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(-) Description

Title :  TREPONEMA DENTICOLA VARIABLE PROTEIN 1
 
Authors :  J. Le Coq, P. Ghosh
Date :  20 Dec 10  (Deposition) - 31 Aug 11  (Release) - 02 Nov 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Unknown Function, Periodontal Disease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Le Coq, P. Ghosh
Conservation Of The C-Type Lectin Fold For Massive Sequence Variation In A Treponema Diversity-Generating Retroelement.
Proc. Natl. Acad. Sci. Usa V. 108 14649 2011
PubMed-ID: 21873231  |  Reference-DOI: 10.1073/PNAS.1105613108

(-) Compounds

Molecule 1 - TREPONEMA DENTICOLA VARIABLE PROTEIN 1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28B
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 39-329
    Organism Scientific: TREPONEMA DENTICOLA
    Organism Taxid: 158
    Other Details: DISUFIDE BOND BETWEEN C318 SIDE CHAIN AND BETA-MERCAPTOETHANOL. C318 WAS REPLACED BY A MODIFIED AMINO ACID CME318.
    Strain: 35405

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 13)

Asymmetric/Biological Unit (4, 13)
No.NameCountTypeFull Name
1ACT9Ligand/IonACETATE ION
2CA2Ligand/IonCALCIUM ION
3CME1Mod. Amino AcidS,S-(2-HYDROXYETHYL)THIOCYSTEINE
4NA1Ligand/IonSODIUM ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:178 , SER A:180 , ASN A:181 , ASN A:182 , TYR A:254 , HOH A:2116BINDING SITE FOR RESIDUE ACT A1330
02AC2SOFTWAREHOH A:2245 , HOH A:2246BINDING SITE FOR RESIDUE ACT A1331
03AC3SOFTWAREHIS A:79 , TYR A:82 , LYS A:216 , HOH A:2036 , HOH A:2247BINDING SITE FOR RESIDUE ACT A1332
04AC4SOFTWARESER A:300 , ACT A:1338 , HOH A:2248 , HOH A:2249 , HOH A:2250 , HOH A:2251BINDING SITE FOR RESIDUE ACT A1333
05AC5SOFTWARETHR A:222 , GLU A:223 , ALA A:224 , CME A:318 , SER A:319 , HOH A:2252BINDING SITE FOR RESIDUE ACT A1334
06AC6SOFTWARESER A:234 , ASN A:235 , TYR A:303 , VAL A:310 , ILE A:312 , HOH A:2228 , HOH A:2253 , HOH A:2254BINDING SITE FOR RESIDUE ACT A1335
07AC7SOFTWAREVAL A:167 , ASP A:168 , HOH A:2106BINDING SITE FOR RESIDUE ACT A1336
08AC8SOFTWARETHR A:59 , GLY A:61 , LYS A:151BINDING SITE FOR RESIDUE ACT A1337
09AC9SOFTWARELYS A:247 , SER A:313 , ACT A:1333 , HOH A:2255 , HOH A:2256BINDING SITE FOR RESIDUE ACT A1338
10BC1SOFTWAREVAL A:306 , HOH A:2037 , HOH A:2145 , HOH A:2247BINDING SITE FOR RESIDUE NA A1339
11BC2SOFTWAREGLU A:101 , ASP A:255 , ILE A:256 , GLY A:258 , VAL A:260 , GLU A:262 , CA A:1341BINDING SITE FOR RESIDUE CA A1340
12BC3SOFTWAREGLU A:101 , ASP A:255 , ILE A:256 , GLY A:258 , VAL A:260 , GLU A:262 , GLY A:294 , GLY A:295 , CA A:1340BINDING SITE FOR RESIDUE CA A1341

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Y3C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Y3C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Y3C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Y3C)

(-) Exons   (0, 0)

(no "Exon" information available for 2Y3C)

(-) 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:278
 aligned with Q73KE9_TREDE | Q73KE9 from UniProtKB/TrEMBL  Length:329

    Alignment length:278
                                    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        
         Q73KE9_TREDE    52 TPVDKTYTVGSVEFTMKGIAAVNAQLGHNDYSINQPHTVSLSAYLIGETEVTQELWQAVMGNNPSHFNGSPAVGETQGKRPVENVNWYQAIAFCNKLSIKLNLEPCYTVNVGGNPVDFAALSFDQIPDSNNADWDKAELDINKKGFRLPTEAEWEWAAKGGTDDKWSGTNTEAELKNYAWYGSNSGSKTHEVKKKKPNWYGLYDIAGNVAEWCWDWRADIHTGDSFPQDYPGPASGSGRVLRGGSWAGSADYCAVGERVNISPGVRCSDLGFRLACRP 329
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee..eeeeeeee..eeeee..........eeeee..eeee....hhhhhhhhhh..............hhhhh.....hhhhhhhhhhhhhhhh.....ee.ee..ee......hhhhh....hhhhhh.ee..........hhhhhhhhhhh..........hhhhhh.................................eeeeeee......................eeee.......hhhhh....eee........ee...ee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y3c A  52 TPVDKTYTVGSVEFTMKGIAAVNAQLGHNDYSINQPHTVSLSAYLIGETEVTQELWQAVMGNNPSHFNGSPAVGETQGKRPVENVNWYQAIAFCNKLSIKLNLEPCYTVNVGGNPVDFAALSFDQIPDSNNADWDKAELDINKKGFRLPTEAEWEWAAKGGTDDKWSGTNTEAELKNYAWYGSNSGSKTHEVKKKKPNWYGLYDIAGNVAEWCWDWRADIHTGDSFPQDYPGPASGSGRVLRGGSWAGSADYCAVGERVNISPGVRcSDLGFRLACRP 329
                                    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        
                                                                                                                                                                                                                                                                                                    318-CME
   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 2Y3C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2Y3C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2Y3C)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q73KE9_TREDE | Q73KE9)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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  2y3c
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