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(-) Description

Title :  CRYSTAL STRUCTURE OF CONSERVED PROTEIN OF UNKNOWN FUNCTION AF0625
 
Authors :  Y. Liu, T. Skarina, A. Dong, M. Kudritskam, A. Savchenko, E. F. Pai, A. Edwards, Midwest Center For Structural Genomics (Mcsg)
Date :  01 Feb 05  (Deposition) - 15 Mar 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym./Biol. Unit :  A
Keywords :  Af0625, Sulfur Sad, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Liu, T. Skarina, A. Dong, M. Kudritskam, A. Savchenko, E. F. Pai, A. Edwards
Crystal Structure Of Conserved Hypothetical Protein Af0625
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL UPF0204 PROTEIN AF0625
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GI|2649994
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 2234

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1POP1Ligand/IonPYROPHOSPHATE 2-

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:50 , ILE A:52 , ARG A:75 , HIS A:76 , SER A:77 , HIS A:139 , HOH A:4043BINDING SITE FOR RESIDUE POP A 3000

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:140 -Pro A:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1YQE)

(-) 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:282
 aligned with DTDA_ARCFU | O29630 from UniProtKB/Swiss-Prot  Length:278

    Alignment length:282
                                1                                                                                                                                                                                                                                                                                     
                                |    6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276  
           DTDA_ARCFU     - ----MKLVVCSESDTAGQNIKDNLLTFADFEEKDVGEFKLYLSDEFYIAETKERLIYADHIDEKLAKYIDFEEILFASRHSSKDGRKIFTVHVSGNVGTADFGGKPYSLAKPSPQTMKNYVLALRERLDRKPEFEFTMEVTHHGPSEISKPSAFYEIGSTEEEWKDREAAEVVAEAMLDAIRAEKMDWNVAVGVGGTHYAPRQTEIMLTTTFTFGHNFAKYTFEHLTAEFLVKAVKLSEAEYIIIDEKSVNSAVKKIVNEAAEVAGVEVLKSKKVKKDFRLV 278
               SCOP domains ----d1yqea1 A:1-278 Hypothetical protein AF0625                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1yqeA01 A:-3-182 AF0625-like                                                                                                                                                              1yqeA02 A:183-278 AF0625-like                                                                    CATH domains
               Pfam domains -------------------------------------------------------tRNA_deacylase-1yqeA01 A:52-268                                                                                                                                                                                          ---------- Pfam domains
         Sec.struct. author .....eeeeee..hhhhhhhhhhhh.....eeeee..eeeee....eeeee..hhhhh.hhhhhhh......eeeeeeeee......eeeee....................hhhhhhhhhhhhhhhhhhh...eeee.............eeeeeeeehhhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.....hhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhhhhh.eeeehhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1yqe A  -3 FQGHMKLVVCSESDTAGQNIKDNLLTFADFEEKDVGEFKLYLSDEFYIAETKERLIYADHIDEKLAKYIDFEEILFASRHSSKDGRKIFTVHVSGNVGTADFGGKPYSLAKPSPQTMKNYVLALRERLDRKPEFEFTMEVTHHGPSEISKPSAFYEIGSTEEEWKDREAAEVVAEAMLDAIRAEKMDWNVAVGVGGTHYAPRQTEIMLTTTFTFGHNFAKYTFEHLTAEFLVKAVKLSEAEYIIIDEKSVNSAVKKIVNEAAEVAGVEVLKSKKVKKDFRLV 278
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: tRNA_deacylase] (1)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DTDA_ARCFU | O29630)
molecular function
    GO:0051499    D-aminoacyl-tRNA deacylase activity    Catalysis of the reaction: D-aminoacyl-tRNA = D-amino acid + tRNA. Hydrolysis of the removal of D-amino acids from residues in charged tRNA.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0019478    D-amino acid catabolic process    The chemical reactions and pathways resulting in the breakdown of D-amino acids, the D-enantiomers of amino acids.

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