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(-) Description

Title :  STRUCTURAL ANALYSIS OF A PROBABLE EUKARYOTIC D-AMINO ACID TRNA DEACYLASE
 
Authors :  M. A. Robien, W. G. J. Hol, Structural Genomics Of Pathogenic Proto Consortium (Sgpp)
Date :  20 May 04  (Deposition) - 08 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Biol. Unit 3:  D  (2x)
Keywords :  Sgpp, Structural Genomics, Psi, Protein Structure Initiative, Structural Genomics Of Pathogenic Protozoa Consortium, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Robien, W. G. J. Hol, Structural Genomics Of Pathogenic Protozoa
Structural Analysis Of Lmaj005534Aaa, A Probable Eukaryotic D-Amino Acid Trna Deacylase From Leishmania Major
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PROBABLE EUKARYOTIC D-AMINO ACID TRNA DEACYLASE, LMAJ005534AAA
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET14B
    Expression System Strain: BL21STAR/DE3
    Expression System Taxid: 562
    Expression System Vector Type: T7 SYSTEM
    Gene: L4171.5
    Organism Scientific: LEISHMANIA MAJOR
    Organism Taxid: 5664

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (2x):   C 
Biological Unit 3 (2x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1TC5)

(-) Sites  (0, 0)

(no "Site" information available for 1TC5)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1TC5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1TC5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1TC5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1TC5)

(-) Exons   (0, 0)

(no "Exon" information available for 1TC5)

(-) 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:187
 aligned with DTD_LEIMA | P84066 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:187
                                  1                                                                                                                                                                                    
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       
            DTD_LEIMA     - ------MLQAMDQGHLLVNNVDKYVRAGRGVMVYIAFLSDRDSAPITDEALRHAVGVLLHTKIFTHFSPEKMINQPQSLEECPEMDILIVPQASLGGKVKGRSVQFHQLVAKDVGAALYDRFCHFVRVARGVDESRVDANGAPRSEGDAPKAEGWIKYNSRVISGTFGNRQGLRFESEGPFTHMFDI 181
               SCOP domains d1tc5a_ A: probable eukaryotic D-amino acid tRNA deacylase                                                                                                                                  SCOP domains
               CATH domains 1tc5A00 A:8-194  [code=3.50.80.10, no name defined]                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.eeeee......eeee..eeeeeeeee........hhhhhhhhhhhhhhh........................eeeeee.hhhhheee..eee.....hhhhhhhhhhhhhhhhhhhh..............hhhhh............eee........eeeee.....eeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tc5 A   8 HMTIRVMLQAMDQGHLLVNNVDKYVRAGRGVMVYIAFLSDRDSAPITDEALRHAVGVLLHTKIFTHFSPEKMINQPQSLEECPEMDILIVPQASLGGKVKGRSVQFHQLVAKDVGAALYDRFCHFVRVARGVDESRVDANGAPRSEGDAPKAEGWIKYNSRVISGTFGNRQGLRFESEGPFTHMFDI 194
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       


Chain B from PDB  Type:PROTEIN  Length:187
 aligned with DTD_LEIMA | P84066 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:187
                                  1                                                                                                                                                                                    
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       
            DTD_LEIMA     - ------MLQAMDQGHLLVNNVDKYVRAGRGVMVYIAFLSDRDSAPITDEALRHAVGVLLHTKIFTHFSPEKMINQPQSLEECPEMDILIVPQASLGGKVKGRSVQFHQLVAKDVGAALYDRFCHFVRVARGVDESRVDANGAPRSEGDAPKAEGWIKYNSRVISGTFGNRQGLRFESEGPFTHMFDI 181
               SCOP domains d1tc5b_ B: probable eukaryotic D-amino acid tRNA deacylase                                                                                                                                  SCOP domains
               CATH domains 1tc5B00 B:8-194  [code=3.50.80.10, no name defined]                                                                                                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeee.eeeee......eeee..eeeeeeeee........hhhhhhhhhhhhhhh........................eeeeee.hhhhheee..eee.....hhhhhhhhhhhhhhhhhhhh..............hhhhh............eee........eeeee.....eeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tc5 B   8 HMTIRVMLQAMDQGHLLVNNVDKYVRAGRGVMVYIAFLSDRDSAPITDEALRHAVGVLLHTKIFTHFSPEKMINQPQSLEECPEMDILIVPQASLGGKVKGRSVQFHQLVAKDVGAALYDRFCHFVRVARGVDESRVDANGAPRSEGDAPKAEGWIKYNSRVISGTFGNRQGLRFESEGPFTHMFDI 194
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       


Chain C from PDB  Type:PROTEIN  Length:186
 aligned with DTD_LEIMA | P84066 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:186
                                 1                                                                                                                                                                                    
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175      
            DTD_LEIMA     - -----MLQAMDQGHLLVNNVDKYVRAGRGVMVYIAFLSDRDSAPITDEALRHAVGVLLHTKIFTHFSPEKMINQPQSLEECPEMDILIVPQASLGGKVKGRSVQFHQLVAKDVGAALYDRFCHFVRVARGVDESRVDANGAPRSEGDAPKAEGWIKYNSRVISGTFGNRQGLRFESEGPFTHMFDI 181
               SCOP domains d1tc5c_ C: probable eukaryotic D-amino acid tRNA deacylase                                                                                                                                 SCOP domains
               CATH domains 1tc5C00 C:9-194  [code=3.50.80.10, no name defined]                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeee.eeeee......eeee..eeeeeeeee........hhhhhhhhhhhhhhh........................eeeeee.hhhhheee..eee.....hhhhhhhhhhhhhhhhhhhh...............................eee........eeee......eeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tc5 C   9 MTIRVMLQAMDQGHLLVNNVDKYVRAGRGVMVYIAFLSDRDSAPITDEALRHAVGVLLHTKIFTHFSPEKMINQPQSLEECPEMDILIVPQASLGGKVKGRSVQFHQLVAKDVGAALYDRFCHFVRVARGVDESRVDANGAPRSEGDAPKAEGWIKYNSRVISGTFGNRQGLRFESEGPFTHMFDI 194
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188      


Chain D from PDB  Type:PROTEIN  Length:186
 aligned with DTD_LEIMA | P84066 from UniProtKB/Swiss-Prot  Length:181

    Alignment length:186
                                 1                                                                                                                                                                                    
                                 |   5        15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175      
            DTD_LEIMA     - -----MLQAMDQGHLLVNNVDKYVRAGRGVMVYIAFLSDRDSAPITDEALRHAVGVLLHTKIFTHFSPEKMINQPQSLEECPEMDILIVPQASLGGKVKGRSVQFHQLVAKDVGAALYDRFCHFVRVARGVDESRVDANGAPRSEGDAPKAEGWIKYNSRVISGTFGNRQGLRFESEGPFTHMFDI 181
               SCOP domains d1tc5d_ D: probable eukaryotic D-amino acid tRNA deacylase                                                                                                                                 SCOP domains
               CATH domains 1tc5D00 D:9-194  [code=3.50.80.10, no name defined]                                                                                                                                        CATH domains
           Pfam domains (1) -----Tyr_Deacylase-1tc5D01 D:14-194                                                                                                                                                        Pfam domains (1)
           Pfam domains (2) -----Tyr_Deacylase-1tc5D02 D:14-194                                                                                                                                                        Pfam domains (2)
           Pfam domains (3) -----Tyr_Deacylase-1tc5D03 D:14-194                                                                                                                                                        Pfam domains (3)
           Pfam domains (4) -----Tyr_Deacylase-1tc5D04 D:14-194                                                                                                                                                        Pfam domains (4)
         Sec.struct. author .eeeeeeeee.eeeee......eeee..eeeeeeeee........hhhhhhhhhhhhhhh........................eeeeee.hhhhheee..eee.....hhhhhhhhhhhhhhhhhhhh...............................eee........eeee......eeeee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tc5 D   9 MTIRVMLQAMDQGHLLVNNVDKYVRAGRGVMVYIAFLSDRDSAPITDEALRHAVGVLLHTKIFTHFSPEKMINQPQSLEECPEMDILIVPQASLGGKVKGRSVQFHQLVAKDVGAALYDRFCHFVRVARGVDESRVDANGAPRSEGDAPKAEGWIKYNSRVISGTFGNRQGLRFESEGPFTHMFDI 194
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: no clan defined [family: Tyr_Deacylase] (12)

(-) Gene Ontology  (4, 4)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (DTD_LEIMA | P84066)
molecular function
    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.
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.
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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