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(-) Description

Title :  CRYSTAL STRUCTURE OF VIBRIO PROTEOLYTICUS CHITOBIOSE PHOSPHORYLASE
 
Authors :  M. Hidaka, Y. Honda, S. Nirasawa, M. Kitaoka, K. Hayashi, T. Wakagi, H. S S. Fushinobu
Date :  24 Dec 03  (Deposition) - 22 Jun 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Beta-Sandwich, (Alpha/Alpha)6 Barrel, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Hidaka, Y. Honda, M. Kitaoka, S. Nirasawa, K. Hayashi, T. Wakagi, H. Shoun, S. Fushinobu
Chitobiose Phosphorylase From Vibrio Proteolyticus, A Membe Of Glycosyl Transferase Family 36, Has A Clan Gh-L-Like (Alpha/Alpha)(6) Barrel Fold.
Structure V. 12 937 2004
PubMed-ID: 15274915  |  Reference-DOI: 10.1016/J.STR.2004.03.027
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHITOBIOSE PHOSPHORYLASE
    Chains: A
    EC Number: 2.4.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET30B-CHBP
    Expression System Strain: BL21GOLD(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: CHBP
    Organism Scientific: VIBRIO PROTEOLYTICUS
    Organism Taxid: 671

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric Unit (1, 3)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:186 , LEU A:187 , ASN A:190 , GLY A:196 , PHE A:197 , HOH A:1227BINDING SITE FOR RESIDUE CA A 1001
2AC2SOFTWAREGLY A:127 , GLY A:791 , ASP A:793 , HOH A:1048 , HOH A:1088 , HOH A:1341BINDING SITE FOR RESIDUE CA A 1002
3AC3SOFTWARETHR A:140 , GLU A:459 , HOH A:1279 , HOH A:1412 , HOH A:1435 , HOH A:1678BINDING SITE FOR RESIDUE CA A 1003

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:424 -A:493

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Arg A:66 -Pro A:67
2Gln A:87 -Pro A:88
3Ala A:615 -Pro A:616

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1V7V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1V7V)

(-) Exons   (0, 0)

(no "Exon" information available for 1V7V)

(-) 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:779
 aligned with CHBP_VIBPR | Q76IQ9 from UniProtKB/Swiss-Prot  Length:801

    Alignment length:801
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800 
           CHBP_VIBPR     1 MKYGYFDNDNREYVITRPDVPAPWTNYLGTEKFCTVISHNAGGYSFYNSPEYNRVTKFRPNATFDRPGHYVYLRDDDSGDYWSISWQPVAKSLDEAQYQIRHGLSYSKFQCDYNGIHARKTLFVPKGEDAEIWDVVIKNTSDQVRTISAFSFVEFSFSHIQSDNQNHQMSLYSAGTAYRPGLIEYDLYYNTDDFEGFYYLASTFDPDSYDGQRDRFLGLYRDEANPLAVEQGRCSNSAQTCYNHCGSLHKQFTLQPGEEIRFAYILGIGKGNGERLREHYQDVANIDAAFAAIKAHWDERCAKFQVKSPNQGLDTMINAWTLYQAETCVVWSRFASFIEVGGRTGLGYRDTAQDAISVPHANPEMTRKRIVDLLRGQVKAGYGLHLFDPDWFDPEKEDVAPSKSPTVVPTPSDEDKIHGIKDTCSDDHLWLIPTICKYVMETGETSFFDQMIPYADGGEASVYEHMKAALDFSAEYVGQTGICKGLRADWNDCLNLGGGESSMVSFLHFWALQEFIDLAKFLGKDQDVNTYTEMAANVREACETHLWDDEGGWYIRGLTKNGDKIGTAQQQEGRVHLESNTLAVLSGLASQERGEQAMDAVDEHLFSPYGLHLNAPSFSTPNDDIGFVTRVYQGVKENGAIFSHPNPWAWVAETKLGRGDRAMKFYDALNPYNQNDIIEKRIAEPYSYVQFIMGRDHQDHGRANHPWLTGTSGWAYFAVTNYILGVQSGFTGLSVDPCIPSDWPGFEVTRQWRGATYHIQVENPDHVSKGVKSITLNGAPIQGRIPPQAQGSDNQVVVVLG 801
               SCOP domains d1v7va2 A:1-270 Chitobiose phosphorylase ChbP                                                                                                                                                                                                                                 d1v7va1 A:271-801 Chitobiose phosphorylase ChbP                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....eeee.........eeee....eeeeee....eeeee......................eeeeee.....eee............eeeeeeee..eeeeeeee..eeeeeeee......eeeeeeeeee.....eeeeeeee......hhhhhhhhhhhhh..eeeeee..eeeeee.........eeeeee.....eeeeehhhhhh.......hhhhhhh...........eeeeeeeeeee....eeeeeeeeee..hhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhhhhhhhhhhhhhhhhhhh.............eehhhhhhhh......hhhhhhhhhhhhhhh.........eehhhhhh.----------------------..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.eee.....eeehhhhhhhhhhhhhhh.......eee........eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhee....ee..ee.....ee.........eehhhhhhhhhh...hhhhhhhhhhhhhhhhee..ee..ee..........hhhhhh.........ee..hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh.hhhhhh......eeee..........eeee...hhhhhhhhhhhhh...eee....eee.........eeeeeeee..eeeeeeee........eeeeee..eee...........eeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1v7v A   1 MKYGYFDNDNREYVITRPDVPAPWTNYLGTEKFCTVISHNAGGYSFYNSPEYNRVTKFRPNATFDRPGHYVYLRDDDSGDYWSISWQPVAKSLDEAQYQIRHGLSYSKFQCDYNGIHARKTLFVPKGEDAEIWDVVIKNTSDQVRTISAFSFVEFSFSHIQSDNQNHQMSLYSAGTAYRPGLIEYDLYYNTDDFEGFYYLASTFDPDSYDGQRDRFLGLYRDEANPLAVEQGRCSNSAQTCYNHCGSLHKQFTLQPGEEIRFAYILGIGKGNGERLREHYQDVANIDAAFAAIKAHWDERCAKFQVKSPNQGLDTMINAWTLYQAETCVVWSRFASFIEVGGRTGLGYRDTAQDAISVPHANPEMTRKRIVDLLRGQVKAGYGLHLFDPDWFDP----------------------IHGIKDTCSDDHLWLIPTICKYVMETGETSFFDQMIPYADGGEASVYEHMKAALDFSAEYVGQTGICKGLRADWNDCLNLGGGESSMVSFLHFWALQEFIDLAKFLGKDQDVNTYTEMAANVREACETHLWDDEGGWYIRGLTKNGDKIGTAQQQEGRVHLESNTLAVLSGLASQERGEQAMDAVDEHLFSPYGLHLNAPSFSTPNDDIGFVTRVYQGVKENGAIFSHPNPWAWVAETKLGRGDRAMKFYDALNPYNQNDIIEKRIAEPYSYVQFIMGRDHQDHGRANHPWLTGTSGWAYFAVTNYILGVQSGFTGLSVDPCIPSDWPGFEVTRQWRGATYHIQVENPDHVSKGVKSITLNGAPIQGRIPPQAQGSDNQVVVVLG 801
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390   |     -         -      |420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800 
                                                                                                                                                                                                                                                                                                                                                                                                                                   394                    417
   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  (2, 2)

Asymmetric Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1V7V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1V7V)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A   (CHBP_VIBPR | Q76IQ9)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
biological process
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.

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  1v7v
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 Related Entries

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

UniProtKB/Swiss-Prot
        CHBP_VIBPR | Q76IQ9: 1v7w 1v7x

(-) Related Entries Specified in the PDB File

1v7w THE SAME PROTEIN WITH GLCNAC
1v7x THE SAME PROTEIN WITH GLCNAC AND SULFATE