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(-) Description

Title :  CRYSTAL STRUCTURE OF A GLYCOSYLTRANSFERASE INVOLVED IN THE GLYCOSYLATION OF THE MAJOR CAPSID OF PBCV-1
 
Authors :  Y. Zhang, Y. Xiang, J. L. Van Etten, M. G. Rossmann
Date :  19 Mar 07  (Deposition) - 21 Aug 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Glycosyltransferase, Pbcv-1, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhang, Y. Xiang, J. L. Van Etten, M. G. Rossmann
Structure And Function Of A Chlorella Virus-Encoded Glycosyltransferase.
Structure V. 15 1031 2007
PubMed-ID: 17850743  |  Reference-DOI: 10.1016/J.STR.2007.07.006

(-) Compounds

Molecule 1 - PUTATIVE GLYCOSYLTRANSFERASE (MANNOSYLTRANSFERASE) INVOLVED IN GLYCOSYLATING THE PBCV-1 MAJOR CAPSID PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTYB-1
    Expression System Strain: BL21(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL FRAGMENT
    Gene: A64R
    Organism Scientific: PARAMECIUM BURSARIA CHLORELLA VIRUS 1
    Organism Taxid: 10506
    Synonym: VP54

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1MN2Ligand/IonMANGANESE (II) ION
2UPG1Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2UPG-1Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2UPG1Ligand/IonURIDINE-5'-DIPHOSPHATE-GLUCOSE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:78 , ASP A:80 , HIS A:193 , HOH A:283 , HOH A:284BINDING SITE FOR RESIDUE MN A 214
2AC2SOFTWAREASP B:78 , ASP B:80 , HIS B:193 , UPG B:215 , HOH B:225 , HOH B:283BINDING SITE FOR RESIDUE MN B 214
3AC3SOFTWAREGLY B:11 , HIS B:12 , PHE B:13 , LEU B:53 , HIS B:54 , ARG B:57 , TRP B:76 , ASP B:78 , SER B:79 , ASP B:80 , ASN B:119 , GLN B:152 , CYS B:195 , ARG B:202 , MN B:214 , HOH B:220 , HOH B:225 , HOH B:247 , HOH B:259 , HOH B:260 , HOH B:261 , HOH B:281 , HOH B:283BINDING SITE FOR RESIDUE UPG B 215

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2P72)

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Ala A:111 -Pro A:112
2Ala A:143 -Pro A:144
3Phe A:148 -Pro A:149
4Phe B:13 -Pro B:14
5Ala B:111 -Pro B:112
6Ala B:143 -Pro B:144
7Phe B:148 -Pro B:149

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2P72)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2P72)

(-) Exons   (0, 0)

(no "Exon" information available for 2P72)

(-) 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:199
 aligned with Q89399_PBCV1 | Q89399 from UniProtKB/TrEMBL  Length:638

    Alignment length:203
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203   
         Q89399_PBCV1     4 PCITILSGHFPKETIYARKTKELVEEYCSIHGYNFYYEESEPLETEEHALHFRRSWIIQQAAEKFPSTEWFLWLDSDVYVNPKNKNKPITSFIDLSDPNILYHTFHEAPWGSYPINTGVKFVHKDALEIEKIVWSLRNEAPWNTFPYEQKTVYEYVFPRIPGRYIVHDPYTLNCIVKAYPEHVKDALFVHMCGTSRAERDEHM 206
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..---hhhhhhhhhhhhhhhhhhh.eeeee.......hhhhhhhhhhhhhhhhhhhh....eeeee...eee.hhhh..hhhhh.........eeee..........eeeeeeee..hhhhhhhhhhh..........hhhhhhhhhhhhhh...eeee......ee......hhhhh.eee...-hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p72 A   4 PCITILSGHF---TIYARKTKELVEEYCSIHGYNFYYEESEPLETEEHALHFRRSWIIQQAAEKFPSTEWFLWLDSDVYVNPKNKNKPITSFIDLSDPNILYHTFHEAPWGSYPINTGVKFVHKDALEIEKIVWSLRNEAPWNTFPYEQKTVYEYVFPRIPGRYIVHDPYTLNCIVKAYPEHVKDALFVHMCG-SRAERDEHM 206
                                    13   |    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193  | |  203   
                                    13  17                                                                                                                                                                                196 |        
                                                                                                                                                                                                                            198        


Chain B from PDB  Type:PROTEIN  Length:204
 aligned with Q89399_PBCV1 | Q89399 from UniProtKB/TrEMBL  Length:638

    Alignment length:205
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203     
         Q89399_PBCV1     4 PCITILSGHFPKETIYARKTKELVEEYCSIHGYNFYYEESEPLETEEHALHFRRSWIIQQAAEKFPSTEWFLWLDSDVYVNPKNKNKPITSFIDLSDPNILYHTFHEAPWGSYPINTGVKFVHKDALEIEKIVWSLRNEAPWNTFPYEQKTVYEYVFPRIPGRYIVHDPYTLNCIVKAYPEHVKDALFVHMCGTSRAERDEHMEM 208
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------Glyco_transf_34-2p72B01 B:11-106                                                                ------------------------------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) -------Glyco_transf_34-2p72B02 B:11-106                                                                ------------------------------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ..eeeee......hhhhhhhhhhhhhhhhhhh.eeee........hhhhhhhhhhhhhhhhhhhh....eeeee...eee.hhhh..hhhhh.........eeee.............eeeee..hhhhhhhhhhh..........hhhhhhhhhhhhhh...eeee......ee......hhhhh.eee..-.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2p72 B   4 PCITILSGHFPKETIYARKTKELVEEYCSIHGYNFYYEESEPLETEEHALHFRRSWIIQQAAEKFPSTEWFLWLDSDVYVNPKNKNKPITSFIDLSDPNILYHTFHEAPWGSYPINTGVKFVHKDALEIEKIVWSLRNEAPWNTFPYEQKTVYEYVFPRIPGRYIVHDPYTLNCIVKAYPEHVKDALFVHMC-TSRAERDEHMEM 208
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193 | |   203     
                                                                                                                                                                                                                         195 |           
                                                                                                                                                                                                                           197
   Legend:   → Mismatch (orange background)
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  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 2P72)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2P72)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: GT-A (172)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q89399_PBCV1 | Q89399)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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).
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.

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  2p72
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 Related Entries

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

UniProtKB/TrEMBL
        Q89399_PBCV1 | Q89399: 2p6w 2p73

(-) Related Entries Specified in the PDB File

2p6w 2p73