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(-) Description

Title :  CRYSTAL STRUCTURE OF ESCHERICHIA COLI FLAVIN TRAFFICKING PROTEIN, AN FMN TRANSFERASE, Y60N MUTANT, ADP-INHIBITED
 
Authors :  D. R. Tomchick, C. A. Brautigam, R. K. Deka, M. V. Norgard
Date :  02 Jan 15  (Deposition) - 16 Dec 15  (Release) - 16 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Flavin Transferase, Bimetal Center, Lipoprotein, Transferase- Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. K. Deka, C. A. Brautigam, W. Z. Liu, D. R. Tomchick, M. V. Norgard
Molecular Insights Into The Enzymatic Diversity Of Flavin-Trafficking Protein (Ftp; Formerly Apbe) In Flavoprotein Biogenesis In The Bacterial Periplasm.
Microbiologyopen V. 5 21 2016
PubMed-ID: 26626129  |  Reference-DOI: 10.1002/MBO3.306

(-) Compounds

Molecule 1
    Chains: A, B
    EC Number: 2.7.1.180
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-21 NESG
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: SOLUBLE FRAGMENT (UNP RESIDUES 21-351)
    Gene: APBE, YOJK, YOJL, B2214, JW5368
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: FLAVIN TRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 19)

Asymmetric/Biological Unit (4, 19)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
2EDO4Ligand/Ion1,2-ETHANEDIOL
3MG4Ligand/IonMAGNESIUM ION
4NO39Ligand/IonNITRATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:166 , ASP A:280 , THR A:284 , HOH A:589 , HOH A:617binding site for residue MG A 401
02AC2SOFTWAREGLU A:169 , TYR A:239 , ARG A:240 , ADP A:403binding site for residue MG A 402
03AC3SOFTWAREALA A:101 , ASP A:103 , VAL A:106 , ASP A:163 , THR A:166 , SER A:238 , TYR A:239 , ARG A:240 , HIS A:252 , ILE A:254 , MG A:402 , HOH A:522 , HOH A:544 , HOH A:589 , HOH A:591 , HOH A:614binding site for residue ADP A 403
04AC4SOFTWAREARG A:93 , ILE A:94 , LYS A:97 , GLU A:278 , TRP A:282 , HOH A:510 , HOH A:521binding site for residue NO3 A 404
05AC5SOFTWAREGLN A:147binding site for residue NO3 A 405
06AC6SOFTWAREHIS A:231 , ILE A:272 , ALA A:273 , PRO A:274 , PHE A:326 , HOH A:561 , ARG B:178 , GLU B:181binding site for residue NO3 A 406
07AC7SOFTWARETHR A:89 , ARG A:93 , NO3 A:408 , ASP B:86binding site for residue NO3 A 407
08AC8SOFTWAREASP A:86 , NO3 A:407 , ASP B:86 , THR B:89 , THR B:90 , ARG B:93 , HOH B:534binding site for residue NO3 A 408
09AC9SOFTWAREASP A:227 , ILE A:228 , ASN A:229 , HIS A:231 , SER B:186 , ARG B:199 , GLY B:200binding site for residue EDO A 409
10AD1SOFTWAREASP A:174 , ARG A:178 , GLU A:181 , HOH A:545 , HOH A:601 , PRO B:274 , EDO B:409binding site for residue EDO A 410
11AD2SOFTWARETHR B:166 , ASP B:280 , THR B:284 , HOH B:647binding site for residue MG B 401
12AD3SOFTWAREGLU B:169 , TYR B:239 , ADP B:403binding site for residue MG B 402
13AD4SOFTWAREALA B:101 , ASP B:103 , VAL B:106 , ASP B:163 , SER B:165 , THR B:166 , GLY B:237 , SER B:238 , TYR B:239 , ARG B:240 , HIS B:252 , VAL B:253 , ILE B:254 , MG B:402 , NO3 B:405 , HOH B:502 , HOH B:519 , HOH B:540 , HOH B:568binding site for residue ADP B 403
14AD5SOFTWAREPRO B:77 , GLN B:147binding site for residue NO3 B 404
15AD6SOFTWARESER B:236 , GLY B:237 , VAL B:253 , ASP B:283 , THR B:284 , ADP B:403 , HOH B:647binding site for residue NO3 B 405
16AD7SOFTWAREGLU A:82 , ARG B:93 , LYS B:97 , GLU B:278 , TRP B:282 , HOH B:574binding site for residue NO3 B 406
17AD8SOFTWAREASP B:174 , GLU B:181 , EDO B:408binding site for residue NO3 B 407
18AD9SOFTWAREASP B:174 , HIS B:175 , NO3 B:407 , HOH B:573binding site for residue EDO B 408
19AE1SOFTWAREARG A:199 , GLY A:230 , EDO A:410 , GLY B:230 , HIS B:231 , HOH B:571binding site for residue EDO B 409

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4XGX)

(-) 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:290
                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.....eeehhhhhhhhhhhhhhhhhh.......hhhhhhhh.....hhhhhhhhhhhhhhh.eeeee....eeeee........hhhhhhhhhhhhhhhhhhhh....eeeee..eeeee.....................eeee.........ee....ee....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeehhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xgx A  13 TEVTVLEGKTMGTFWRASIPGIDAKRSAELKEKIQTQLDADDQLLSTNKKDSALMRFNDSQSLSPWPVSEAMADIVTTSLRIGAKTDGAMDITVGPLVNLWGVQIPSQEQIDAMKAKTGLQHLTVINQSHQQYLQKDLPDLYVDLSTVGEGYAADHLARLMEQEGISRYLVSVGGALNSRGMNGEGLPWRVAIAVVDINGHGISTSGSYRNSHVIDPQTGRPIEHNLVSVTVIAPTALEADAWDTGLMVLGPEKAKEVVRREGLAVYMITKEGDSFKTWMSPQFKSFLVS 329
                                    22        32        42        52        62        72        82        92       102       112 ||    129       139       149       159       169       179       189       199       209  ||   230       240||     259       269       279       289       299       309       319       329
                                                                                                                               114|                                                                                       212|              241|                                                                              
                                                                                                                                122                                                                                        224               251                                                                              


Chain B from PDB  Type:PROTEIN  Length:293
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.....eeehhhhhhhhhhhhhhhhhh.......hhhhhhhh.......hhhhhhhhhhhhhhh.eeeee....eeeee........hhhhhhhhhhhhhhhhhhhh....eeeee..eeeee..........ee....ee.....eeee........ee....ee....eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeee..eeeeeehhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4xgx B  13 TEVTVLEGKTMGTFWRASIPGIDAKRSAELKEKIQTQLDADDQLLSTNKKDSALMRFNDSQSLSPWPVSEAMADIVTTSLRIGAKTDGAMDITVGPLVNLWGFPVQIPSQEQIDAMKAKTGLQHLTVINQSHQQYLQKDLPDLYVDLSTVGEGYAADHLARLMEQEGISRYLVSVGGALNSRGMNGEGLPWRVAIQKAVVDINGHGISTSGSYRNHVIDPQTGRPIEHNLVSVTVIAPTALEADAWDTGLMVLGPEKAKEVVRREGLAVYMITKEGDSFKTWMSPQFKSFLVS 329
                                    22        32        42        52        62        72        82        92       102       112  ||   127       137       147       157       167       177       187       197       207      |226       236    || 256       266       276       286       296       306       316       326   
                                                                                                                                115|                                                                                          214|              241|                                                                             
                                                                                                                                 121                                                                                           224               252
   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 4XGX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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        APBE_ECOLI | P0AB85: 2o18 4xgv 4xgw

(-) Related Entries Specified in the PDB File

4xgv 4XGV CONTAINS THE WILD-TYPE PROTEIN.