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(-) Description

Title :  CRYSTAL STRUCTURE OF GFP-LIKE PROTEIN ACEGFP_G222E (A. COERULESCENS). COLORLESS FORM.
 
Authors :  N. V. Pletneva, V. Z. Pletnev, S. V. Pletnev
Date :  19 Feb 10  (Deposition) - 09 Mar 10  (Release) - 09 Jun 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.14
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Colorless Gfp-Like Protein, Chromophore Biosynthesis, Fluorescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. V. Pletneva, V. Z. Pletnev, K. A. Lukyanov, N. G. Gurskaya, E. A. Goryacheva, V. I. Martynov, A. Wlodawer, Z. Dauter, S. Pletnev
Structural Evidence For A Dehydrated Intermediate In Green Fluorescent Protein Chromophore Biosynthesis.
J. Biol. Chem. V. 285 15978 2010
PubMed-ID: 20220148  |  Reference-DOI: 10.1074/JBC.M109.092320

(-) Compounds

Molecule 1 - GREEN FLUORESCENT PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: JM109
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: AEQUOREA COERULESCENS
    Organism Taxid: 210840

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A 
Biological Unit 3 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2GYS2Mod. Amino Acid[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
Biological Unit 1 (2, 7)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL
2GYS2Mod. Amino Acid[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2GYS1Mod. Amino Acid[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID
Biological Unit 3 (2, 5)
No.NameCountTypeFull Name
1GOL4Ligand/IonGLYCEROL
2GYS1Mod. Amino Acid[(4Z)-2-(1-AMINO-2-HYDROXYETHYL)-4-(4-HYDROXYBENZYLIDENE)-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL]ACETIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:148 , ASN A:149 , LYS A:166 , ARG A:168 , HOH A:261 , HOH A:347 , HOH B:271BINDING SITE FOR RESIDUE GOL A 239
2AC2SOFTWAREHIS B:148 , ASN B:149 , LYS B:166 , ARG B:168 , HOH B:260 , HOH B:263 , HOH B:406 , HOH B:445BINDING SITE FOR RESIDUE GOL B 239
3AC3SOFTWARELYS A:166 , ASP A:180 , TYR A:182 , GLU B:95 , ARG B:96 , THR B:97 , TYR B:182 , GLN B:184 , HOH B:304 , HOH B:414BINDING SITE FOR RESIDUE GOL B 240
4AC4SOFTWARELYS B:107 , SER B:108 , ARG B:109 , GLU B:124 , LEU B:125 , THR B:126 , HOH B:460BINDING SITE FOR RESIDUE GOL B 241
5AC5SOFTWAREPRO A:89 , PHE A:114 , GLU A:115 , GLY A:116 , LYS B:52 , LYS B:214 , ASP B:216 , HOH B:249 , HOH B:293BINDING SITE FOR RESIDUE GOL B 242

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Met A:88 -Pro A:89
2Met B:88 -Pro B:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3LVC)

(-) 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:227
 aligned with Q6YGZ0_9CNID | Q6YGZ0 from UniProtKB/TrEMBL  Length:238

    Alignment length:229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         
         Q6YGZ0_9CNID     1 MSKGAELFTGVVPILIELNGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYIQERTIFFKDDGNYKSRAEVKFEGDTLVNRIELTGTDFKEDGNILGNKMEYNYNAHNVYIMTDKAKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSTLSKDPNEKRDHMIYFEFVTAAAI 229
               SCOP domains d3lvca_ A: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh..eeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh....--hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lvc A   1 MSKGAELFTGIVPILIELNGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLs--VQCFSRYPDHMKQHDFFKSAMPEGYIQERTIFFEDDGNYKSRAEVKFEGDTLVNRIELTGTDFKEDGNILGNKMEYNYNAHNVYIMTDKAKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMIYFEFVTAAAI 229
                                    10        20        30        40        50        60    |  |70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         
                                                                                           65-GYS                                                                                                                                                                


Chain B from PDB  Type:PROTEIN  Length:227
 aligned with Q6YGZ0_9CNID | Q6YGZ0 from UniProtKB/TrEMBL  Length:238

    Alignment length:229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         
         Q6YGZ0_9CNID     1 MSKGAELFTGVVPILIELNGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYIQERTIFFKDDGNYKSRAEVKFEGDTLVNRIELTGTDFKEDGNILGNKMEYNYNAHNVYIMTDKAKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSTLSKDPNEKRDHMIYFEFVTAAAI 229
               SCOP domains d3lvcb_ B: automated matches                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----GFP-3lvcB01 B:5-229                                                                                                                                                                                                               Pfam domains (1)
           Pfam domains (2) ----GFP-3lvcB02 B:5-229                                                                                                                                                                                                               Pfam domains (2)
         Sec.struct. author ..hhhhhhh..eeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh....--hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3lvc B   1 MSKGAELFTGIVPILIELNGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTLs--VQCFSRYPDHMKQHDFFKSAMPEGYIQERTIFFEDDGNYKSRAEVKFEGDTLVNRIELTGTDFKEDGNILGNKMEYNYNAHNVYIMTDKAKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMIYFEFVTAAAI 229
                                    10        20        30        40        50        60    |  |70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         
                                                                                           65-GYS
   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  (0, 0)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: GFP (101)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q6YGZ0_9CNID | Q6YGZ0)
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
        Q6YGZ0_9CNID | Q6YGZ0: 3lva 3lvd

(-) Related Entries Specified in the PDB File

3lva CRYSTAL STRUCTURE OF GFP-LIKE PROTEIN ACEGFP (A. COERULESCENS)
3lvd CRYSTAL STRUCTURE OF GFP-LIKE PROTEIN ACEGFP_G222E (A. COERULESCENS). UV-PHOTOCONVERTED GREEN FORM.