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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GT DOMAIN OF CLOSTRIDIUM DIFFICILE TOXIN A (TCDA) IN COMPLEX WITH UDP AND MANGANESE
 
Authors :  E. Malito, N. D'Urzo, M. J. Bottomley, M. Biancucci, M. Scarselli, D. Ma M. Martinelli
Date :  08 Feb 12  (Deposition) - 18 Jul 12  (Release) - 31 Oct 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Glucosyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. D'Urzo, E. Malito, M. Biancucci, M. J. Bottomley, D. Maione, M. Scarselli, M. Martinelli
The Structure Of Clostridium Difficile Toxin A Glucosyltransferase Domain Bound To Mn2+ And Udp Provides Insights Into Glucosyltransferase Activity And Product Release.
Febs J. V. 279 3085 2012
PubMed-ID: 22747490  |  Reference-DOI: 10.1111/J.1742-4658.2012.08688.X

(-) Compounds

Molecule 1 - TOXIN A
    Chains: A
    EC Number: 2.4.1.-
    Engineered: YES
    Expression System: BREVIBACILLUS CHOSHINENSIS
    Expression System Taxid: 54911
    Fragment: GLUCOSYLTRANSFERASE DOMAIN (UNP RESIDUES 1-541)
    Gene: TOXA, TCDA
    Organism Scientific: CLOSTRIDIUM DIFFICILE
    Organism Taxid: 1496
    Synonym: TCDA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1MN1Ligand/IonMANGANESE (II) ION
2UDP1Ligand/IonURIDINE-5'-DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:287 , GLU A:514 , UDP A:602 , HOH A:763BINDING SITE FOR RESIDUE MN A 601
2AC2SOFTWAREVAL A:100 , TRP A:101 , ILE A:102 , LEU A:264 , SER A:268 , TYR A:283 , ASP A:285 , VAL A:286 , ASP A:287 , SER A:517 , MN A:601 , HOH A:719BINDING SITE FOR RESIDUE UDP A 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DMW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4DMW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DMW)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DMW)

(-) Exons   (0, 0)

(no "Exon" information available for 4DMW)

(-) 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:535
 aligned with TOXA_CLODI | P16154 from UniProtKB/Swiss-Prot  Length:2710

    Alignment length:537
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       
           TOXA_CLODI     2 SLISKEELIKLAYSIRPRENEYKTILTNLDEYNKLTTNNNENKYLQLKKLNESIDVFMNKYKTSSRNRALSNLKKDILKEVILIKNSNTSPVEKNLHFVWIGGEVSDIALEYIKQWADINAEYNIKLWYDSEAFLVNTLKKAIVESSTTEALQLLEEEIQNPQFDNMKFYKKRMEFIYDRQKRFINYYKSQINKPTVPTIDDIIKSHLVSEYNRDETVLESYRTNSLRKINSNHGIDIRANSLFTEQELLNIYSQELLNRGNLAAASDIVRLLALKNFGGVYLDVDMLPGIHSDLFKTISRPSSIGLDRWEMIKLEAIMKYKKYINNYTSENFDKLDQQLKDNFKLIIESKSEKSEIFSKLENLNVSDLEIKIAFALGSVINQALISKQGSYLTNLVIEQVKNRYQFLNQHLNPAIESDNNFTDTTKIFHDSLFNSATAENSMFLTKIAPYLQVGFMPEARSTISLSGPGAYASAYYDFINLQENTIEKTLKASDLIEFKFPENNLSQLTEQEINSLWSFDQASAKYQFEKYVRDYT 538
               SCOP domains d4dmwa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh......hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh..eee...eeeee......hhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..--..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eee........hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhheeee......................hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh...hhhhh.......eee...eeeeee..eeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh......hhhhh..hhhhhhhhhhhhhh..........hhhhhhhhh.hhhhh...hhhhhhh....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dmw A   2 SLISKEELIKLAYSIRPRENEYKTILTNLDEYNKLTTNNNENKYLQLKKLNESIDVFMNKYKTSSRNRALSNLKKDILKEVILIKNSNTSPVEKNLHFVWIGGEVSDIALEYIKQWADINAEYNIKLWYDSEAFLVNTLKKAIVESSTTEALQLLEEEIQNPQFDNMKFYKKRMEFIYDRQKRFINYYKSQINK--VPTIDDIIKSHLVSEYNRDETVLESYRTNSLRKINSNHGIDIRANSLFTEQELLNIYSQELLNRGNLAAASDIVRLLALKNFGGVYLDVDMLPGIHSDLFKTISRPSSIGLDRWEMIKLEAIMKYKKYINNYTSENFDKLDQQLKDNFKLIIESKSEKSEIFSKLENLNVSDLEIKIAFALGSVINQALISKQGSYLTNLVIEQVKNRYQFLNQHLNPAIESDNNFTDTTKIFHDSLFNSATAENSMFLTKIAPYLQVGFMPEARSTISLSGPGAYASAYYDFINLQENTIEKTLKASDLIEFKFPENNLSQLTEQEINSLWSFDQASAKYQFEKYVRDYT 538
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191   |  |201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       
                                                                                                                                                                                                                           195  |                                                                                                                                                                                                                                                                                                                                                    
                                                                                                                                                                                                                              198
   Legend:   → Mismatch (orange background)
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  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 4DMW)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DMW)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TOXA_CLODI | P16154)
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: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.

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  4dmw
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  2.4.1.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        TOXA_CLODI | P16154: 2f6e 2g7c 2qj6 3ho6 4dmv 4r04 5uqk 5uql

(-) Related Entries Specified in the PDB File

3srz CLOSTRIDIUM DIFFICILE TOXIN A (TCDA) GLUCOLSYLTRANSFERASE DOMAIN BOUND TO UDP-GLUCOSE
3ss1 CLOSTRIDIUM DIFFICILE TOXIN A (TCDA) GLUCOLSYLTRANSFERASE DOMAIN
4dmv CRYSTAL STRUCTURE OF APO GT DOMAIN OF CLOSTRIDIUM DIFFICILE TOXIN A (TCDA)