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(-) Description

Title :  ALPHA-GLUCOSYLTRANSFERASE (AGT) IN COMPLEX WITH UDP
 
Authors :  L. Lariviere, N. Sommer, S. Morera
Date :  27 Oct 04  (Deposition) - 30 Aug 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.73
Chains :  Asym./Biol. Unit :  A
Keywords :  Transferase (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 - DNA ALPHA-GLUCOSYLTRANSFERASE
    Chains: A
    EC Number: 2.4.1.26
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ENTEROBACTERIA PHAGE T4
    Organism Taxid: 10665
    Synonym: AGT

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (5, 9)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2CME2Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
3EDO3Ligand/Ion1,2-ETHANEDIOL
4GOL2Ligand/IonGLYCEROL
5UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:447 , GLU A:1012 , CME A:1014 , GLY A:1015 , VAL A:1016 , THR A:1017BINDING SITE FOR RESIDUE CL A 1401
2AC2SOFTWAREHOH A:30 , HOH A:33 , HOH A:40 , GLY A:1013 , CME A:1014 , GLY A:1015 , LYS A:1018 , ARG A:1046 , SER A:1049 , HIS A:1050 , ARG A:1204 , LYS A:1209 , TYR A:1275 , ASN A:1277 , GLU A:1306 , TYR A:1307 , THR A:1308 , GLU A:1311 , EDO A:1403 , GOL A:2002BINDING SITE FOR RESIDUE UDP A 1402
3AC3SOFTWAREHOH A:37 , CME A:1014 , ASP A:1115 , UDP A:1402 , GOL A:2002BINDING SITE FOR RESIDUE EDO A 1403
4AC4SOFTWAREHOH A:445 , HOH A:446 , GLU A:1393 , EDO A:1405BINDING SITE FOR RESIDUE EDO A 1404
5AC5SOFTWAREHOH A:260 , HOH A:445 , ARG A:1332 , PHE A:1389 , EDO A:1404BINDING SITE FOR RESIDUE EDO A 1405
6AC6SOFTWAREHOH A:28 , HOH A:37 , HOH A:100 , GLY A:1015 , HIS A:1114 , HIS A:1140 , GLU A:1306 , UDP A:1402 , EDO A:1403BINDING SITE FOR RESIDUE GOL A 2002
7AC7SOFTWAREASN A:1030 , HIS A:1032 , LYS A:1392BINDING SITE FOR RESIDUE GOL A 2003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1XV5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1XV5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1XV5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1XV5)

(-) Exons   (0, 0)

(no "Exon" information available for 1XV5)

(-) 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:401
 aligned with GSTA_BPT4 | P04519 from UniProtKB/Swiss-Prot  Length:400

    Alignment length:401
                             1                                                                                                                                                                                                                                                                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399 
           GSTA_BPT4      - -MRICIFMARGLEGCGVTKFSLEQRDWFIKNGHEVTLVYAKDKSFTRTSSHDHKSFSIPVILAKEYDKALKLVNDCDILIINSVPATSVQEATINNYKKLLDNIKPSIRVVVYQHDHSVLSLRRNLGLEETVRRADVIFSHSDNGDFNKVLMKEWYPETVSLFDDIEEAPTVYNFQPPMDIVKVRSTYWKDVSEINMNINRWIGRTTTWKGFYQMFDFHEKFLKPAGKSTVMEGLERSPAFIAIKEKGIPYEYYGNREIDKMNLAPNQPAQILDCYINSEMLERMSKSGFGYQLSKLNQKYLQRSLEYTHLELGACGTIPVFWKSTGENLKFRVDNTPLTSHDSGIIWFDENDMESTFERIKELSSDRALYDREREKAYEFLYQHQDSSFCFKEQFDIITK  400
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......hhhhhhhhhhhhhhhhh..eeeeeee.................eee....hhhhhhhhhh...eeeeee......hhhhhhhhhhhhhhh....eeeeee...hhhhhh...hhhhhhhhh.eeee....hhhhhhhhhhhh...............eee.....hhhhhhhhhh.hhhhheeeeeeee...hhhhhhhhhhhhhhhh......eeeee....hhhhhhhhhh...eeeehhhhhhhh.......eeee...hhhhhhhhhhheeeeee....hhhhh....hhhhhhhhhhh.eeeeehhhhhhh.......hhhhh....eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1xv5 A 1000 SMRICIFMARGLEGcGVTKFSLEQRDWFIKNGHEVTLVYAKDKSFTRTSSHDHKSFSIPVILAKEYDKALKLVNDCDILIINSVPATSVQEATINNYKKLLDNIKPSIRVVVYQHDHSVLSLRRNLGLEETVRRADVIFSHSDNGDFNKVLMKEWYPETVSLFDDIEEAPTVYNFQPPMDIVKVRSTYWKDVSEINMNINRWIGRTTTWKGFYQMFDFHEKFLKPAGKSTVMEGLERSPAFIAIKEKGIPYEYYGNREIDKMNLAPNQPAQILDcYINSEMLERMSKSGFGYQLSKLNQKYLQRSLEYTHLELGACGTIPVFWKSTGENLKFRVDNTPLTSHDSGIIWFDENDMESTFERIKELSSDRALYDREREKAYEFLYQHQDSSFCFKEQFDIITK 1400
                                  1009    | 1019      1029      1039      1049      1059      1069      1079      1089      1099      1109      1119      1129      1139      1149      1159      1169      1179      1189      1199      1209      1219      1229      1239      1249      1259      1269    | 1279      1289      1299      1309      1319      1329      1339      1349      1359      1369      1379      1389      1399 
                                       1014-CME                                                                                                                                                                                                                                                            1274-CME
   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 1XV5)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1XV5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1XV5)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (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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  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: 1y6f 1y6g 1y8z 1ya6

(-) Related Entries Specified in the PDB File

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
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