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(-) Description

Title :  CRYSTAL STRUCTURE OF N66D MUTANT OF GREEN FLUORESCENT PROTEIN FROM ZOANTHUS SP. AT 2.4 A RESOLUTION (TRANSITION STATE)
 
Authors :  S. V. Pletnev, N. V. Pletneva, T. V. Tikhonova, V. Z. Pletnev
Date :  14 May 07  (Deposition) - 25 Sep 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  B  (4x)
Keywords :  Zoanthus Family, Red Fluorescent Protein, Green Fluorescent Protein, Chromophore Structure (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Pletneva, V. Pletnev, T. Tikhonova, A. A. Pakhomov, V. Popov, V. I. Martynov, A. Wlodawer, Z. Dauter, S. Pletnev
Refined Crystal Structures Of Red And Green Fluorescent Proteins From The Button Polyp Zoanthus.
Acta Crystallogr. , Sect. D V. 63 1082 2007
PubMed-ID: 17881826  |  Reference-DOI: 10.1107/S0907444907042461
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GFP-LIKE FLUORESCENT CHROMOPROTEIN FP506
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30-ZGFP506_N66D
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: ZOANTHUS SP.
    Organism Taxid: 105402
    Synonym: ZFP506

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (4x): A 
Biological Unit 2 (4x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1DYG2Mod. Amino Acid(3S)-3-AMINO-3-[(4Z)-1-(CARBOXYMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-IMIDAZOL-2-YL]PROPANOIC ACID
2XYG2Mod. Residue[(4Z)-2-[(1Z)-ETHANIMIDOYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1DYG4Mod. Amino Acid(3S)-3-AMINO-3-[(4Z)-1-(CARBOXYMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-IMIDAZOL-2-YL]PROPANOIC ACID
2XYG4Mod. Residue[(4Z)-2-[(1Z)-ETHANIMIDOYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1DYG4Mod. Amino Acid(3S)-3-AMINO-3-[(4Z)-1-(CARBOXYMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-IMIDAZOL-2-YL]PROPANOIC ACID
2XYG4Mod. Residue[(4Z)-2-[(1Z)-ETHANIMIDOYL]-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID

(-) Sites  (0, 0)

(no "Site" information available for 2PXW)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:52 -Pro A:53
2Cys A:87 -Pro A:88
3Gly B:52 -Pro B:53
4Cys B:87 -Pro B:88

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PXW)

(-) 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:226
 aligned with GFPL1_ZOASP | Q9U6Y5 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:228
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
          GFPL1_ZOASP     4 SKHGLTKEMTMKYRMEGCVDGHKFVITGEGIGYPFKGKQAINLCVVEGGPLPFAEDILSAAFNYGNRVFTEYPQDIVDYFKNSCPAGYTWDRSFLFEDGAVCICNADITVSVEENCMYHESKFYGVNFPADGPVMKKMTDNWEPSCEKIIPVPKQGILKGDVSMYLLLKDGGRLRCQFDTVYKAKSVPRKMPDWHFIQHKLTREDRSDAKNQKWHLTEHAIASGSALP 231
               SCOP domains d2pxwa_ A: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains 2pxwA00 A:4-231 Green Fluorescent Protein                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhh...eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhh....--............hhhhhh....eeeeeeeee....eeeeeeeeeee....eeeeeeeeeee............eeee..eeeeeee......eeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeee.......eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pxw A   4 SKHGLTKEMTMKYRMEGCVDGHKFVITGEGIGYPFKGKQAINLCVVEGGPLPFAEDILSAAFd--NRVFTEYPQDIVDYFKNSCPAGYTWDRSFLFEDGAVCICNADITVSVEENCMYHESKFYGVNFPADGPVMKKMTDNWEPSCEKIIPVPKQGILKGDVSMYLLLKDGGRLRCQFDTVYKAKSVPRKMPDWHFIQHKLTREDRSDAKNQKWHLTEHAIASGSALP 231
                                    13        23        33        43        53        63  |  |  73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
                                                                                         66-DYG                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:226
 aligned with GFPL1_ZOASP | Q9U6Y5 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:228
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
          GFPL1_ZOASP     4 SKHGLTKEMTMKYRMEGCVDGHKFVITGEGIGYPFKGKQAINLCVVEGGPLPFAEDILSAAFNYGNRVFTEYPQDIVDYFKNSCPAGYTWDRSFLFEDGAVCICNADITVSVEENCMYHESKFYGVNFPADGPVMKKMTDNWEPSCEKIIPVPKQGILKGDVSMYLLLKDGGRLRCQFDTVYKAKSVPRKMPDWHFIQHKLTREDRSDAKNQKWHLTEHAIASGSALP 231
               SCOP domains d2pxwb_ B: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains 2pxwB00 B:4-231 Green Fluorescent Protein                                                                                                                                                                                            CATH domains
           Pfam domains (1) -GFP-2pxwB01 B:5-228                                                                                                                                                                                                             --- Pfam domains (1)
           Pfam domains (2) -GFP-2pxwB02 B:5-228                                                                                                                                                                                                             --- Pfam domains (2)
         Sec.struct. author hhhhh...eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhh....--............hhhhhh....eeeeeeeee....eeeeeeeeeee....eeeeeeeeeee............eeee..eeeeeee......eeeeeeeeeee....eeeeeeeeeeee..........eeeeeeeeeee.......eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pxw B   4 SKHGLTKEMTMKYRMEGCVDGHKFVITGEGIGYPFKGKQAINLCVVEGGPLPFAEDILSAAFd--NRVFTEYPQDIVDYFKNSCPAGYTWDRSFLFEDGAVCICNADITVSVEENCMYHESKFYGVNFPADGPVMKKMTDNWEPSCEKIIPVPKQGILKGDVSMYLLLKDGGRLRCQFDTVYKAKSVPRKMPDWHFIQHKLTREDRSDAKNQKWHLTEHAIASGSALP 231
                                    13        23        33        43        53        63  |  |  73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223        
                                                                                         66-DYG
   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, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: GFP (101)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GFPL1_ZOASP | Q9U6Y5)
biological process
    GO:0008218    bioluminescence    The production of light by certain enzyme-catalyzed reactions in cells.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.

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  Cis Peptide Bonds
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 Related Entries

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

UniProtKB/Swiss-Prot
        GFPL1_ZOASP | Q9U6Y5: 2icr 2ojk 2pxs

(-) Related Entries Specified in the PDB File

2fl1 CRYSTAL STRUCTURE OF RED FLUORESCENT PROTEIN FROM ZOANTHUS SP2 AT 2.4 A RESOLUTION
2icr CRYSTAL STRUCTURE OF RED FLUORESCENT PROTEIN FROM ZOANTHUS SP2 AT 1.5 A RESOLUTION
2ogr CRYSTAL STRUCTURE OF YELLOW FLUORESCENT PROTEIN FROM ZOANTHUS SP AT 1.8 A RESOLUTION
2ojk CRYSTAL STRUCTURE OF GREEN FLUORESCENT PROTEIN FROM ZOANTHUS SP AT 2.2 A RESOLUTION
2pxs CRYSTAL STRUCTURE OF N66D MUTANT OF GREEN FLUORESCENT PROTEIN FROM ZOANTHUS SP IN MATURE STATE AT 2.2 A RESOLUTION