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(-) Description

Title :  CRYSTAL STRUCTURE OF LACTOBACILLUS HELVETICUS PURINE DEOXYRIBOSYL TRANSFERASE (PDT) WITH THE TRICYCLIC PURINE 8,9-DIHYDRO-9-OXOIMIDAZO[2,1-B]PURINE (N2,3-ETHENOGUANINE)
 
Authors :  D. Paul, J. Seckute, S. E. Ealick
Date :  26 Aug 13  (Deposition) - 15 Oct 14  (Release) - 15 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Purine Deoxyribosyl Transferase (Pdt), Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Ye, D. Paul, L. Gao, J. Seckute, R. Sangaiah, J. Karupiah, Z. Zhang, A. P. Kaminski, S. E. Ealick, A. Gold, L. M. Ball
Glycosylation Of A Tricyclic Purine Analog At Alternative Sites By Nucleoside 2 -Deoxyribosyltransferases
Plos One 2014
PubMed: search

(-) Compounds

Molecule 1 - NUCLEOSIDE DEOXYRIBOSYLTRANSFERASE
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: LBHH_1694
    Organism Scientific: LACTOBACILLUS HELVETICUS
    Organism Taxid: 767462
    Strain: H10

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
128Y3Ligand/Ion3H-IMIDAZO[2,1-B]PURIN-4(5H)-ONE
2SO42Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:5 , HOH A:322 , HOH A:326 , PRO C:6 , THR C:7BINDING SITE FOR RESIDUE SO4 A 201
2AC2SOFTWAREPRO A:44 , PHE A:45 , TRP A:67 , THR A:71 , ASP A:75 , HOH A:341 , HOH A:367 , HOH A:379 , ASN C:128 , LEU C:129 , MET C:130 , TYR C:167BINDING SITE FOR RESIDUE 28Y A 202
3AC3SOFTWAREASN A:128 , LEU A:129 , MET A:130 , TYR A:167 , PRO B:44 , TRP B:67 , THR B:71 , ASP B:75 , LEU B:129 , TYR B:167 , 28Y B:202 , PRO C:44 , PHE C:45 , THR C:71 , ASP C:75BINDING SITE FOR RESIDUE 28Y B 201
4AC4SOFTWARELEU A:129 , TYR A:167 , PRO B:44 , TRP B:67 , THR B:71 , ASP B:75 , ASN B:128 , LEU B:129 , TYR B:167 , 28Y B:201 , PRO C:44 , PHE C:45 , THR C:71 , ASP C:75BINDING SITE FOR RESIDUE 28Y B 202
5AC5SOFTWARELYS A:9 , LYS B:9 , LYS C:9 , ASN C:81 , HOH C:314 , HOH C:318 , HOH C:322BINDING SITE FOR RESIDUE SO4 C 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4MEJ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly C:60 -Gly C:61

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MEJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MEJ)

(-) Exons   (0, 0)

(no "Exon" information available for 4MEJ)

(-) 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:167
                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee....hhhhhhhhhhhhhhhhh...eeeee.....................hhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhh...eeeeee........eeehhhhhhh.ee.....hhhhhhh..............eee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mej A   1 MKAVVPTGKIYLGSPFYSDAQRERAAKAKELLAKNPSIAHVFFPFDDGFTDPDEKNPEIGGIRSMVWRDATYQNDLTGISNATCGVFLYDMDQLDDGSAFEIGFMRAMHKPVILVPFTEHPEKEKKMNLMIAQGVTTIIDGNTEFEKLADYNFNECPSNPVRGYGIY 167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       


Chain B from PDB  Type:PROTEIN  Length:167
                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee......hhhhhhhhhhhhhhh...eeeee.....................hhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhh...eeeeee........eeehhhhhhh.ee.....hhhhhhh..............eee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mej 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
                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee......hhhhhhhhhhhhhhh...eeeee.....................hhhhhhhhhhhhhhhhhhh.eeeeeee....hhhhhhhhhhhhhh...eeeeee........eeehhhhhhh.ee.hhhhhhhhhhh..............eee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mej C   1 MKAVVPTGKIYLGSPFYSDAQRERAAKAKELLAKNPSIAHVFFPFDDGFTDPDEKNPEIGGIRSMVWRDATYQNDLTGISNATCGVFLYDMDQLDDGSAFEIGFMRAMHKPVILVPFTEHPEKEKKMNLMIAQGVTTIIDGNTEFEKLADYNFNECPSNPVRGYGIY 167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4MEJ)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MEJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MEJ)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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1s2l