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(-) Description

Title :  ALPHA-GLUCOSYLTRANSFERASE IN COMPLEX WITH UDP AND A 13_MER DNA CONTAINING A HMU BASE AT 2.8 A RESOLUTION
 
Authors :  L. Lariviere, N. Sommer, S. Morera
Date :  06 Dec 04  (Deposition) - 30 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
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 For 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
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*GP*AP*TP*AP*CP*TP*(5HU)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*T)-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, 12)

Asymmetric Unit (5, 12)
No.NameCountTypeFull Name
15HU1Mod. Nucleotide5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE
2CL1Ligand/IonCHLORIDE ION
3EDO1Ligand/Ion1,2-ETHANEDIOL
4NCO7Ligand/IonCOBALT HEXAMMINE(III)
5UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (3, 5)
No.NameCountTypeFull Name
15HU1Mod. Nucleotide5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3EDO-1Ligand/Ion1,2-ETHANEDIOL
4NCO3Ligand/IonCOBALT HEXAMMINE(III)
5UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 2 (3, 6)
No.NameCountTypeFull Name
15HU-1Mod. Nucleotide5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3EDO1Ligand/Ion1,2-ETHANEDIOL
4NCO4Ligand/IonCOBALT HEXAMMINE(III)
5UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS B:1114 , NCO B:2019BINDING SITE FOR RESIDUE CL B 2017
02AC2SOFTWAREARG A:1132 , ALA A:1134 , ASP A:1135BINDING SITE FOR RESIDUE NCO A 1401
03AC3SOFTWAREARG B:1132 , ARG B:1133 , ALA B:1134 , ASP B:1135BINDING SITE FOR RESIDUE NCO B 2018
04AC4SOFTWARETYR B:1252 , GLU B:1257 , DT D:10BINDING SITE FOR RESIDUE NCO D 1003
05AC5SOFTWARETHR A:1086 , SER A:1087 , VAL A:1088 , GLU A:1090BINDING SITE FOR RESIDUE NCO A 1402
06AC6SOFTWAREHIS B:1114 , ASP B:1115 , HIS B:1116 , ARG B:1204 , CL B:2017 , UDP B:2021BINDING SITE FOR RESIDUE NCO B 2019
07AC7SOFTWAREHIS A:1114 , ASP A:1115 , HIS A:1116 , ARG A:1204 , GLU A:1306 , UDP A:1404BINDING SITE FOR RESIDUE NCO A 1403
08AC8SOFTWAREHOH A:2014 , ASP B:1101 , ASN B:1102BINDING SITE FOR RESIDUE NCO B 2020
09AC9SOFTWARECYS A:1014 , GLY A:1015 , ARG A:1046 , SER A:1049 , HIS A:1050 , ARG A:1204 , LYS A:1209 , CYS A:1274 , TYR A:1275 , ASN A:1277 , GLU A:1306 , TYR A:1307 , THR A:1308 , GLU A:1311 , NCO A:1403BINDING SITE FOR RESIDUE UDP A 1404
10BC1SOFTWARECYS B:1014 , GLY B:1015 , ARG B:1046 , SER B:1049 , HIS B:1050 , ARG B:1204 , LYS B:1209 , CYS B:1274 , TYR B:1275 , ASN B:1277 , GLU B:1306 , TYR B:1307 , THR B:1308 , GLU B:1311 , NCO B:2019BINDING SITE FOR RESIDUE UDP B 2021
11BC2SOFTWARELYS B:1246BINDING SITE FOR RESIDUE EDO B 2022

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y6G)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ala A:1168 -Pro A:1169
2Ala B:1168 -Pro B:1169

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y6G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y6G)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y6G)

(-) 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:392
 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.................eee....hhhhhhhhhh...eeee........hhhhhhhhhhhhhhh....eeeee......hhhhh..hhhhhhhhh.eeee........hhhhhhhh.-----------....ee.....hhhhhhhhhh......eeeeeeee...hhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhh...eeee...............eeee...hhhhhhhhhh.eeeeee.............hhhhhhhhhhh.eeeeehhhhhhh................eee...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1y6g A  998 MGSMRICIFMARGLEGCGVTKFSLEQRDWFIKNGHEVTLVYAKDKSFTRTSSHDHKSFSIPVILAKEYDKALKLVNDCDILIINSVPATSVQEATINNYKKLLDNIKPSIRVVVYQHDHSVLSLRRNLGLEETVRRADVIFSHSDNGDFNKVLMKEWYP-----------APTVYNFQPPMDIVKVRSTYWKDVSEINMNINRWIGRTTTWKGFYQMFDFHEKFLKPAGKSTVMEGLERSPAFIAIKEKGIPYEYYGNREIDKMNLAPNQPAQILDCYINSEMLERMSKSGFGYQLSKLNQKYLQRSLEYTHLELGACGTIPVFWKSTGENLKFRVDNTPLTSHDSGIIWFDENDMESTFERIKELSSDRALYDREREKAYEFLYQHQDSSFCFKEQFDIITK 1400
                                  1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147        |-         -|     1177      1187      1197      1207      1217      1227      1237      1247      1257      1267      1277      1287      1297      1307      1317      1327      1337      1347      1357      1367      1377      1387      1397   
                                                                                                                                                                                       1156        1168                                                                                                                                                                                                                                        


Chain B from PDB  Type:PROTEIN  Length:393
 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 (1) ----------------AGT-1y6gB01 B:1014-1368                                                                                                                                                                                                                                                                                                                                            -------------------------------- Pfam domains (1)
           Pfam domains (2) ----------------AGT-1y6gB02 B:1014-1368                                                                                                                                                                                                                                                                                                                                            -------------------------------- Pfam domains (2)
         Sec.struct. author ....eeeeee......hhhhhhhhhhhhhhhhh..eeeeeee................eeeehhhhhhhhhhhhhh...eeeeee......hhhhhhhhhhhhhh.....eeeee....hhhhhh...hhhhhhhhh.eeee.........hhhhhhh..----------...eee.....hhhhhhhhhh.hhhhheeeeeeee...hhhhhhhhhhhhhhhhhhhhh.eeeee.....hhhhhhhh....ee.....hhhhh.......eeee...hhhhhhhhhhheeeeee....hhhhh....hhhhhhhhhh..eeeehhhhhhhh......................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1y6g B  998 MGSMRICIFMARGLEGCGVTKFSLEQRDWFIKNGHEVTLVYAKDKSFTRTSSHDHKSFSIPVILAKEYDKALKLVNDCDILIINSVPATSVQEATINNYKKLLDNIKPSIRVVVYQHDHSVLSLRRNLGLEETVRRADVIFSHSDNGDFNKVLMKEWYPE----------APTVYNFQPPMDIVKVRSTYWKDVSEINMNINRWIGRTTTWKGFYQMFDFHEKFLKPAGKSTVMEGLERSPAFIAIKEKGIPYEYYGNREIDKMNLAPNQPAQILDCYINSEMLERMSKSGFGYQLSKLNQKYLQRSLEYTHLELGACGTIPVFWKSTGENLKFRVDNTPLTSHDSGIIWFDENDMESTFERIKELSSDRALYDREREKAYEFLYQHQDSSFCFKEQFDIITK 1400
                                  1007      1017      1027      1037      1047      1057      1067      1077      1087      1097      1107      1117      1127      1137      1147      1157         -|     1177      1187      1197      1207      1217      1227      1237      1247      1257      1267      1277      1287      1297      1307      1317      1327      1337      1347      1357      1367      1377      1387      1397   
                                                                                                                                                                                        1157       1168                                                                                                                                                                                                                                        


Chain C from PDB  Type:DNA  Length:13
                                              
                1y6g C    1 GATACTxAGATAG   13
                                  | 10   
                                  7-5HU  


Chain D from PDB  Type:DNA  Length:12
                                             
                1y6g D    1 CTATCTGAGTAT   12
                                    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 1Y6G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Y6G)

(-) 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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  1y6g
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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 1y6f 1y8z 1ya6

(-) Related Entries Specified in the PDB File

1xv5 THE SAME PROTEIN IN COMPLEX WITH UDP
1y6f THE SAME PROTEIN IN COMPLEX WITH UDP-GLUCOSE AND DNA CONTAINING AN ABASIC SITE
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