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(-) Description

Title :  CRYSTAL STRUCTURE OF A 2:1 COMPLEX OF TREPONEMA PALLIDUM TATP(T) (TP0957) BOUND TO TATT (TP0956)
 
Authors :  C. A. Brautigam, R. K. Deka, M. V. Norgard
Date :  30 Jan 12  (Deposition) - 23 May 12  (Release) - 20 Jun 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.05
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Protein-Protein Complex, Trap Transporter, Tpat, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. A. Brautigam, R. K. Deka, P. Schuck, D. R. Tomchick, M. V. Norgard
Structural And Thermodynamic Characterization Of The Interaction Between Two Periplasmic Treponema Pallidum Lipoproteins That Are Components Of A Tpr-Protein-Associate Trap Transporter (Tpat).
J. Mol. Biol. V. 420 70 2012
PubMed-ID: 22504226  |  Reference-DOI: 10.1016/J.JMB.2012.04.001

(-) Compounds

Molecule 1 - TP33 PROTEIN
    Chains: D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: SOLUBLE FRAGMENT, UNP RESIDUES 21-342
    Gene: TP_0957
    Mutation: YES
    Organism Scientific: TREPONEMA PALLIDUM SUBSP. PALLIDUM
    Organism Taxid: 243276
    Strain: NICHOLS
 
Molecule 2 - UNCHARACTERIZED PROTEIN TP_0956
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: SOLUBLE FRAGMENT, UNP RESIDUES 23-323
    Gene: TP_0956
    Organism Scientific: TREPONEMA PALLIDUM SUBSP. PALLIDUM
    Organism Taxid: 243276
    Strain: NICHOLS

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4DI3)

(-) Sites  (0, 0)

(no "Site" information available for 4DI3)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4DI3)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ser D:91 -Gly D:92
2Ser E:65 -Ser E:66
3Ser E:66 -Arg E:67

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4DI3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4DI3)

(-) Exons   (0, 0)

(no "Exon" information available for 4DI3)

(-) 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:273
 aligned with Y956_TREPA | O83922 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:273
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319   
           Y956_TREPA    50 DADFTRVFTEEDDLDLVAQSLPLVLKVYEALHLQNPAHRGLSLAVGRLYIMYANAFVQTPAQYLPEDEFEAQNEAYSRARKLYLRGARYALSSLETAYPGFTREVFSGDEQRLHKVLSRCTRVDVGTLYWVGTGYVAAFALTPLGSALPDTVHAAVMMLERACDLWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAGFDEALDRALAIDPESVPHNKLLVILSQKRARWLKAHVQDFFL 322
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4di3 A  29 DADFTRVFTEEDDLDLVAQSLPLVLKVYEALHLQNPAHRGLSLAVGRLYIMYANAFVQTPAQYLPEDEFEAQNEAYSRARKLYLRGARYALSSLETAYPGFTREVFSGDEQRLHKVLSRCTRVDVGTLYWVGTGYVAAFALTPLGSALPDTVHAAVMMLERACDLWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAGFDEALDRALAIDPESVPHNKLLVILSQKRARWLKAHVQDFFL 301
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298   


Chain B from PDB  Type:PROTEIN  Length:273
 aligned with Y956_TREPA | O83922 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:273
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319   
           Y956_TREPA    50 DADFTRVFTEEDDLDLVAQSLPLVLKVYEALHLQNPAHRGLSLAVGRLYIMYANAFVQTPAQYLPEDEFEAQNEAYSRARKLYLRGARYALSSLETAYPGFTREVFSGDEQRLHKVLSRCTRVDVGTLYWVGTGYVAAFALTPLGSALPDTVHAAVMMLERACDLWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAGFDEALDRALAIDPESVPHNKLLVILSQKRARWLKAHVQDFFL 322
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4di3 B  29 DADFTRVFTEEDDLDLVAQSLPLVLKVYEALHLQNPAHRGLSLAVGRLYIMYANAFVQTPAQYLPEDEFEAQNEAYSRARKLYLRGARYALSSLETAYPGFTREVFSGDEQRLHKVLSRCTRVDVGTLYWVGTGYVAAFALTPLGSALPDTVHAAVMMLERACDLWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAGFDEALDRALAIDPESVPHNKLLVILSQKRARWLKAHVQDFFL 301
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298   


Chain C from PDB  Type:PROTEIN  Length:273
 aligned with Y956_TREPA | O83922 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:273
                                    59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319   
           Y956_TREPA    50 DADFTRVFTEEDDLDLVAQSLPLVLKVYEALHLQNPAHRGLSLAVGRLYIMYANAFVQTPAQYLPEDEFEAQNEAYSRARKLYLRGARYALSSLETAYPGFTREVFSGDEQRLHKVLSRCTRVDVGTLYWVGTGYVAAFALTPLGSALPDTVHAAVMMLERACDLWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAGFDEALDRALAIDPESVPHNKLLVILSQKRARWLKAHVQDFFL 322
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhh..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4di3 C  29 DADFTRVFTEEDDLDLVAQSLPLVLKVYEALHLQNPAHRGLSLAVGRLYIMYANAFVQTPAQYLPEDEFEAQNEAYSRARKLYLRGARYALSSLETAYPGFTREVFSGDEQRLHKVLSRCTRVDVGTLYWVGTGYVAAFALTPLGSALPDTVHAAVMMLERACDLWPSYQEGAVWNVLTKFYAAAPESFGGGMEKAHTAFEHLTRYCSAHDPDHHITYADALCIPLNNRAGFDEALDRALAIDPESVPHNKLLVILSQKRARWLKAHVQDFFL 301
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298   


Chain D from PDB  Type:PROTEIN  Length:303
 aligned with O83923_TREPA | O83923 from UniProtKB/TrEMBL  Length:342

    Alignment length:312
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333  
         O83923_TREPA    24 VVLKIASIAPARSIWETELKKLSAEWSEITGGLVSMKFYDMSSLGGEREGIRKLKSSRPGQAAPLDGAVFSCLGLSELAPDSGIYTLSVPFLIQNEKDLERVLHELREDLDRPFRAAGFRVITWTNAGWLSFYTRAPYASLGQLKKQTIALSSLDSSVLGTCFRICGFDIKDAPNARLAPLLKAGSIDGFLSVHLFTWATGFYRYISYALDTKICPAVIGMLISDGSWARIPSRYHDAMLQAATRVRQRLANNLETLDRECSNNIQKAGVSIVHLTPQEIQEWRTEFAADVKRIQARLPGMLNMTLYEKIKH 335
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeee......hhhhhhhhhhhhhhhhh....eeeeee.....hhhhhhhh...-----......eeeehhhhhhhh...hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeeee.....hhhhhhh.eee..----............eee.....hhhhhhhh....eeeeehhhhhhhhhhhhh.eee.....eeeeeeeeehhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4di3 D  10 VVLKIASIAPARSIWETELKKLSAEWSEITGGLVSMKFYDMSSLGGEREGIRKLKS-----AAPLDGAVFSCLGLSELAPDSGIYTLSVPFLIQNEKDLERVLHELREDLDRPFRAAGFRVITWTNAGWLSFYTRAPYASLGQLKKQTIALS----SVLGTCFRICGFDIKDAPNVRLAPLLKAGSIDGFLSVHLFTWATGFYRYISYALDTKICPAVIGMLISDGSWARIPSRYHDAMLQAATRVRQRLANNLETLDRECSNNIQKAGVSIVHLTPQEIQEWRTEFAADVKRIQARLPGMLNMTLYEKIKH 321
                                    19        29        39        49        59     |   - |      79        89        99       109       119       129       139       149       159 |    |169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319  
                                                                                  65    71                                                                                       161  166                                                                                                                                                           


Chain E from PDB  Type:PROTEIN  Length:317
 aligned with O83923_TREPA | O83923 from UniProtKB/TrEMBL  Length:342

    Alignment length:317
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       
         O83923_TREPA    23 KVVLKIASIAPARSIWETELKKLSAEWSEITGGLVSMKFYDMSSLGGEREGIRKLKSSRPGQAAPLDGAVFSCLGLSELAPDSGIYTLSVPFLIQNEKDLERVLHELREDLDRPFRAAGFRVITWTNAGWLSFYTRAPYASLGQLKKQTIALSSLDSSVLGTCFRICGFDIKDAPNARLAPLLKAGSIDGFLSVHLFTWATGFYRYISYALDTKICPAVIGMLISDGSWARIPSRYHDAMLQAATRVRQRLANNLETLDRECSNNIQKAGVSIVHLTPQEIQEWRTEFAADVKRIQARLPGMLNMTLYEKIKHLLYS 339
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhhhhh...eeeeeee.....hhhhhhhh.............eeeeehhhhhhhh...hhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeeee.....hhhhhhh.eeee.hhhhhhhhhhhh....eeee....hhhhhhhh....eeeeehhhhhhhhhhhhh.eee.....eeeeeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhh.hhhhhhhh....hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4di3 E   9 KVVLKIASIAPARSIWETELKKLSAEWSEITGGLVSMKFYDMSSLGGEREGIRKLKSSRPGQAAPLDGAVFSCLGLSELAPDSGIYTLSVPFLIQNEKDLERVLHELREDLDRPFRAAGFRVITWTNAGWLSFYTRAPYASLGQLKKQTIALSSLDSSVLGTCFRICGFDIKDAPNVRLAPLLKAGSIDGFLSVHLFTWATGFYRYISYALDTKICPAVIGMLISDGSWARIPSRYHDAMLQAATRVRQRLANNLETLDRECSNNIQKAGVSIVHLTPQEIQEWRTEFAADVKRIQARLPGMLNMTLYEKIKHLLYS 325
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318
   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  (0, 0)

(no "SCOP Domain" information available for 4DI3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4DI3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4DI3)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (Y956_TREPA | O83922)

Chain D,E   (O83923_TREPA | O83923)
biological process
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0030288    outer membrane-bounded periplasmic space    The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.

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  Cis Peptide Bonds
    Ser D:91 - Gly D:92   [ RasMol ]  
    Ser E:65 - Ser E:66   [ RasMol ]  
    Ser E:66 - Arg E:67   [ RasMol ]  
 

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  4di3
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  O83923_TREPA | O83923
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  Y956_TREPA | O83922
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 Related Entries

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

UniProtKB/Swiss-Prot
        Y956_TREPA | O83922: 3u64 4di4
UniProtKB/TrEMBL
        O83923_TREPA | O83923: 3u65 4di4

(-) Related Entries Specified in the PDB File

3di4 TATP(T) (TP0957) BOUND TO TATT (TP0956)
3u64 STRUCTURE OF TATT ALONE
3u65 STRUCTURE OF TATP(T) ALONE