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(-) Description

Title :  CRYSTAL STRUCTURE OF A FUNCTIONAL UNIT OF INTERPHOTORECEPTOR RETINOID-BINDING PROTEIN (IRBP)
 
Authors :  A. Loew, F. Gonzalez-Fernandez
Date :  19 May 01  (Deposition) - 20 Feb 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Beta Alpha Spiral, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Loew, F. Gonzalez-Fernandez
Crystal Structure Of The Functional Unit Of Interphotoreceptor Retinoid Binding Protein.
Structure V. 10 43 2002
PubMed-ID: 11796109  |  Reference-DOI: 10.1016/S0969-2126(01)00698-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - INTERPHOTORECEPTOR RETINOID-BINDING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTHIOHIS
    Expression System Strain: TOP 10
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: AFRICAN CLAWED FROG
    Organism Scientific: XENOPUS LAEVIS
    Organism Taxid: 8355
    Synonym: IRBP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1MSE4Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1J7X)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J7X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J7X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J7X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1J7X)

(-) Exons   (0, 0)

(no "Exon" information available for 1J7X)

(-) 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:302
 aligned with RET3_XENLA | Q7SZI7 from UniProtKB/Swiss-Prot  Length:1219

    Alignment length:305
                                   326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616     
           RET3_XENLA   317 RSSVTHVLHQLCDILANNYAFSERIPTLLQHLPNLDYSTVISEEDIAAKLNYELQSLTEDPRLVLKSKTDTLVMPGDSIQAENIPEDEAMLQALVNTVFKVSILPGNIGYLRFDQFADVSVIAKLAPFIVNTVWEPITITENLIIDLRYNVGGSSTAVPLLLSYFLDPETKIHLFTLHNRQQNSTDEVYSHPKVLGKPYGSKKGVYVLTSHQTATAAEEFAYLMQSLSRATIIGEITSGNLMHSKVFPFDGTQLSVTVPIINFIDSNGDYWLGGGVVPDAIVLADEALDKAKEIIAFHPSIFPLV 621
               SCOP domains d1j7xa_ A: Interphotoreceptor retinoid-binding protein IRBP                                                                                                                                                                                                                                                       SCOP domains
               CATH domains 1j7xA01 A:2-73,A:245-260  [code=3.30.750.34, no name defined]           1j7xA02 A:74-244,A:261-303 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                        1j7xA01         1j7xA02 A:74-244,A:261-303                     CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh....eeee.hhh........hhhhh..hhhhhhhhhhhhheeeee...eeeee.....hhhhhhhhhhhhhhhhhhhhh...eeeee..........hhhhhhhh........eeeeeee......eeee..............eeeeee.....hhhhhhhhhhhhh...eeee.........eeeee.....eeeeee.eeeee..............ee.hhhhhhhhhhhhhhh..---... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j7x A   2 DPSVTHVLHQLCDILANNYAFSERIPTLLQHLPNLDYSTVISEEDIAAKLNYELQSLTEDPRLVLKSKTDTLVmPGDSIQAENIPEDEAmLQALVNTVFKVSILPGNIGYLRFDQFADVSVIAKLAPFIVNTVWEPITITENLIIDLRYNVGGSSTAVPLLLSYFLDPETKIHLFTLHNRQQNSTDEVYSHPKVLGKPYGSKKGVYVLTSHQTATAAEEFAYLmQSLSRATIIGEITSGNLmHSKVFPFGDTQLSVTVPIINFIDSNGDYWLGGGVVPDAIVLADEALDKAKEIIAFHP---PLA 303
                                    11        21        31        41        51        61        71   |    81        91       101       111       121       131       141       151       161       171       181       191       201       211       221   |   231       241 |     251       261       271       281       291        |-  |  
                                                                                                    75-MSE          91-MSE                                                                                                                               225-MSE           243-MSE                                                  300 301
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J7X)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RET3_XENLA | Q7SZI7)
molecular function
    GO:0005501    retinoid binding    Interacting selectively and non-covalently with retinoids, any member of a class of isoprenoids that contain or are derived from four prenyl groups linked head-to-tail. Retinoids include retinol and retinal and structurally similar natural derivatives or synthetic compounds, but need not have vitamin A activity.
    GO:0008236    serine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0007601    visual perception    The series of events required for an organism to receive a visual stimulus, convert it to a molecular signal, and recognize and characterize the signal. Visual stimuli are detected in the form of photons and are processed to form an image.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0033165    interphotoreceptor matrix    A specialized extracellularc matrix that surrounds the photoreceptors of the retina and lies between them and the apical surface of the retinal pigment epithelium. The IPM has been implicated in several important activities required for photoreceptor function and maintenance.
    GO:0005578    proteinaceous extracellular matrix    A layer consisting mainly of proteins (especially collagen) and glycosaminoglycans (mostly as proteoglycans) that forms a sheet underlying or overlying cells such as endothelial and epithelial cells. The proteins are secreted by cells in the vicinity. An example of this component is found in Mus musculus.

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