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(-) Description

Title :  THE 2.0 ANGSTROMS CRYSTAL STRUCTURE OF A POCILLOPORIN AT PH 3.5: THE STRUCTURAL BASIS FOR THE LINKAGE BETWEEN COLOR TRANSITION AND HALIDE BINDING
 
Authors :  P. G. Wilmann, J. Battad, T. Beddoe, S. Olsen, S. C. Smith, S. Dove, R. J. D J. Rossjohn, M. Prescott
Date :  19 Aug 05  (Deposition) - 05 Sep 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Chromophore, Luminescence, Luminescent Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. G. Wilmann, J. Battad, T. Beddoe, S. Olsen, S. C. Smith, S. Dove, R. J. Devenish, J. Rossjohn, M. Prescott
The 2. 0 Angstroms Crystal Structure Of A Pocilloporin At Ph 3. 5: The Structural Basis For The Linkage Between Color Transition And Halide Binding
Photochem. Photobiol. V. 82 359 2006
PubMed-ID: 16613486  |  Reference-DOI: 10.1562/2005-05-02-RA-509

(-) Compounds

Molecule 1 - GFP-LIKE NON-FLUORESCENT CHROMOPROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PRSETBN
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: MONTIPORA EFFLORESCENS
    Organism Taxid: 105610
    Synonym: RTMS 5, NON-FLUORESCENT POCILLOPORIN

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric Unit (4, 12)
No.NameCountTypeFull Name
1ACY5Ligand/IonACETIC ACID
2CL2Ligand/IonCHLORIDE ION
3CRQ1Mod. Amino Acid[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETICACID
4IOD4Ligand/IonIODIDE ION
Biological Unit 1 (3, 40)
No.NameCountTypeFull Name
1ACY20Ligand/IonACETIC ACID
2CL-1Ligand/IonCHLORIDE ION
3CRQ4Mod. Amino Acid[2-(3-CARBAMOYL-1-IMINO-PROPYL)-4-(4-HYDROXY-BENZYLIDENE)-5-OXO-4,5-DIHYDRO-IMIDAZOL-1-YL]-ACETICACID
4IOD16Ligand/IonIODIDE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:146BINDING SITE FOR RESIDUE IOD A 502
02AC2SOFTWARELYS A:182BINDING SITE FOR RESIDUE IOD A 503
03AC3SOFTWAREPRO A:88BINDING SITE FOR RESIDUE IOD A 504
04AC4SOFTWAREGLY A:155BINDING SITE FOR RESIDUE CL A 511
05AC5SOFTWAREGLY A:191BINDING SITE FOR RESIDUE CL A 512
06AC6SOFTWAREASN A:23 , PRO A:131 , LYS A:182BINDING SITE FOR RESIDUE ACY A 521
07AC7SOFTWAREPHE A:151 , ALA A:152 , HIS A:172 , PRO A:190 , GLY A:191 , TYR A:192 , HOH A:579BINDING SITE FOR RESIDUE ACY A 522
08AC8SOFTWARELYS A:34 , GLY A:35 , THR A:43 , ACY A:525BINDING SITE FOR RESIDUE ACY A 523
09AC9SOFTWAREASP A:101 , PRO A:134 , HOH A:631 , HOH A:678BINDING SITE FOR RESIDUE ACY A 524
10BC1SOFTWAREGLN A:11 , LYS A:34 , LYS A:36 , ACY A:523BINDING SITE FOR RESIDUE ACY A 525

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:52 -Pro A:53
2Phe A:87 -Pro A:88

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2ARL)

(-) 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:219
 aligned with NFCP_MONEF | P83690 from UniProtKB/Swiss-Prot  Length:221

    Alignment length:221
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220 
           NFCP_MONEF     1 MSVIATQMTYKVYMSGTVNGHYFEVEGDGKGRPYEGEQTVKLTVTKGGPLPFAWDILSPQCQYGSIPFTKYPEDIPDYVKQSFPEGFTWERIMNFEDGAVCTVSNDSSIQGNCFTYHVKFSGLNFPPNGPVMQKKTQGWEPHSERLFARGGMLIGNNFMALKLEGGGHYLCEFKTTYKAKKPVKMPGYHYVDRKLDVTNHNKDYTSVEQCEISIARKPVVA 221
               SCOP domains d2arla_ A: Pocilloporin pigment Rtms5                                                                                                                                                                                         SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeeeeeeee..eeeeeeeeeeee....eeeeeeeeee......hhhhhhhhh.--............hhhhhh....eeeeeeeee....eeeeeeeeeee..eeeeeeeeeee............eeee..eeeeeeee..eeeeeeeeeeee....eeeeeeeeeeee.........eeeeeeeeeeee.....eeeeeeeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2arl A   5 GSVIATQMTYKVYMSGTVNGHYFEVEGDGKGKPYEGEQTVKLTVTKGGPLPFAWDILSPQCq--SIPFTKYPEDIPDYVKQSFPEGFTWERIMNFEDGAVCTVSNDSSIQGNCFTYHVKFSGLNFPPNGPVMQKKTQGWEPSSERLFARGGMLIGNNFMALKLEGGGHYLCEFKTTYKAKKPVKMPGYHYVDRKLDVTNHNKDYTSVEQCEISIARKPVVA 225
                                    14        24        34        44        54        64 |  |   74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224 
                                                                                        66-CRQ
   Legend:   → Mismatch (orange background)
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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 Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ARL)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (NFCP_MONEF | P83690)
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:0010117    photoprotection    Protection mechanism used by plants under conditions of excess energy absorption as a consequence of the light reactions of photosynthesis.
    GO:0018298    protein-chromophore linkage    The covalent or noncovalent attachment of a chromophore to a protein.
cellular component
    GO:0018995    host    Any organism in which another organism, especially a parasite or symbiont, spends part or all of its life cycle and from which it obtains nourishment and/or protection.

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  2arl
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 Related Entries

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UniProtKB/Swiss-Prot
        NFCP_MONEF | P83690: 1mou 1mov 2p4m 3vic 3vk1

(-) Related Entries Specified in the PDB File

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