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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF TOXIN B FROM CLOSTRIDIUM DIFFICILE IN COMPLEX WITH UDP, GLC AND MANGANESE ION
 
Authors :  D. J. Reinert, T. Jank, K. Aktories, G. E. Schulz
Date :  30 Jun 05  (Deposition) - 03 Aug 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Toxin, Glycosyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. J. Reinert, T. Jank, K. Aktories, G. E. Schulz
Structural Basis For The Function Of Clostridium Difficile Toxin B.
J. Mol. Biol. V. 351 973 2005
PubMed-ID: 16054646  |  Reference-DOI: 10.1016/J.JMB.2005.06.071

(-) Compounds

Molecule 1 - TOXIN B
    Chains: A
    EC Number: 2.4.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Fragment: CATALYTIC DOMAIN, RESIDUES 1-543
    Mutation: YES
    Organism Scientific: CLOSTRIDIUM DIFFICILE
    Organism Taxid: 1496
    Strain: VPI 10463

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 8)

Asymmetric/Biological Unit (5, 8)
No.NameCountTypeFull Name
1GLC1Ligand/IonALPHA-D-GLUCOSE
2MN1Ligand/IonMANGANESE (II) ION
3SO41Ligand/IonSULFATE ION
4TBR4Ligand/IonHEXATANTALUM DODECABROMIDE
5UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:266 , ASP A:270 , ARG A:273 , ASP A:286 , ILE A:383 , ASN A:384 , GLN A:385 , GLY A:470 , PRO A:471 , TRP A:520 , UDP A:1545 , HOH A:2289BINDING SITE FOR RESIDUE GLC A1546
2AC2SOFTWAREASP A:288 , GLU A:515 , UDP A:1545 , HOH A:2347 , HOH A:2348BINDING SITE FOR RESIDUE MN A1544
3AC3SOFTWAREMET A:516 , ALA A:517 , SER A:518 , PHE A:522 , ASP A:523 , ARG A:526 , HOH A:2354BINDING SITE FOR RESIDUE SO4 A1547
4AC4SOFTWAREVAL A:101 , TRP A:102 , ILE A:103 , ASN A:139 , LEU A:265 , ALA A:266 , SER A:269 , TYR A:284 , ASP A:286 , VAL A:287 , ASP A:288 , GLU A:515 , SER A:518 , LEU A:519 , TRP A:520 , MN A:1544 , GLC A:1546 , HOH A:2327 , HOH A:2347 , HOH A:2348 , HOH A:2349 , HOH A:2350 , HOH A:2351 , HOH A:2352BINDING SITE FOR RESIDUE UDP A1545
5AC5SOFTWAREASP A:29 , GLU A:32 , GLU A:33 , ASN A:134 , ASP A:239 , ARG A:241 , ASN A:242BINDING SITE FOR RESIDUE TBR A1548
6AC6SOFTWAREARG A:16 , ASP A:310 , ASN A:378 , SER A:379 , LYS A:380 , GLU A:515 , MET A:516 , HOH A:2084BINDING SITE FOR RESIDUE TBR A1549
7AC7SOFTWAREGLU A:77 , VAL A:80 , THR A:81 , LEU A:84 , ILE A:494 , ASP A:497 , HOH A:2143 , HOH A:2308BINDING SITE FOR RESIDUE TBR A1550
8AC8SOFTWAREARG A:173 , ASN A:425 , THR A:428 , ASN A:429 , ILE A:432 , ARG A:455 , GLU A:533 , ARG A:536 , ASN A:537 , HOH A:2280BINDING SITE FOR RESIDUE TBR A1551

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asp A:163 -Pro A:164

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2BVL)

(-) 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:543
 aligned with TOXB_CLODI | P18177 from UniProtKB/Swiss-Prot  Length:2366

    Alignment length:543
                                    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   
           TOXB_CLODI     1 MSLVNRKQLEKMANVRFRTQEDEYVAILDALEEYHNMSENTVVEKYLKLKDINSLTDIYIDTYKKSGRNKALKKFKEYLVTEVLELKNNNLTPVEKNLHFVWIGGQINDTAINYINQWKDVNSDYNVNVFYDSNAFLINTLKKTVVESAINDTLESFRENLNDPRFDYNKFFRKRMEIIYDKQKNFINYYKAQREENPELIIDDIVKTYLSNEYSKEIDELNTYIEESLNKITQNSGNDVRNFEEFKNGESFNLYEQELVERWNLAAASDILRISALKEIGGMYLDVDMLPGIQPDLFESIEKPSSVTVDFWEMTKLEAIMKYKEYIPEYTSEHFDMLDEEVQSSFESVLASKSDKSEIFSSLGDMEASPLEVKIAFNSKGIINQGLISVKDSYCSNLIVKQIENRYKILNNSLNPAISEDNDFNTTTNTFIDSIMAEANADNGRFMMELGKYLRVGFFPDVKTTINLSGPEAYAAAYQDLLMFKEGSMNIHLIEADLRNFEISKTNISQSTEQEMASLWSFDDARAKAQFEEYKRNYFEGSL 543
               SCOP domains d2bvla1 A:1-542 Toxin B                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       - SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh.......hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.ee...eeeee......hhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..eee...hhhhhh..hhhhhhhhhhh..hhhhhhhhhhhhhhhhhheeee....ee................hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh..hhhhh.......ee.....eeeee..eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh.........hhhhhh....hhh.ee...hhhhh.....hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2bvl A   1 MSLVNRKQLEKMANVRFRTQEDEYVAILDALEEYHNMSENTVVEKYLKLKDINSLTDICIDTYKKSGRNKALKKFKEYLVTEVLELKNNNLTPVEKNLHFVWIGGQINDTAINYINQWKDVNSDYNVNVFYDSNAFLINTLKKTVVESAINDTLESFRENLNDPRFDYNKFFRKRMEIIYDKQKNFINYYKAQREENPELIIDDIVKTYLSNEYSKEIDELNTYIEESLNKITQNSGNDVRNFGEFKNGESFNLYEQELVERWNLAAASDILRISALKEIGGMYLDVDMLPGIQPDLFESIEKPSSVTVDFWEMTKLEAIMKYKEYIPEYTSEHFDMLDEEVQSSFESVLASKSDKSEIFSSLGDMEASPLEVKIAFNSKGIINQGLISVKDSYCSNLIVKQIENRYKILNNSLNPAISEDNDFNTTTNTFIDSIMAEANADNGRFMMELGKYLRVGFFPDVKTTINLSGPEAYAAAYQDLLMFKEGSMNIHLIEADLRNFEISKTNISQSTEQEMASLWSFDDARAKAQFEEYKRNYFEGAL 543
                                    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
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BVL)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TOXB_CLODI | P18177)
molecular function
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0046527    glucosyltransferase activity    Catalysis of the transfer of a glucosyl group to an acceptor molecule, typically another carbohydrate or a lipid.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    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:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0020002    host cell plasma membrane    The plasma membrane surrounding a host cell.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TOXB_CLODI | P18177: 2bvm 4nc2 4np4 5uqm 5uqn 5uqt

(-) Related Entries Specified in the PDB File

2bvm CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF TOXIN B FROM CLOSTRIDIUM DIFFICILE IN COMPLEX WITH UDP, GLC AND MANGANESE ION