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(-) Description

Title :  CRYSTAL STRUCTURE OF TREPONEMA PALLIDUM TP0796 FLAVIN TRAFFICKING PROTEIN,A BIFUNCTIONAL FMN TRANSFERASE/FAD PYROPHOSPHATASE, N55Y MUTANT, ADP BOUND FORM
 
Authors :  D. R. Tomchick, C. A. Brautigam, R. K. Deka, M. V. Norgard
Date :  20 Dec 14  (Deposition) - 14 Oct 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A
Keywords :  Fmn Transferase, Fad Pyrophosphatase, Hydrolase, Bimetal Center, Flavin Turnover, Treponema Pallidum, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. K. Deka, C. A. Brautigam, W. Z. Liu, D. R. Tomchick, M. V. Norgard
Evidence For Posttranslational Protein Flavinylation In The Syphilis Spirochete Treponema Pallidum: Structural And Biochemical Insights From The Catalytic Core Of A Periplasmic Flavin-Trafficking Protein.
Mbio V. 6 00519 2015
PubMed-ID: 25944861  |  Reference-DOI: 10.1128/MBIO.00519-15

(-) Compounds

Molecule 1
    Chains: A
    EC Number: 2.7.1.180
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: APBE, TP_0796
    Mutation: YES
    Organism Scientific: TREPONEMA PALLIDUM (STRAIN NICHOLS)
    Organism Taxid: 243276
    Strain: NICHOLS
    Synonym: FLAVIN TRANSFERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric/Biological Unit (5, 10)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3EDO3Ligand/Ion1,2-ETHANEDIOL
4MG2Ligand/IonMAGNESIUM ION
5NA2Ligand/IonSODIUM ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:162 , ASP A:284 , THR A:288 , MG A:502 , ADP A:505binding site for residue MG A 501
02AC2SOFTWAREASP A:284 , MG A:501 , ADP A:505 , HOH A:717 , HOH A:718 , HOH A:850binding site for residue MG A 502
03AC3SOFTWAREHIS A:267 , EDO A:508 , HOH A:735 , HOH A:816 , HOH A:823 , HOH A:851binding site for residue NA A 503
04AC4SOFTWARETHR A:239 , GLU A:244 , ADP A:505 , HOH A:787 , HOH A:789binding site for residue NA A 504
05AC5SOFTWAREALA A:96 , PHE A:97 , ASN A:98 , LEU A:101 , ASP A:159 , GLY A:161 , ALA A:162 , LYS A:165 , SER A:240 , GLU A:244 , HIS A:256 , ILE A:257 , ILE A:258 , ASP A:284 , THR A:288 , MG A:501 , MG A:502 , NA A:504 , HOH A:717 , HOH A:718 , HOH A:733 , HOH A:751 , HOH A:803 , HOH A:811 , HOH A:826 , HOH A:836 , HOH A:850binding site for residue ADP A 505
06AC6SOFTWAREPHE A:276 , GLY A:307 , ASP A:309 , HOH A:828 , HOH A:841binding site for residue EDO A 506
07AC7SOFTWARETYR A:295 , ALA A:321 , SER A:322binding site for residue EDO A 507
08AC8SOFTWAREHIS A:267 , ASP A:269 , LEU A:293 , NA A:503 , HOH A:612 , HOH A:735binding site for residue EDO A 508
09AC9SOFTWAREARG A:24 , LEU A:185 , LYS A:198 , ASN A:213binding site for residue ACT A 509
10AD1SOFTWARESER A:27 , LYS A:28 , ALA A:180 , LEU A:181 , ASP A:182 , HOH A:723 , HOH A:809binding site for residue ACT A 510

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XDU)

(-) 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    
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(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:330
                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeeeee..eeeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.....eeehhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.eeeee.......eeeee...........hhhhhhhhhhhhhhhhh....eeeee..eeeee..ee...ee.eeeeee........eeeeeee..eeeeeee....eeee..eeee................eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee....eeee...hhh.eee.....ee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4xdu A   5 ARVREYSRAELVIGTLCRVRVYSKRPAAEVHAALEEVFTLLQQQEMVLSAYRDDSALAALNAQAGSAPVVVDRSLYALLERALFFAEKSGGAFNPALGAVVKLWNIGFDRAAVPDPDALKEALTRCDFRQVHLRAGVSVGAPHTVQLAQAGMQLDLGAIAKGFLADKIVQLLTAHALDSALVDLGGNIFALGLKYGAQRLEWNVGIRDPHGTGQKPALVVSVRDCSVVTSGAYERFFERDGVRYHHIIDPVTGFPAHTDVDSVSIFAPRSTDADALATACFVLGYEKSCALLREFPGVDALFIFPDKRVRASAGIVDRVRVLDARFVLER 340
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194     ||210       220       230       240       250       260       270       280       290       300       310       320       330       340
                                                                                                                                                                                                                             200|                                                                                                                                     
                                                                                                                                                                                                                              207
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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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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  2.7.1.180
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 Related Entries

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

UniProtKB/Swiss-Prot
        APBE_TREPA | O83774: 4ifu 4ifw 4ifx 4ifz 4ig1 4xdr 4xdt

(-) Related Entries Specified in the PDB File

4ifu 4IFU CONTAINS THE WILD TYPE PROTEIN, APO FORM.