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(-) Description

Title :  CRYSTAL STRUCTURE OF THE THIOREDOXIN-FOLD DOMAIN OF HUMAN PHOSDUCIN-LIKE PROTEIN 2
 
Authors :  X. Lou, R. Bao, C. Zhou, Y. Chen
Date :  13 Oct 08  (Deposition) - 03 Mar 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Alpha Beta, 3-Layer(Aba) Sandwich, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Lou, R. Bao, C. Z. Zhou, Y. Chen
Structure Of The Thioredoxin-Fold Domain Of Human Phosducin-Like Protein 2
Acta Crystallogr. , Sect. F V. 65 67 2009
PubMed-ID: 19193988  |  Reference-DOI: 10.1107/S1744309108037342

(-) Compounds

Molecule 1 - PHOSDUCIN-LIKE PROTEIN 2
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: P28
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: THIOREDOXIN-FOLD DOMAIN, UNP RESIDUES 88-205
    Gene: PDCL2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 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, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1NA2Ligand/IonSODIUM ION
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:24 , PHE A:165 , ASN B:106BINDING SITE FOR RESIDUE PEG A 2
2AC2SOFTWARETYR B:100 , LYS B:175 , HOH B:207 , HOH B:220BINDING SITE FOR RESIDUE PEG B 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Leu A:161 -Pro A:162
2Leu B:161 -Pro B:162

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 3EVI)

(-) 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:118
 aligned with PDCL2_HUMAN | Q8N4E4 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:118
                                    97       107       117       127       137       147       157       167       177       187       197        
          PDCL2_HUMAN    88 KFGELREISGNQYVNEVTNAEEDVWVIIHLYRSSIPMCLLVNQHLSLLARKFPETKFVKAIVNSCIQHYHDNCLPTIFVYKNGQIEAKFIGIIECGGINLKLEELEWKLAEVGAIQTD 205
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.hhhhhhhhh.......eeeeeee...hhhhhhhhhhhhhhhhhh...eeeeee.hhh....hhhhh.eeeeee..eeeeeee..........hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3evi A  88 KFGELREISGNQYVNEVTNAEEDVWVIIHLYRSSIPMCLLVNQHLSLLARKFPETKFVKAIVNSCIQHYHDNCLPTIFVYKNGQIEAKFIGIIECGGINLKLEELEWKLAEVGAIQTD 205
                                    97       107       117       127       137       147       157       167       177       187       197        


Chain B from PDB  Type:PROTEIN  Length:118
 aligned with PDCL2_HUMAN | Q8N4E4 from UniProtKB/Swiss-Prot  Length:241

    Alignment length:118
                                    97       107       117       127       137       147       157       167       177       187       197        
          PDCL2_HUMAN    88 KFGELREISGNQYVNEVTNAEEDVWVIIHLYRSSIPMCLLVNQHLSLLARKFPETKFVKAIVNSCIQHYHDNCLPTIFVYKNGQIEAKFIGIIECGGINLKLEELEWKLAEVGAIQTD 205
               SCOP domains ---------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee.hhhhhhhhh.......eeeeeee...hhhhhhhhhhhhhhhhhh...eeeeee.hhh....hhhhh.eeeeee..eeeeeeehhhhh.....hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------- Transcript
                 3evi B  88 KFGELREISGNQYVNEVTNAEEDVWVIIHLYRSSIPMCLLVNQHLSLLARKFPETKFVKAIVNSCIQHYHDNCLPTIFVYKNGQIEAKFIGIIECGGINLKLEELEWKLAEVGAIQTD 205
                                    97       107       117       127       137       147       157       167       177       187       197
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3EVI)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PDCL2_HUMAN | Q8N4E4)
molecular function
    GO:0008479    queuine tRNA-ribosyltransferase activity    Catalysis of the reaction: tRNA guanine + queuine = tRNA queuine + guanine.
biological process
    GO:0008616    queuosine biosynthetic process    The chemical reactions and pathways resulting in the formation of queuosines, any of a series of nucleosides found in tRNA and having an additional pentenyl ring added via an NH group to the methyl group of 7-methylguanosine. The pentenyl ring may carry other substituents.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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