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(-) Description

Title :  ALPHA-GLUCOSYLTRANSFERASE IN COMPLEX WITH UDP-GLUCOSE AND DNA CONTAINING AN ABASIC SITE
 
Authors :  L. Lariviere, N. Sommer, S. Morera
Date :  06 Dec 04  (Deposition) - 30 Aug 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Transferase, Transferase-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Lariviere, N. Sommer, S. Morera
Structural Evidence Of A Passive Base-Flipping Mechanism Fo Agt, An Unusual Gt-B Glycosyltransferase.
J. Mol. Biol. V. 352 139 2005
PubMed-ID: 16081100  |  Reference-DOI: 10.1016/J.JMB.2005.07.007

(-) Compounds

Molecule 1 - 5'-D(*GP*AP*TP*AP*CP*TP*(3DR)P*AP*GP*AP*TP*AP*G)-3'
    Chains: C
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - 5'-D(*CP*TP*AP*TP*CP*TP*GP*AP*GP*TP*AP*TP*C)-3'
    Chains: D
    Engineered: YES
    Synthetic: YES
 
Molecule 3 - DNA ALPHA-GLUCOSYLTRANSFERASE
    Chains: A, B
    EC Number: 2.4.1.26
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PROEXHTB
    Expression System Strain: XL1BLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Synonym: AGT

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 9)

Asymmetric Unit (5, 9)
No.NameCountTypeFull Name
13DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2GOL4Ligand/IonGLYCEROL
3PEG2Ligand/IonDI(HYDROXYETHYL)ETHER
4UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
5UPG1Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE
Biological Unit 1 (4, 5)
No.NameCountTypeFull Name
13DR1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2GOL2Ligand/IonGLYCEROL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4UDP-1Ligand/IonURIDINE-5'-DIPHOSPHATE
5UPG1Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
13DR-1Mod. Nucleotide1',2'-DIDEOXYRIBOFURANOSE-5'-PHOSPHATE
2GOL2Ligand/IonGLYCEROL
3PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
4UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
5UPG-1Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:1014 , GLY A:1015 , ARG A:1046 , SER A:1049 , HIS A:1050 , HIS A:1114 , HIS A:1116 , HIS A:1140 , ARG A:1204 , TRP A:1208 , LYS A:1209 , CYS A:1274 , TYR A:1275 , ASN A:1277 , GLU A:1306 , TYR A:1307 , THR A:1308 , GLU A:1311BINDING SITE FOR RESIDUE UPG A 501
2AC2SOFTWAREHOH B:149 , GOL B:602 , CYS B:1014 , GLY B:1015 , ARG B:1046 , HIS B:1050 , ARG B:1204 , LYS B:1209 , TYR B:1275 , ASN B:1277 , GLU B:1306 , TYR B:1307 , THR B:1308 , GLU B:1311BINDING SITE FOR RESIDUE UDP B 601
3AC3SOFTWAREHOH B:149 , UDP B:601 , HIS B:1114 , HIS B:1140 , GLU B:1306BINDING SITE FOR RESIDUE GOL B 602
4AC4SOFTWAREGOL A:702 , ARG A:1108 , ASP A:1135 , ARG B:1108BINDING SITE FOR RESIDUE GOL A 701
5AC5SOFTWAREGOL A:701 , ARG A:1108 , ASP B:1135BINDING SITE FOR RESIDUE GOL A 702
6AC6SOFTWARELYS B:1295 , TRP B:1322 , SER B:1324BINDING SITE FOR RESIDUE GOL B 703
7AC7SOFTWAREARG B:1236 , SER B:1237 , PHE B:1240 , LYS B:1244 , TYR B:1250BINDING SITE FOR RESIDUE PEG B 801
8AC8SOFTWAREHOH A:98 , ARG A:1024 , ILE A:1028BINDING SITE FOR RESIDUE PEG A 802

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y6F)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y6F)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y6F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y6F)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y6F)

(-) 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:394
 aligned with GSTA_BPT4 | P04519 from UniProtKB/Swiss-Prot  Length:400

    Alignment length:403
                               1                                                                                                                                                                                                                                                                                                                                                                                                               
                               |     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397   
           GSTA_BPT4      - ---MRICIFMARGLEGCGVTKFSLEQRDWFIKNGHEVTLVYAKDKSFTRTSSHDHKSFSIPVILAKEYDKALKLVNDCDILIINSVPATSVQEATINNYKKLLDNIKPSIRVVVYQHDHSVLSLRRNLGLEETVRRADVIFSHSDNGDFNKVLMKEWYPETVSLFDDIEEAPTVYNFQPPMDIVKVRSTYWKDVSEINMNINRWIGRTTTWKGFYQMFDFHEKFLKPAGKSTVMEGLERSPAFIAIKEKGIPYEYYGNREIDKMNLAPNQPAQILDCYINSEMLERMSKSGFGYQLSKLNQKYLQRSLEYTHLELGACGTIPVFWKSTGENLKFRVDNTPLTSHDSGIIWFDENDMESTFERIKELSSDRALYDREREKAYEFLYQHQDSSFCFKEQFDIITK  400
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee......hhhhhhhhhhhhhhhhh..eeeeeee.................eeehhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhh.......eeeee....hhhhhh...hhhhhhhhh.eeee....hhhhhhhhhhhh.---------......ee.....hhhhhhhhhh.hhhhheeeeeeee...hhhhhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhh...eeee...hhhhh.......eeee...hhhhhhhhhh.eeeeee....hhhhh....hhhhhhhhhh..eeeeehhhhhhh.......hhhhh....eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1y6f A  998 MGSMRICIFMARGLEGCGVTKFSLEQRDWFIKNGHEVTLVYAKDKSFTRTSSHDHKSFSIPVILAKEYDKALKLVNDCDILIINSVPATSVQEATINNYKKLLDNIKPSIRVVVYQHDHSVLSLRRNLGLEETVRRADVIFSHSDNGDFNKVLMKEWYP---------EEAPTVYNFQPPMDIVKVRSTYWKDVSEINMNINRWIGRTTTWKGFYQMFDFHEKFLKPAGKSTVMEGLERSPAFIAIKEKGIPYEYYGNREIDKMNLAPNQPAQILDCYINSEMLERMSKSGFGYQLSKLNQKYLQRSLEYTHLELGACGTIPVFWKSTGENLKFRVDNTPLTSHDSGIIWFDENDMESTFERIKELSSDRALYDREREKAYEFLYQHQDSSFCFKEQFDIITK 1400
                                  1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147        |-      1167      1177      1187      1197      1207      1217      1227      1237      1247      1257      1267      1277      1287      1297      1307      1317      1327      1337      1347      1357      1367      1377      1387      1397   
                                                                                                                                                                                       1156      1166                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:394
 aligned with GSTA_BPT4 | P04519 from UniProtKB/Swiss-Prot  Length:400

    Alignment length:402
                              1                                                                                                                                                                                                                                                                                                                                                                                                               
                              |      8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398  
           GSTA_BPT4      - --MRICIFMARGLEGCGVTKFSLEQRDWFIKNGHEVTLVYAKDKSFTRTSSHDHKSFSIPVILAKEYDKALKLVNDCDILIINSVPATSVQEATINNYKKLLDNIKPSIRVVVYQHDHSVLSLRRNLGLEETVRRADVIFSHSDNGDFNKVLMKEWYPETVSLFDDIEEAPTVYNFQPPMDIVKVRSTYWKDVSEINMNINRWIGRTTTWKGFYQMFDFHEKFLKPAGKSTVMEGLERSPAFIAIKEKGIPYEYYGNREIDKMNLAPNQPAQILDCYINSEMLERMSKSGFGYQLSKLNQKYLQRSLEYTHLELGACGTIPVFWKSTGENLKFRVDNTPLTSHDSGIIWFDENDMESTFERIKELSSDRALYDREREKAYEFLYQHQDSSFCFKEQFDIITK  400
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) ---------------AGT-1y6fB01 B:1014-1368                                                                                                                                                                                                                                                                                                                                            -------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------AGT-1y6fB02 B:1014-1368                                                                                                                                                                                                                                                                                                                                            -------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeee......hhhhhhhhhhhhhhhhh..eeeeeee.................eee....hhhhhhhhhh...eeeeee.........hhhhhhhhhhh.....eeeeee...hhhhhh...hhhhhhhh..eeee....hhhhhhhhhhhh...--------.....ee.....hhhhhhhhhh.hhhhheeeeeeee...hhhhhhhhhhhhhhhh......eeeee.....hhhhhhhh....eeeehhhhhhhh.......eeee...hhhhhhhhhhheeeeee....hhhhh....hhhhhhhhhh..eeeeehhhhhhh................eee...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1y6f B  999 GSMRICIFMARGLEGCGVTKFSLEQRDWFIKNGHEVTLVYAKDKSFTRTSSHDHKSFSIPVILAKEYDKALKLVNDCDILIINSVPATSVQEATINNYKKLLDNIKPSIRVVVYQHDHSVLSLRRNLGLEETVRRADVIFSHSDNGDFNKVLMKEWYPET--------EAPTVYNFQPPMDIVKVRSTYWKDVSEINMNINRWIGRTTTWKGFYQMFDFHEKFLKPAGKSTVMEGLERSPAFIAIKEKGIPYEYYGNREIDKMNLAPNQPAQILDCYINSEMLERMSKSGFGYQLSKLNQKYLQRSLEYTHLELGACGTIPVFWKSTGENLKFRVDNTPLTSHDSGIIWFDENDMESTFERIKELSSDRALYDREREKAYEFLYQHQDSSFCFKEQFDIITK 1400
                                  1008      1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148      1158      1168      1178      1188      1198      1208      1218      1228      1238      1248      1258      1268      1278      1288      1298      1308      1318      1328      1338      1348      1358      1368      1378      1388      1398  
                                                                                                                                                                                        1158     1167                                                                                                                                                                                                                                         


Chain C from PDB  Type:DNA  Length:13
                                              
                1y6f C    1 GATACTxAGATAG   13
                                  | 10   
                                  7-3DR  


Chain D from PDB  Type:DNA  Length:13
                                              
                1y6f D    1 CTATCTGAGTATC   13
                                    10
   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  (0, 0)

(no "SCOP Domain" information available for 1Y6F)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Y6F)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: AGT] (4)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (GSTA_BPT4 | P04519)
molecular function
    GO:0033820    DNA alpha-glucosyltransferase activity    Catalysis of the transfer of an alpha-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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  1y6f
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  GSTA_BPT4 | P04519
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  2.4.1.26
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 Related Entries

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

UniProtKB/Swiss-Prot
        GSTA_BPT4 | P04519: 1xv5 1y6g 1y8z 1ya6

(-) Related Entries Specified in the PDB File

1xv5 THE SAME PROTEIN IN COMPLEX WITH UDP
1y6g THE SAME PROTEIN IN COMPLEX WITH UDP AND A 13_MER DNA CONTAINING A HMU BASE AT 2.8 A RESOLUTION
1y8z THE SAME PROTEIN IN COMPLEX WITH UDP AND A 13-MER DNA CONTAINING A HMU BASE AT 1.9 A RESOLUTION
1ya6 THE SAME PROTEIN IN COMPLEX WITH UDP AND A 13-MER DNA CONTAINING A CENTRAL A:G MISMATCH