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(-) Description

Title :  ALPHA-GLUCOSYLTRANSFERASE IN COMPLEX WITH UDP AND A 13-MER DNA CONTAINING A HMU BASE AT 1.9 A RESOLUTION
 
Authors :  L. Lariviere, N. Sommer, S. Morera
Date :  14 Dec 04  (Deposition) - 30 Aug 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
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*(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*G)-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  (6, 17)

Asymmetric Unit (6, 17)
No.NameCountTypeFull Name
15HU1Mod. Nucleotide5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE
2CL1Ligand/IonCHLORIDE ION
3CME4Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
4GOL4Ligand/IonGLYCEROL
5NCO5Ligand/IonCOBALT HEXAMMINE(III)
6UDP2Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 1 (5, 9)
No.NameCountTypeFull Name
15HU1Mod. Nucleotide5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3CME2Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
4GOL3Ligand/IonGLYCEROL
5NCO2Ligand/IonCOBALT HEXAMMINE(III)
6UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE
Biological Unit 2 (4, 7)
No.NameCountTypeFull Name
15HU-1Mod. Nucleotide5-HYDROXYMETHYLURIDINE-2'-DEOXY-5'-MONOPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3CME2Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
4GOL1Ligand/IonGLYCEROL
5NCO3Ligand/IonCOBALT HEXAMMINE(III)
6UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH B:489 , GLU B:1012 , CME B:1014 , GLY B:1015 , VAL B:1016 , THR B:1017BINDING SITE FOR RESIDUE CL B 4001
02AC2SOFTWAREHOH A:420 , ARG A:1132 , ARG A:1133 , ALA A:1134 , ASP A:1135 , LYS B:1400BINDING SITE FOR RESIDUE NCO A 3001
03AC3SOFTWARELYS A:1400 , ARG B:1132 , ARG B:1133 , ALA B:1134 , ASP B:1135BINDING SITE FOR RESIDUE NCO B 3002
04AC4SOFTWARETYR B:1252 , GLU B:1257 , DG D:9BINDING SITE FOR RESIDUE NCO D 3003
05AC5SOFTWAREHOH B:287 , ASP B:1101 , ASN B:1102BINDING SITE FOR RESIDUE NCO B 3004
06AC6SOFTWARETHR A:1086 , VAL A:1088 , GLU A:1090 , LEU A:1125BINDING SITE FOR RESIDUE NCO A 3005
07AC7SOFTWAREHOH A:46 , HOH A:424 , HOH A:479 , GLY A:1013 , CME A:1014 , GLY A:1015 , ARG A:1046 , SER A:1049 , HIS A:1050 , ARG A:1204 , LYS A:1209 , CME A:1274 , TYR A:1275 , ASN A:1277 , MET A:1280 , GLU A:1306 , TYR A:1307 , THR A:1308 , GLU A:1311BINDING SITE FOR RESIDUE UDP A 3006
08AC8SOFTWAREHOH B:71 , HOH B:278 , HOH B:334 , GLY B:1013 , CME B:1014 , GLY B:1015 , LYS B:1018 , ARG B:1046 , SER B:1049 , HIS B:1050 , ARG B:1204 , LYS B:1209 , CME B:1274 , TYR B:1275 , ASN B:1277 , GLU B:1306 , TYR B:1307 , THR B:1308 , GLU B:1311BINDING SITE FOR RESIDUE UDP B 2001
09AC9SOFTWAREGLY A:1247 , ILE A:1248 , TYR A:1250BINDING SITE FOR RESIDUE GOL A 5001
10BC1SOFTWARESER A:1000BINDING SITE FOR RESIDUE GOL A 5002
11BC2SOFTWARESER A:1340 , HIS A:1341 , ASP A:1342BINDING SITE FOR RESIDUE GOL A 5003
12BC3SOFTWARESER B:1139 , SER B:1141 , VAL B:1171BINDING SITE FOR RESIDUE GOL B 5004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Y8Z)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Y8Z)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Y8Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Y8Z)

(-) Exons   (0, 0)

(no "Exon" information available for 1Y8Z)

(-) 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:391
 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 ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeee......hhhhhhhhhhhhhhhhh..eeeeeee....hhhhhh......eeee....hhhhhhhhhh...eeee........hhhhhhhhhhhhhh.....eeeee....hhhhhh...hhhhhhhhh.eeee....hhhhhhhhhhhh.-----------...eee.....hhhhhhhhhh.hhhhheeeeeeee...hhhhhhhhhhhhhhhh......eeeee......hhhhhhhhh...eee...hhhhh........eee...hhhhhhhhhh.eeeeee....hhhhh....hhhhhhhhhhh.eeeeehhhhhhh.......hhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1y8z A  999 GSMRICIFMARGLEGcGVTKFSLEQRDWFIKNGHEVTLVYAKDKSFTRTSSHDHKSFSIPVILAKEYDKALKLVNDCDILIINSVPATSVQEATINNYKKLLDNIKPSIRVVVYQHDHSVLSLRRNLGLEETVRRADVIFSHSDNGDFNKVLMKEWYP-----------APTVYNFQPPMDIVKVRSTYWKDVSEINMNINRWIGRTTTWKGFYQMFDFHEKFLKPAGKSTVMEGLERSPAFIAIKEKGIPYEYYGNREIDKMNLAPNQPAQILDcYINSEMLERMSKSGFGYQLSKLNQKYLQRSLEYTHLELGACGTIPVFWKSTGENLKFRVDNTPLTSHDSGIIWFDENDMESTFERIKELSSDRALYDREREKAYEFLYQHQDSSFCFKEQFDIITK 1400
                                  1008     |1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138      1148       | -      1168      1178      1188      1198      1208      1218      1228      1238      1248      1258      1268     |1278      1288      1298      1308      1318      1328      1338      1348      1358      1368      1378      1388      1398  
                                        1014-CME                                                                                                                                      1156        1168                                                                                                      1274-CME                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:373
 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-1y8zB01 B:1014-1368                                                                                                                                                                                                                                                                                                                                            -------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------AGT-1y8zB02 B:1014-1368                                                                                                                                                                                                                                                                                                                                            -------------------------------- Pfam domains (2)
         Sec.struct. author ...eeeeee......hhhhhhhhhhhhhhhhh..eeeeeee.................eee....hhhhhhhhhh...eeee........hhhhhhhhhhhhhhh....eeeeee...hhhhhh...hhhhhhhhh.eeee..-----------------------------.ee.....hhhhhhhhhh.hhhhheeeeeeee...hhhhhhhhhhhhhhhh......eeeee.....hhhhhhhhh...eeee...hhhhh.......eeee...hhhhhhhhhh.eeeeee.............hhhhhhhhhh..eeeeehhhhhhh.......hhhhh....eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                1y8z B  999 GSMRICIFMARGLEGcGVTKFSLEQRDWFIKNGHEVTLVYAKDKSFTRTSSHDHKSFSIPVILAKEYDKALKLVNDCDILIINSVPATSVQEATINNYKKLLDNIKPSIRVVVYQHDHSVLSLRRNLGLEETVRRADVIFSHS-----------------------------VYNFQPPMDIVKVRSTYWKDVSEINMNINRWIGRTTTWKGFYQMFDFHEKFLKPAGKSTVMEGLERSPAFIAIKEKGIPYEYYGNREIDKMNLAPNQPAQILDcYINSEMLERMSKSGFGYQLSKLNQKYLQRSLEYTHLELGACGTIPVFWKSTGENLKFRVDNTPLTSHDSGIIWFDENDMESTFERIKELSSDRALYDREREKAYEFLYQHQDSSFCFKEQFDIITK 1400
                                  1008     |1018      1028      1038      1048      1058      1068      1078      1088      1098      1108      1118      1128      1138  |      -         -         -  |   1178      1188      1198      1208      1218      1228      1238      1248      1258      1268     |1278      1288      1298      1308      1318      1328      1338      1348      1358      1368      1378      1388      1398  
                                        1014-CME                                                                                                                       1141                          1171                                                                                                   1274-CME                                                                                                                          


Chain C from PDB  Type:DNA  Length:13
                                              
                1y8z C    1 GATACTxAGATAG   13
                                  | 10   
                                  7-5HU  


Chain D from PDB  Type:DNA  Length:9
                                          
                1y8z D    1 CTATCTGAG    9
   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 1Y8Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1Y8Z)

(-) 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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  1y8z
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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 1y6f 1y6g 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
1y6g THE SAME PROTEIN IN COMPLEX WITH UDP AND A 13_MER DNA CONTAINING A HMU BASE AT 2.8 A RESOLUTION
1ya6 THE SAME PROTEIN IN COMPLEX WITH UDP AND A 13-MER DNA CONTAINING A CENTRAL A:G MISMATCH