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(-) Description

Title :  ENGINEERED MEDIUM-AFFINITY HALIDE-BINDING PROTEIN DERIVED FROM YFP: BROMIDE COMPLEX
 
Authors :  W. Wang, J. S. Grimley, L. S. Beese, H. W. Hellinga
Date :  12 Jul 11  (Deposition) - 18 Jul 12  (Release) - 18 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Barrel, Luminescent Protein, Yellow Fluorescent Protein, Imaging Reagent, Halide Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Wang, J. S. Grimley, G. J. Augustine, L. S. Beese, H. W. Hellinga
Determination Of Engineered Chloride-Binding Site Structure In Fluorescent Proteins Reveals Principles Of Halide Recognition
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GREEN FLUORESCENT PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PUC19
    Expression System Strain: KRX
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GFP
    Mutation: YES
    Organism Common: JELLYFISH
    Organism Scientific: AEQUOREA VICTORIA
    Organism Taxid: 6100

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
1BR5Ligand/IonBROMIDE ION
2CR21Mod. Amino Acid{(4Z)-2-(AMINOMETHYL)-4-[(4-HYDROXYPHENYL)METHYLIDENE]-5-OXO-4,5-DIHYDRO-1H-IMIDAZOL-1-YL}ACETIC ACID
3EDO1Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECR2 A:66 , THR A:69 , GLN A:94 , ARG A:96 , GLN A:183 , TYR A:203BINDING SITE FOR RESIDUE EDO A 260
2AC2SOFTWARECR2 A:66 , VAL A:68 , THR A:69 , TYR A:203BINDING SITE FOR RESIDUE BR A 261
3AC3SOFTWAREGLN A:94 , THR A:108 , HOH A:356BINDING SITE FOR RESIDUE BR A 262
4AC4SOFTWARETRP A:57 , HOH A:318BINDING SITE FOR RESIDUE BR A 263
5AC5SOFTWARESER A:175 , VAL A:176BINDING SITE FOR RESIDUE BR A 264
6AC6SOFTWAREARG A:79 , ARG A:215BINDING SITE FOR RESIDUE BR A 265

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Met A:88 -Pro A:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_GFP_AEQVI_001 *F100YGFP_AEQVI  ---  ---AF100Y
2UniProtVAR_GFP_AEQVI_002 *T108SGFP_AEQVI  ---  ---AT108S
3UniProtVAR_GFP_AEQVI_003 *L141MGFP_AEQVI  ---  ---AL141M
4UniProtVAR_GFP_AEQVI_004 *V219IGFP_AEQVI  ---  ---AV219I
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3SVD)

(-) 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:230
 aligned with GFP_AEQVI | P42212 from UniProtKB/Swiss-Prot  Length:238

    Alignment length:232
                             1                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229  
            GFP_AEQVI     - -MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITH 231
               SCOP domains d3svda_ A: Green fluorescent protein, GFP                                                                                                                                                                                                SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh...eeeeeeeeeeee..eeeeeeeeeeee....eeeeeeee.......hhhhhh...--.hhhhh..hhhhhhhhhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee...................eeeeeeeehhhheeeeeeeeeee.....eeeeeeeeeeee...........eeeeeeeeee........eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------Y-------S--------------------------------M-----------------------------------------------------------------------------I------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3svd A   0 MVSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTF--gVTCFARYPDHMRQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKANFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSYQSALSKDPNEKRDHMVLLEFVTAAGITL 231
                                     9        19        29        39        49        59    |  |69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229  
                                                                                           64  ||                                                                                                                                                                   
                                                                                              66-CR2                                                                                                                                                                
                                                                                               68
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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, 1)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GFP_AEQVI | P42212)
molecular function
    GO:0003674    molecular_function    Elemental activities, such as catalysis or binding, describing the actions of a gene product at the molecular level. A given gene product may exhibit one or more molecular functions.
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.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
cellular component
    GO:0005575    cellular_component    The part of a cell, extracellular environment or virus in which a gene product is located. A gene product may be located in one or more parts of a cell and its location may be as specific as a particular macromolecular complex, that is, a stable, persistent association of macromolecules that function together.

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  GFP_AEQVI | P42212
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 Related Entries

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

UniProtKB/Swiss-Prot
        GFP_AEQVI | P42212: 1b9c 1bfp 1c4f 1cv7 1ema 1emb 1emc 1eme 1emf 1emg 1emk 1eml 1emm 1f09 1f0b 1gfl 1h6r 1hcj 1huy 1jby 1jbz 1jc0 1jc1 1kp5 1kyp 1kyr 1kys 1myw 1q4a 1q4b 1q4c 1q4d 1q4e 1q73 1qxt 1qy3 1qyf 1qyo 1qyq 1rm9 1rmm 1rmo 1rmp 1rrx 1s6z 1w7s 1w7t 1w7u 1yfp 1yhg 1yhh 1yhi 1yj2 1yjf 1z1p 1z1q 2ah8 2aha 2awj 2awk 2awl 2awm 2b3p 2b3q 2due 2duf 2dug 2duh 2dui 2emd 2emn 2emo 2fwq 2fzu 2g16 2g2s 2g3d 2g5z 2g6e 2h6v 2h9w 2hcg 2hfc 2hgd 2hgy 2hjo 2hqz 2hrs 2jad 2o24 2o29 2o2b 2okw 2oky 2q57 2q6p 2qrf 2qt2 2qu1 2qz0 2wsn 2wso 2wur 2y0g 2ydz 2ye0 2ye1 2yfp 3cb9 3cbe 3cd1 3cd9 3dpw 3dpx 3dpz 3dq1 3dq2 3dq3 3dq4 3dq5 3dq6 3dq7 3dq8 3dq9 3dqa 3dqc 3dqd 3dqe 3dqf 3dqh 3dqi 3dqj 3dqk 3dql 3dqm 3dqn 3dqo 3dqu 3ed8 3ek4 3ek7 3ek8 3ekh 3ekj 3evp 3evr 3evu 3evv 3g9a 3gex 3gj1 3gj2 3i19 3k1k 3la1 3o77 3o78 3ogo 3osq 3osr 3p28 3sg2 3sg3 3sg4 3sg5 3sg6 3sg7 3sry 3ss0 3ssh 3ssk 3ssl 3ssp 3sst 3ssv 3ssy 3st0 3sv5 3svb 3svc 3sve 3u8p 3ufz 3ug0 3v3d 3vht 3w1c 3w1d 3wlc 3wld 3ztf 4anj 4ar7 4as8 4b5y 4bdu 4en1 4eul 4ges 4gf6 4h47 4h48 4ik1 4ik3 4ik4 4ik5 4ik8 4ik9 4j88 4j89 4j8a 4jfg 4jrb 4ka9 4kag 4kex 4kf5 4kw4 4kw8 4kw9 4l12 4l13 4l1i 4lqt 4lqu 4lw5 4n3d 4ndj 4ndk 4ogs 4orn 4p1q 4p7h 4pa0 4pfe 4u2v 4xbi 4xgy 4xl5 4xov 4xow 4xvp 4z4k 4z4m 4zf3 4zf4 4zf5 5aqb 5dpg 5dph 5dpi 5dpj 5dqb 5dqm 5drf 5drg 5dtx 5dty 5dtz 5du0 5ehu 5f9g 5fgu 5fji 5hbd 5hge 5hw9 5hzo 5j2o 5j3n 5ktg 5t3i

(-) Related Entries Specified in the PDB File

3sry ENGINEERED HIGH-AFFINITY HALIDE-BINDING PROTEIN DERIVED FROM YFP: HALIDE-FREE
3ss0 ENGINEERED HIGH-AFFINITY HALIDE-BINDING PROTEIN DERIVED FROM YFP: FLUORIDE COMPLEX
3ssh ENGINEERED HIGH-AFFINITY HALIDE-BINDING PROTEIN DERIVED FROM YFP: CHLORIDE COMPLEX
3ssk ENGINEERED HIGH-AFFINITY HALIDE-BINDING PROTEIN DERIVED FROM YFP: BROMIDE COMPLEX
3ssl ENGINEERED HIGH-AFFINITY HALIDE-BINDING PROTEIN DERIVED FROM YFP: IODIDE COMPLEX
3ssp ENGINEERED LOW-AFFINITY HALIDE-BINDING PROTEIN DERIVED FROM YFP: HALIDE-FREE
3sst ENGINEERED LOW-AFFINITY HALIDE-BINDING PROTEIN DERIVED FROM YFP: CHLORIDE COMPLEX
3ssv ENGINEERED LOW-AFFINITY HALIDE-BINDING PROTEIN DERIVED FROM YFP: FLUORIDE COMPLEX
3ssy ENGINEERED LOW-AFFINITY HALIDE-BINDING PROTEIN DERIVED FROM YFP: IODIDE COMPLEX
3st0 ENGINEERED MEDIUM-AFFINITY HALIDE-BINDING PROTEIN DERIVED FROM YFP: HALIDE-FREE
3sv5 ENGINEERED MEDIUM-AFFINITY HALIDE-BINDING PROTEIN DERIVED FROM YFP: IODIDE COMPLEX
3svb ENGINEERED MEDIUM-AFFINITY HALIDE-BINDING PROTEIN DERIVED FROM YFP: FLUORIDE COMPLEX
3svc ENGINEERED MEDIUM-AFFINITY HALIDE-BINDING PROTEIN DERIVED FROM YFP: CHLORIDE COMPLEX
3sve ENGINEERED LOW-AFFINITY HALIDE-BINDING PROTEIN DERIVED FROM YFP: BROMIDE COMPLEX