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(-) Description

Title :  T4 PHAGE BGT-D100A MUTANT IN COMPLEX WITH UDP-GLUCOSE: FORM II
 
Authors :  L. Lariviere, S. Morera
Date :  17 Feb 03  (Deposition) - 09 Sep 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Glycosyltransferase, Gt-B, Udp-Glucose, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Lariviere, V. Gueguen-Chaignon, S. Morera
Crystal Structures Of The T4 Phage Beta-Glucosyltransferase And The D100A Mutant In Complex With Udp-Glucose: Glucose Binding And Identification Of The Catalytic Base For A Direct Displacement Mechanism.
J. Mol. Biol. V. 330 1077 2003
PubMed-ID: 12860129  |  Reference-DOI: 10.1016/S0022-2836(03)00635-1

(-) Compounds

Molecule 1 - DNA BETA-GLYCOSYLTRANSFERASE
    Chains: A
    EC Number: 2.4.1.27
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PBSK
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BGT
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Synonym: BGT

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GOL2Ligand/IonGLYCEROL
3UPG1Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:101 , ARG A:102 , TYR A:261 , HOH A:610BINDING SITE FOR RESIDUE CL A 352
2AC2SOFTWARELYS A:166 , MET A:240 , VAL A:243 , SER A:244BINDING SITE FOR RESIDUE CL A 353
3AC3SOFTWAREVAL A:18 , GLU A:22 , THR A:99 , GLN A:137 , GLY A:187 , 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 , THR A:267 , LEU A:268 , ARG A:269 , GLU A:272 , GOL A:355 , HOH A:364 , HOH A:373 , HOH A:395 , HOH A:398 , HOH A:473 , HOH A:505 , HOH A:549 , HOH A:551BINDING SITE FOR RESIDUE UPG A 354
4AC4SOFTWAREGLU A:22 , ARG A:102 , LEU A:103 , UPG A:354 , HOH A:504 , HOH A:516 , HOH A:541 , HOH A:559BINDING SITE FOR RESIDUE GOL A 355
5AC5SOFTWAREASP A:38 , ILE A:39 , VAL A:46 , TYR A:47 , THR A:48 , LYS A:49 , ASP A:317 , LYS A:321BINDING SITE FOR RESIDUE GOL A 356

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1NZF)

(-) 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: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 d1nzfa_ A: beta-Glucosyltransferase (DNA-modifying)                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1nzfA01 A:1-166,A:333-349 Glycogen Phosphorylase B;                                                                                                                   1nzfA02 A:167-332 Glycogen Phosphorylase B;                                                                                                                           1nzfA01          -- CATH domains
               Pfam domains T4-Gluco-transf-1nzfA01 A:1-38        ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.........hhhhhhhhhhhhhhhh....eeeee......eee.hhhhhhhh.eeeee.....hhhhh.hhhhhhhhhhhhhh...eeeee.........hhhhhh.hhhhhhhhhhhhh....eeeee...hhhhhhhhh.....eeeeee.hhhhhh...............eeeeee.....hhhhhhhhhhhh.....eeee...hhhhh...........ee....hhhhhhhhhh.eeeeee...........hhhhhhhhh...eeeee.hhhh......hhh.ee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1nzf A   1 MKIAIINMGNNVINFKTVPSSETIYLFKVISEMGLNVDIISLKNGVYTKSFDEVDVNDYDRLIVVNSSINFFGGKPNLAILSAQKFMAKYKSKIYYLFTAIRLPFSQSWPNVKNRPWAYLYTEEELLIKSPIKVISQGINLDIAKAAHKKVDNVIEFEYFPIEQYKIHMNDFQLSKPTKKTLDVIYGGSFRSGQRESKMVEFLFDTGLNIEFFGNAREKQFKNPKYPWTKAPVFTGKIPMNMVSEKNSQAIAALIIGDKNYNDNFITLRVWETMASDAVMLIDEEFDTKHRIINDARFYVNNRAELIDRVNELKHSDVLRKEMLSIQHDILNKTRAKKAEWQDAFKKAIDL 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
   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, 1)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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 1qkj 1sxp 1sxq 2bgt 2bgu

(-) Related Entries Specified in the PDB File

1j39 CRYSTAL STRUCTURE OF T4 PHAGE BGT IN COMPLEX WITH UDP- GLUCOSE
1nzd T4 PHAGE BGT-D100A MUTANT IN COMPLEX WITH UDP-GLUCOSE