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(-) Description

Title :  BGT IN COMPLEX WITH A 13MER DNA CONTAINING A CENTRAL C:G BASE PAIR AND UDP
 
Authors :  L. Lariviere, S. Morera
Date :  31 Mar 04  (Deposition) - 22 Jun 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,C,E  (1x)
Biol. Unit 2:  B,D,F  (1x)
Keywords :  Flipped-Out Base, Transferase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Lariviere, S. Morera
Structural Evidence Of A Passive Base Flipping Mechanism For {Beta}-Glucosyltransferase
J. Biol. Chem. V. 279 34715 2004
PubMed-ID: 15178685  |  Reference-DOI: 10.1074/JBC.M404394200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*AP*AP*AP*AP*AP*AP*GP*TP*TP*TP*TP*TP*T)-3'
    Chains: C, D
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(*AP*AP*AP*AP*AP*AP*CP*TP*TP*TP*TP*TP*T)-3'
    Chains: E, F
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA BETA-GLUCOSYLTRANSFERASE
    Chains: A, B
    EC Number: 2.4.1.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BGT, BETA-GT
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Synonym: BGT

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): A C E 
Biological Unit 2 (1x):  B D F

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:18 , GLY A:188 , SER A:189 , ARG A:191 , ARG A:195 , PHE A:213 , GLY A:214 , LYS A:237 , ILE A:238 , MET A:240 , VAL A:243 , TYR A:261 , ARG A:269 , GLU A:272 , HOH A:413 , HOH A:419 , HOH A:445 , HOH A:452 , HOH A:469 , HOH A:526 , HOH A:575 , HOH A:685BINDING SITE FOR RESIDUE UDP A 400
2AC2SOFTWAREVAL B:18 , GLY B:188 , SER B:189 , ARG B:191 , ARG B:195 , PHE B:213 , GLY B:214 , LYS B:237 , ILE B:238 , MET B:240 , VAL B:243 , TYR B:261 , ARG B:269 , GLU B:272 , HOH B:408 , HOH B:412 , HOH B:424 , HOH B:474 , HOH B:563 , HOH B:582 , HOH B:586 , HOH B:659BINDING SITE FOR RESIDUE UDP B 400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1SXQ)

(-) 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:351
 aligned with GSTB_BPT4 | P04547 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:351
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350 
            GSTB_BPT4     1 MKIAIINMGNNVINFKTVPSSETIYLFKVISEMGLNVDIISLKNGVYTKSFDEVDVNDYDRLIVVNSSINFFGGKPNLAILSAQKFMAKYKSKIYYLFTDIRLPFSQSWPNVKNRPWAYLYTEEELLIKSPIKVISQGINLDIAKAAHKKVDNVIEFEYFPIEQYKIHMNDFQLSKPTKKTLDVIYGGSFRSGQRESKMVEFLFDTGLNIEFFGNAREKQFKNPKYPWTKAPVFTGKIPMNMVSEKNSQAIAALIIGDKNYNDNFITLRVWETMASDAVMLIDEEFDTKHRIINDARFYVNNRAELIDRVNELKHSDVLRKEMLSIQHDILNKTRAKKAEWQDAFKKAIDL 351
               SCOP domains d1sxqa_ A: beta-Glucosyltransferase (DNA-modifying)                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1sxqA01 A:1-166,A:333-349 Glycogen Phosphorylase B;                                                                                                                   1sxqA02 A:167-332 Glycogen Phosphorylase B;                                                                                                                           1sxqA01          -- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.........hhhhhhhhhhhhhhhh...eeeeee......eee.hhhhhhhh.eeeee.....hhhhh.hhhhhhhhhhhhhh...eeeee.........hhhhh....hhhhhhhhhhh....eeeee...hhhhhhhhh.....eeeeee.hhhhhhhhh............eeeeee..hhhhhhhhhhhhhhh.....eeee...hhhhh...........eee...hhhhhhhhhh.eeeeee..hhhhh....hhhhhhhhh...eeeee.hhh.......hhh.ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sxq A   1 MKIAIINMGNNVINFKTVPSSETIYLFKVISEMGLNVDIISLKNGVYTKSFDEVDVNDYDRLIVVNSSINFFGGKPNLAILSAQKFMAKYKSKIYYLFTDIRLPFSQSWPNVKNRPWAYLYTEEELLIKSPIKVISQGINLDIAKAAHKKVDNVIEFEYFPIEQYKIHMNDFQLSKPTKKTLDVIYGGSFRSGQRESKMVEFLFDTGLNIEFFGNAREKQFKNPKYPWTKAPVFTGKIPMNMVSEKNSQAIAALIIGDKNYNDNFITLRVWETMASDAVMLIDEEFDTKHRIINDARFYVNNRAELIDRVNELKHSDVLRKEMLSIQHDILNKTRAKKAEWQDAFKKAIDL 351
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350 


Chain B from PDB  Type:PROTEIN  Length:351
 aligned with GSTB_BPT4 | P04547 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:351
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350 
            GSTB_BPT4     1 MKIAIINMGNNVINFKTVPSSETIYLFKVISEMGLNVDIISLKNGVYTKSFDEVDVNDYDRLIVVNSSINFFGGKPNLAILSAQKFMAKYKSKIYYLFTDIRLPFSQSWPNVKNRPWAYLYTEEELLIKSPIKVISQGINLDIAKAAHKKVDNVIEFEYFPIEQYKIHMNDFQLSKPTKKTLDVIYGGSFRSGQRESKMVEFLFDTGLNIEFFGNAREKQFKNPKYPWTKAPVFTGKIPMNMVSEKNSQAIAALIIGDKNYNDNFITLRVWETMASDAVMLIDEEFDTKHRIINDARFYVNNRAELIDRVNELKHSDVLRKEMLSIQHDILNKTRAKKAEWQDAFKKAIDL 351
               SCOP domains d1sxqb_ B: beta-Glucosyltransferase (DNA-modifying)                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1sxqB01 B:1-166,B:333-349 Glycogen Phosphorylase B;                                                                                                                   1sxqB02 B:167-332 Glycogen Phosphorylase B;                                                                                                                           1sxqB01          -- CATH domains
           Pfam domains (1) T4-Gluco-transf-1sxqB01 B:1-38        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) T4-Gluco-transf-1sxqB02 B:1-38        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeeeee.........hhhhhhhhhhhhhhhh...eeeeee......eee.hhhhhhhh.eeeee.....hhhhh.hhhhhhhhhhhhhh...eeeee.........hhhhhh...hhhhhhhhhhh....eeeee...hhhhhhhhh.....eeeeee.hhhhhhhhh............eeeeee..hhhhhhhhhhhhhhh.....eeee...hhhhh...........eee...hhhhhhhhhh.eeeeee..hhhhh....hhhhhhhhh...eeeee.hhh.......hhh.ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sxq B   1 MKIAIINMGNNVINFKTVPSSETIYLFKVISEMGLNVDIISLKNGVYTKSFDEVDVNDYDRLIVVNSSINFFGGKPNLAILSAQKFMAKYKSKIYYLFTDIRLPFSQSWPNVKNRPWAYLYTEEELLIKSPIKVISQGINLDIAKAAHKKVDNVIEFEYFPIEQYKIHMNDFQLSKPTKKTLDVIYGGSFRSGQRESKMVEFLFDTGLNIEFFGNAREKQFKNPKYPWTKAPVFTGKIPMNMVSEKNSQAIAALIIGDKNYNDNFITLRVWETMASDAVMLIDEEFDTKHRIINDARFYVNNRAELIDRVNELKHSDVLRKEMLSIQHDILNKTRAKKAEWQDAFKKAIDL 351
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350 


Chain C from PDB  Type:DNA  Length:13
                                             
                 1sxq C   1 AAAAAAGTTTTTT  13
                                    10   


Chain D from PDB  Type:DNA  Length:13
                                             
                 1sxq D   1 AAAAAAGTTTTTT  13
                                    10   


Chain E from PDB  Type:DNA  Length:13
                                             
                 1sxq E  14 AAAAAACTTTTTT  26
                                    23   


Chain F from PDB  Type:DNA  Length:13
                                             
                 1sxq F  14 AAAAAACTTTTTT  26
                                    23
   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, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Architecture: 3-Layer(aba) Sandwich (12045)
(-)
Topology: Rossmann fold (7312)
(-)
Homologous Superfamily: Glycogen Phosphorylase B; (202)
(-)
[unclassified] (4)
1a1sxqA01A:1-166,A:333-349
1b1sxqA02A:167-332
1c1sxqB02B:167-332
1d1sxqB01B:1-166,B:333-349

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: T4-Gluco-transf] (12)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GSTB_BPT4 | P04547)
molecular function
    GO:0033821    DNA beta-glucosyltransferase activity    Catalysis of the transfer of a beta-D-glucosyl residue from UDP-glucose to a hydroxymethylcytosine residue in DNA.
    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:0006304    DNA modification    The covalent alteration of one or more nucleotide sites in DNA, resulting in a change in its properties.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.

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  2.4.1.27
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GSTB_BPT4 | P04547: 1bgt 1bgu 1c3j 1ixy 1j39 1jej 1jg6 1jg7 1jiu 1jiv 1jix 1m5r 1nvk 1nzd 1nzf 1qkj 1sxp 2bgt 2bgu

(-) Related Entries Specified in the PDB File

1ixy 1m5r 1sxp