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(-) Description

Title :  CRYSTAL STRUCTURE OF NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE
 
Authors :  S. R. Armstrong, W. J. Cook, S. A. Short, S. E. Ealick
Date :  05 Jul 00  (Deposition) - 26 Jul 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Active Site, Alpha/Beta Protein, Biocatalyst, Nucleoside, X- Ray Crystallography, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. R. Armstrong, W. J. Cook, S. A. Short, S. E. Ealick
Crystal Structures Of Nucleoside 2-Deoxyribosyltransferase In Native And Ligand-Bound Forms Reveal Architecture Of The Active Site.
Structure V. 4 97 1996
PubMed-ID: 8805514  |  Reference-DOI: 10.1016/S0969-2126(96)00013-5
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NUCLEOSIDE 2-DEOXYRIBOSYLTRANSFERASE
    Chains: A, B
    EC Number: 2.4.2.6
    Organism Scientific: LACTOBACILLUS LEICHMANNII
    Organism Taxid: 28039

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1F8X)

(-) Sites  (0, 0)

(no "Site" information available for 1F8X)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F8X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1F8X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F8X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1F8X)

(-) Exons   (0, 0)

(no "Exon" information available for 1F8X)

(-) 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:156
 aligned with NTD_LACLE | Q9R5V5 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      
            NTD_LACLE     2 PKKTIYFGAGWFTDRQNKAYKEAMEALKENPTIDLENSYVPLDNQYKGIRVDEHPEYLHDKVWATATYNNDLNGIKTNDIMLGVYIPDEEDVGLGMELGYALSQGKYVLLVIPDEDYGKPINLMSWGVSDNVIKMSQLKDFNFNKPRFDFYEGAVY 157
               SCOP domains d1f8xa_ A: Nucleoside 2-deoxyribosyltransferase                                                                                                              SCOP domains
               CATH domains 1f8xA00 A:2-157  [code=3.40.50.1810, no name defined]                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee...hhhhhhhhhhhhhhhhhh...hhhhh.hhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhhhhh.eeeee......hhhhhhhhhhhhhh..eeeeeehhhhh....hhhhhhhh.eeee.hhh.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1f8x A   2 PKKTIYFGAGWFTDRQNKAYKEAMEALKENPTIDLENSYVPLDNQYKGIRVDEHPEYLHDKVWATATYNNDLNGIKTNDIMLGVYIPDEEDVGLGMELGYALSQGKYVLLVIPDEDYGKPINLMSWGVSDNVIKMSQLKDFNFNKPRFDFYEGAVY 157
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      


Chain B from PDB  Type:PROTEIN  Length:156
 aligned with NTD_LACLE | Q9R5V5 from UniProtKB/Swiss-Prot  Length:157

    Alignment length:156
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151      
            NTD_LACLE     2 PKKTIYFGAGWFTDRQNKAYKEAMEALKENPTIDLENSYVPLDNQYKGIRVDEHPEYLHDKVWATATYNNDLNGIKTNDIMLGVYIPDEEDVGLGMELGYALSQGKYVLLVIPDEDYGKPINLMSWGVSDNVIKMSQLKDFNFNKPRFDFYEGAVY 157
               SCOP domains d1f8xb_ B: Nucleoside 2-deoxyribosyltransferase                                                                                                              SCOP domains
               CATH domains 1f8xB00 B:202-357  [code=3.40.50.1810, no name defined]                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee....hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhh..eeeeee.........hhhhhhhh.eeee.hhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1f8x B 202 PKKTIYFGAGWFTDRQNKAYKEAMEALKENPTIDLENSYVPLDNQYKGIRVDEHPEYLHDKVWATATYNNDLNGIKTNDIMLGVYIPDEEDVGLGMELGYALSQGKYVLLVIPDEDYGKPINLMSWGVSDNVIKMSQLKDFNFNKPRFDFYEGAVY 357
                                   211       221       231       241       251       261       271       281       291       301       311       321       331       341       351
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F8X)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NTD_LACLE | Q9R5V5)
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.
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.
    GO:0009117    nucleotide metabolic process    The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
    GO:0043173    nucleotide salvage    Any process which produces a nucleotide, a compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety, from derivatives of it without de novo synthesis.

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 Related Entries

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        NTD_LACLE | Q9R5V5: 1f8y 4hx9

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