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(-) Description

Title :  PURINE 2'DEOXYRIBOSYLTRANSFERASE + 2'-DEOXYADENOSINE
 
Authors :  R. Anand, P. A. Kaminski, S. E. Ealick
Date :  08 Jan 04  (Deposition) - 30 Mar 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Ptd, 2'-Deoxyadenosine, 2'-Purine Deoxyribosyltansferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Anand, P. A. Kaminski, S. E. Ealick
Structures Of Purine 2'-Deoxyribosyltransferase, Substrate Complexes, And The Ribosylated Enzyme Intermediate At 2. 0 A Resolution.
Biochemistry V. 43 2384 2004
PubMed-ID: 14992575  |  Reference-DOI: 10.1021/BI035723K

(-) Compounds

Molecule 1 - PURINE TRANS DEOXYRIBOSYLASE
    Chains: A, B, C
    EC Number: 2.4.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: PURINE 2'-DEOXYRIBOSYLTANSFERASE
    Organism Scientific: LACTOBACILLUS HELVETICUS
    Organism Taxid: 1587

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
13D13Ligand/Ion(2R,3S,5R)-5-(6-AMINO-9H-PURIN-9-YL)-TETRAHYDRO-2-(HYDROXYMETHYL)FURAN-3-OL
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
13D16Ligand/Ion(2R,3S,5R)-5-(6-AMINO-9H-PURIN-9-YL)-TETRAHYDRO-2-(HYDROXYMETHYL)FURAN-3-OL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:11 , GLY A:13 , SER A:14 , TYR A:17 , PRO A:44 , PHE A:45 , THR A:71 , ASP A:75 , ASP A:95 , GLY A:97 , GLU A:101 , HOH A:1214 , ASN C:128 , MET C:130 , TYR C:167 , HOH C:1174BINDING SITE FOR RESIDUE 3D1 A 1168
2AC2SOFTWAREGLY B:13 , SER B:14 , TYR B:17 , PRO B:44 , PHE B:45 , THR B:71 , ASP B:75 , ASP B:95 , GLY B:97 , GLU B:101 , ASN B:128 , LEU B:129 , MET B:130 , TYR B:167 , HOH B:1184BINDING SITE FOR RESIDUE 3D1 B 1169
3AC3SOFTWAREASN A:128 , LEU A:129 , MET A:130 , TYR A:167 , HOH A:1182 , GLY C:13 , SER C:14 , PRO C:44 , PHE C:45 , TRP C:67 , THR C:71 , ASP C:75 , ASP C:95 , GLY C:97 , GLU C:101BINDING SITE FOR RESIDUE 3D1 C 1170

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S2G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1S2G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S2G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1S2G)

(-) Exons   (0, 0)

(no "Exon" information available for 1S2G)

(-) 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:165
 aligned with Q8RLY5_LACHE | Q8RLY5 from UniProtKB/TrEMBL  Length:167

    Alignment length:167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       
         Q8RLY5_LACHE     1 MKAVVPTGKIYLGSPFYSDAQRERAAKAKELLAKNPSIAHVFFPFDDGFTDPDEKNPEIGGIRSMVWRDATYQNDLTGISNATCGVFLYDMDQLDDGSAFEIGFMRAMHKPVILVPFTEHPEKEKKMNLMIAQGVTTIIDGNTEFEKLADYNFNECPSNPVRGYGIY 167
               SCOP domains d1s2ga_ A: Purine transdeoxyribosylase                                                                                                                                  SCOP domains
               CATH domains 1s2gA00 A:1-167  [code=3.40.50.1810, no name d efined]                                                                                                                  CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee....hhhhhhhhhhhhhhhh....eeeee....-........-.......hhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhh...eeeeee........eehhhhhhhh.ee.....hhhhhhh..............ee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s2g A   1 MKAVVPTGKIYLGSPFYSDAQRERAAKAKELLAKNPSIAHVFFPFD-GFTDPDEK-PEIGGIRSMVWRDATYQNDLTGISNATCGVFLYDMDQLDDGSAFEIGFMRAMHKPVILVPFTEHPEKEKKMNLMIAQGVTTIIDGNTEFEKLADYNFNECPSNPVRGYGIY 167
                                    10        20        30        40     | |50    | | 60        70        80        90       100       110       120       130       140       150       160       
                                                                        46 |     55 |                                                                                                              
                                                                          48       57                                                                                                              


Chain B from PDB  Type:PROTEIN  Length:167
 aligned with Q8RLY5_LACHE | Q8RLY5 from UniProtKB/TrEMBL  Length:167

    Alignment length:167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       
         Q8RLY5_LACHE     1 MKAVVPTGKIYLGSPFYSDAQRERAAKAKELLAKNPSIAHVFFPFDDGFTDPDEKNPEIGGIRSMVWRDATYQNDLTGISNATCGVFLYDMDQLDDGSAFEIGFMRAMHKPVILVPFTEHPEKEKKMNLMIAQGVTTIIDGNTEFEKLADYNFNECPSNPVRGYGIY 167
               SCOP domains d1s2gb_ B: Purine transdeoxyribosylase                                                                                                                                  SCOP domains
               CATH domains 1s2gB00 B:1-167  [code=3.40.50.1810, no name defined]                                                                                                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee....hhhhhhhhhhhhhhhhh...eeeee.....................hhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhh...eeeeee........eeehhhhhhh.ee.hhhhhhhhhhh..............eee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s2g B   1 MKAVVPTGKIYLGSPFYSDAQRERAAKAKELLAKNPSIAHVFFPFDDGFTDPDEKNPEIGGIRSMVWRDATYQNDLTGISNATCGVFLYDMDQLDDGSAFEIGFMRAMHKPVILVPFTEHPEKEKKMNLMIAQGVTTIIDGNTEFEKLADYNFNECPSNPVRGYGIY 167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       


Chain C from PDB  Type:PROTEIN  Length:167
 aligned with Q8RLY5_LACHE | Q8RLY5 from UniProtKB/TrEMBL  Length:167

    Alignment length:167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       
         Q8RLY5_LACHE     1 MKAVVPTGKIYLGSPFYSDAQRERAAKAKELLAKNPSIAHVFFPFDDGFTDPDEKNPEIGGIRSMVWRDATYQNDLTGISNATCGVFLYDMDQLDDGSAFEIGFMRAMHKPVILVPFTEHPEKEKKMNLMIAQGVTTIIDGNTEFEKLADYNFNECPSNPVRGYGIY 167
               SCOP domains d1s2gc_ C: Purine transdeoxyribosylase                                                                                                                                  SCOP domains
               CATH domains 1s2gC00 C:1-167  [code=3.40.50.1810, no name defined]                                                                                                                   CATH domains
           Pfam domains (1) ---------Nuc_deoxyrib_tr-1s2gC01 C:10-130                                                                                         ------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------Nuc_deoxyrib_tr-1s2gC02 C:10-130                                                                                         ------------------------------------- Pfam domains (2)
           Pfam domains (3) ---------Nuc_deoxyrib_tr-1s2gC03 C:10-130                                                                                         ------------------------------------- Pfam domains (3)
         Sec.struct. author .......eeeeee....hhhhhhhhhhhhhhhhh...eeeee.....................hhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhh...eeeeee..........hhhhhhhh.ee.hhhhhhhhhhh................. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s2g C   1 MKAVVPTGKIYLGSPFYSDAQRERAAKAKELLAKNPSIAHVFFPFDDGFTDPDEKNPEIGGIRSMVWRDATYQNDLTGISNATCGVFLYDMDQLDDGSAFEIGFMRAMHKPVILVPFTEHPEKEKKMNLMIAQGVTTIIDGNTEFEKLADYNFNECPSNPVRGYGIY 167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
   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, 3)

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

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: Nribosyltransf (19)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (Q8RLY5_LACHE | Q8RLY5)
molecular function
    GO:0070694    deoxyribonucleoside 5'-monophosphate N-glycosidase activity    Catalysis of the reaction: a deoxyribonucleoside 5'-monophosphate + H2O = deoxyribose 5-monophosphate + a purine or pyrimidine base.
    GO:0050144    nucleoside deoxyribosyltransferase activity    Catalysis of the reaction: 2-deoxy-D-ribosyl-base1 + base2 = 2-deoxy-D-ribosyl-base2 + base1.
    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:0009159    deoxyribonucleoside monophosphate catabolic process    The chemical reactions and pathways resulting in the breakdown of a deoxyribonucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with phosphate on the sugar.

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        Q8RLY5_LACHE | Q8RLY5: 1s2d 1s2i 1s2l 1s3f

(-) Related Entries Specified in the PDB File

1f8y STRUCTURE OF 2'-DEOXYRIBOSYLTRANSFERASE(NTD)
1s2d PURINE 2'-DEOXYRIBOSYL COMPLEX WITH ARABINOSIDE: RIBOSYLATED INTERMEDIATE (ARAA)
1s2i PURINE 2'DEOXYRIBOSYLTRANSFERASE + BROMOPURINE
1s2l PURINE 2'DEOXYRIBOSYLTRANSFERASE NATIVE STRUCTURE
1s3f PURINE 2'-DEOXYRIBOSYLTRANSFERASE + SELENOINOSINE