLRVTMAKGGPMPFAFDLVSHV--f-HRPFTKYPEEIPDYFKQAFPEGLSWERSLEFEDGGSASVSAHISLRGNTFYHKSKFTGVNFPADGPIMQNQSVDWEPSTEKITASDGVLKGDVTMYLKLEGGGNHKCQFKTTYKAAKKILKMPGSHYISHRLVRKTEGNITELVEDAVAHS 218
                                    11        21        31        41        51        61 |  | | 71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
                                                                                        63  | |                                                                                                                                                      
                                                                                           66-CFY                                                                                                                                                    
                                                                                             68                                                                                                                                                      


Chain B from PDB  Type:PROTEIN  Length:214
 aligned with Q6I7B2_FUNCO | Q6I7B2 from UniProtKB/TrEMBL  Length:218

    Alignment length:217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
         Q6I7B2_FUNCO     2 VSVIKPEMKMRYYMDGSVNGHEFTIEGEGTGRPYEGHQEMTLRVTMAKGGPMPFAFDLVSHVFCYGHRPFTKYPEEIPDYFKQAFPEGLSWERSLEFEDGGSASVSAHISLRGNTFYHKSKFTGVNFPADGPIMQNQSVDWEPSTEKITASDGVLKGDVTMYLKLEGGGNHKCQFKTTYKAAKKILKMPGSHYISHRLVRKTEGNITELVEDAVAHS 218
               SCOP domains d2zmwb_ B: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeeeee.........hhhhhh.--.-............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zmw B   2 VSVIKPEMKMRYYMDGSVNGHEFTIEGEGTGRPYEGHQEMTLRVTMAKGGPMPFAFDLVSHV--f-HRPFTKYPEEIPDYFKQAFPEGLSWERSLEFEDGGSASVSAHISLRGNTFYHKSKFTGVNFPADGPIMQNQSVDWEPSTEKITASDGVLKGDVTMYLKLEGGGNHKCQFKTTYKAAKKILKMPGSHYISHRLVRKTEGNITELVEDAVAHS 218
                                    11        21        31        41        51        61 |  | | 71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
                                                                                        63  | |                                                                                                                                                      
                                                                                           66-CFY                                                                                                                                                    
                                                                                             68                                                                                                                                                      


Chain C from PDB  Type:PROTEIN  Length:214
 aligned with Q6I7B2_FUNCO | Q6I7B2 from UniProtKB/TrEMBL  Length:218

    Alignment length:217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
         Q6I7B2_FUNCO     2 VSVIKPEMKMRYYMDGSVNGHEFTIEGEGTGRPYEGHQEMTLRVTMAKGGPMPFAFDLVSHVFCYGHRPFTKYPEEIPDYFKQAFPEGLSWERSLEFEDGGSASVSAHISLRGNTFYHKSKFTGVNFPADGPIMQNQSVDWEPSTEKITASDGVLKGDVTMYLKLEGGGNHKCQFKTTYKAAKKILKMPGSHYISHRLVRKTEGNITELVEDAVAHS 218
               SCOP domains d2zmwc_ C: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeeeee.........hhhhhh.--.-............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zmw C   2 VSVIKPEMKMRYYMDGSVNGHEFTIEGEGTGRPYEGHQEMTLRVTMAKGGPMPFAFDLVSHV--f-HRPFTKYPEEIPDYFKQAFPEGLSWERSLEFEDGGSASVSAHISLRGNTFYHKSKFTGVNFPADGPIMQNQSVDWEPSTEKITASDGVLKGDVTMYLKLEGGGNHKCQFKTTYKAAKKILKMPGSHYISHRLVRKTEGNITELVEDAVAHS 218
                                    11        21        31        41        51        61 |  | | 71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
                                                                                        63  | |                                                                                                                                                      
                                                                                           66-CFY                                                                                                                                                    
                                                                                             68                                                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:214
 aligned with Q6I7B2_FUNCO | Q6I7B2 from UniProtKB/TrEMBL  Length:218

    Alignment length:217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
         Q6I7B2_FUNCO     2 VSVIKPEMKMRYYMDGSVNGHEFTIEGEGTGRPYEGHQEMTLRVTMAKGGPMPFAFDLVSHVFCYGHRPFTKYPEEIPDYFKQAFPEGLSWERSLEFEDGGSASVSAHISLRGNTFYHKSKFTGVNFPADGPIMQNQSVDWEPSTEKITASDGVLKGDVTMYLKLEGGGNHKCQFKTTYKAAKKILKMPGSHYISHRLVRKTEGNITELVEDAVAHS 218
               SCOP domains d2zmwd_ D: automated matches                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) GFP-2zmwD01 D:2-218                                                                                                                                                                                                       Pfam domains (1)
           Pfam domains (2) GFP-2zmwD02 D:2-218                                                                                                                                                                                                       Pfam domains (2)
           Pfam domains (3) GFP-2zmwD03 D:2-218                                                                                                                                                                                                       Pfam domains (3)
           Pfam domains (4) GFP-2zmwD04 D:2-218                                                                                                                                                                                                       Pfam domains (4)
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeeehhh.eeeeeeeeee.........hhhhhh.--.-............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeeee..eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2zmw D   2 VSVIKPEMKMRYYMDGSVNGHEFTIEGEGTGRPYEGHQEMTLRVTMAKGGPMPFAFDLVSHV--f-HRPFTKYPEEIPDYFKQAFPEGLSWERSLEFEDGGSASVSAHISLRGNTFYHKSKFTGVNFPADGPIMQNQSVDWEPSTEKITASDGVLKGDVTMYLKLEGGGNHKCQFKTTYKAAKKILKMPGSHYISHRLVRKTEGNITELVEDAVAHS 218
                                    11        21        31        41        51        61 |  | | 71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       
                                                                                        63  | |                                                                                                                                                      
                                                                                           66-CFY                                                                                                                                                    
                                                                                             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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: GFP (101)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q6I7B2_FUNCO | Q6I7B2)
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)

UniProtKB/TrEMBL
        Q6I7B2_FUNCO | Q6I7B2: 2zmu 3mgf

(-) Related Entries Specified in the PDB File

2zmu THE SAME PROTEIN AT PH 9.1