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(-) Description

Title :  CRYSTAL STRUCTURE OF ADENINE PHOSPHORIBOSYLTRANSFERASE (APRT) FROM LEISHMANIA TARENTOLAE
 
Authors :  O. H. Thiemann, M. Silva, G. Oliva, C. H. T. P. Silva, J. Iulek
Date :  10 Oct 02  (Deposition) - 28 Oct 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Alpha/Beta Structure, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Silva, C. H. T. P. Silva, J. Iulek, G. Oliva, O. H. Thiemann
Crystal Structure Of Adenine Phosphoribosyltransferase From Leishmania Tarentolae: Potential Implications For Aprt Catalytic Mechanism.
Biochim. Biophys. Acta V. 1696 31 2004
PubMed-ID: 14726202  |  Reference-DOI: 10.1016/J.BBAPAP.2003.09.003

(-) Compounds

Molecule 1 - ADENINE PHOSPHORIBOSYLTRANSFERASE
    Chains: A
    EC Number: 2.4.2.7
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET29(+)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: LEISHMANIA TARENTOLAE
    Organism Taxid: 5689

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1AMP2Ligand/IonADENOSINE MONOPHOSPHATE
2PO42Ligand/IonPHOSPHATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:80 , ALA A:81 , ARG A:82 , ARG A:102 , LYS A:106 , HOH A:461 , HOH A:506 , HOH A:571 , HOH A:589BINDING SITE FOR RESIDUE PO4 A 401
2AC2SOFTWAREARG A:37 , ARG A:41 , PHE A:42 , ALA A:43 , ARG A:82 , ASP A:146 , ASP A:147 , VAL A:148 , ALA A:150 , THR A:151 , GLY A:152 , GLY A:153 , THR A:154 , HOH A:402 , HOH A:403 , HOH A:514 , HOH A:589BINDING SITE FOR RESIDUE AMP A 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:70 -Pro A:71
2Asp A:80 -Ala A:81

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1MZV)

(-) 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:216
 aligned with O77103_LEITA | O77103 from UniProtKB/TrEMBL  Length:235

    Alignment length:216
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
         O77103_LEITA     2 SLKEIGPNSLLLEDSHSLSQLLKKNYRWYSPIFSPRNVPRFADVSSITESPETLKAIRDFLVERYRTMSPAPTHILGFDARGFLFGPMIAVELGIPFVLMRKADKNAGLLIRSEPYEKEYKEAAPEVMTIRHGSIGKNSRVVLIDDVLATGGTALSGLQLVEASGAEVVEMVSILTIPFLKAAERIHSTAGGRYKNVRFIGLLSEDVLTEANCGDL 217
               SCOP domains d1mzva_ A: Adenine PRTase                                                                                                                                                                                                SCOP domains
               CATH domains 1mzvA00 A:2-217  [code=3.40.50.2020, no name defined]                                                                                                                                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee..eeee...hhhhhhhhhhheeehhhhh......eeehhhhhhhhhhhhhhhhhhhhhhhh......eeeee.hhhhhhhhhhhhhhh..eeee.hhhhh...eee................eee........eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeee.hhhhhhhhhhhhhhhh.....eeeeee.hhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1mzv A   2 SLKEIGPNSLLLEDSHSLSQLLKKNYRWYSPIFSPRNVPRFADVSSITESPETLKAIRDFLVERYRTMSPAPTHILGFDARGFLFGPMIAVELGIPFVLMRKADKNAGLLIRSEPYEKEYKEAAPEVMTIRHGSIGKNSRVVLIDDVLATGGTALSGLQLVEASGAEVVEMVSILTIPFLKAAERIHSTAGGRYKNVRFIGLLSEDVLTEANCGDL 217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (O77103_LEITA | O77103)
molecular function
    GO:0003999    adenine phosphoribosyltransferase activity    Catalysis of the reaction: AMP + diphosphate = adenine + 5-phospho-alpha-D-ribose 1-diphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
    GO:0009116    nucleoside metabolic process    The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).

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(-) Related Entries Specified in the PDB File

1qb7 CRYSTAL STRUCTURES OF ADENINE PHOSPHORIBOSYLTRANSFERASE FROM LEISHMANIA DONOVANI