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(-) Description

Title :  CRYSTAL STRUCTURE OF A THIAMINE BIOSYNTHESIS LIPOPROTEIN APBE, NORTHEAST STRCUTURAL GENOMICS TARGET ER559
 
Authors :  J. Seetharaman, M. Su, D. Wang, Y. Fang, K. Cunningham, L. Ma, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  28 Nov 06  (Deposition) - 05 Dec 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Lipoprotein, Apbe, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Lipid Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Seetharaman, M. Su, D. Wang, Y. Fang, K. Cunningham, L. Ma, R. Xiao, J. Liu, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt, L. Tong
Crystal Structure Of A Thiamine Biosynthesis Lipoprotein Apbe
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THIAMINE BIOSYNTHESIS LIPOPROTEIN APBE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: APBE
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 44)

Asymmetric/Biological Unit (2, 44)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2MSE40Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:166 , ASP A:280 , ASP A:283 , THR A:284 , HOH A:393BINDING SITE FOR RESIDUE CA A 341
2AC2SOFTWARETHR B:166 , ASP B:280 , ASP B:283 , THR B:284 , HOH B:388BINDING SITE FOR RESIDUE CA B 341
3AC3SOFTWARETHR C:166 , ASP C:280 , ASP C:283 , THR C:284BINDING SITE FOR RESIDUE CA C 341
4AC4SOFTWARETHR D:166 , ASP D:280 , ASP D:283 , THR D:284 , HOH D:397BINDING SITE FOR RESIDUE CA D 341

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O18)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gln A:120 -Pro A:121

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O18)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2O18)

(-) Exons   (0, 0)

(no "Exon" information available for 2O18)

(-) 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:307
 aligned with APBE_ECOLI | P0AB85 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:318
                                    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        
           APBE_ECOLI    32 TEVTVLEGKTMGTFWRASIPGIDAKRSAELKEKIQTQLDADDQLLSTYKKDSALMRFNDSQSLSPWPVSEAMADIVTTSLRIGAKTDGAMDITVGPLVNLWGFGPEQQPVQIPSQEQIDAMKAKTGLQHLTVINQSHQQYLQKDLPDLYVDLSTVGEGYAADHLARLMEQEGISRYLVSVGGALNSRGMNGEGLPWRVAIQKPTDKENAVQAVVDINGHGISTSGSYRNYYELDGKRLSHVIDPQTGRPIEHNLVSVTVIAPTALEADAWDTGLMVLGPEKAKEVVRREGLAVYMITKEGDSFKTWMSPQFKSFLVSE 349
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.....eeehhhhhhhhhhhhhhhhhh.......hhhhhhhhh..............hhhhhhhhhhhh.eeeee....eeeee........hhhhhhhhhhhhhhhhhhhh....eeeee..eeeee..........eee......----.eee.....eeeeee....-------.................eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....eeeeehhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2o18 A  13 TEVTVLEGKTmGTFWRASIPGIDAKRSAELKEKIQTQLDADDQLLSTYKKDSALmRFNDSQSLSPWPVSEAmADIVTTSLRIGAKTDGAmDITVGPLVNLWGFGPEQQPVQIPSQEQIDAmKAKTGLQHLTVINQSHQQYLQKDLPDLYVDLSTVGEGYAADHLARLmEQEGISRYLVSVGGALNSRGmNGEGLPWRVAIQKPTDK----QAVVDINGHGISTSGSYRN-------RLSHVIDPQTGRPIEHNLVSVTVIAPTALEADAWDTGLmVLGPEKAKEVVRREGLAVYmITKEGDSFKTWmSPQFKSFLVSE 330
                                    22|       32        42        52        62    |   72        82 |      92       102       112       122       132|      142       152       162       172       182       192       202       212     |   -|      232        |-      |252       262       272       282    |  292       302    |  312      |322        
                                     23-MSE                                      67-MSE           84-MSE           102-MSE                        133-MSE                                        180-MSE              201-MSE          218  223               241     249                                   287-MSE             307-MSE     319-MSE       


Chain B from PDB  Type:PROTEIN  Length:300
 aligned with APBE_ECOLI | P0AB85 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:318
                                    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        
           APBE_ECOLI    32 TEVTVLEGKTMGTFWRASIPGIDAKRSAELKEKIQTQLDADDQLLSTYKKDSALMRFNDSQSLSPWPVSEAMADIVTTSLRIGAKTDGAMDITVGPLVNLWGFGPEQQPVQIPSQEQIDAMKAKTGLQHLTVINQSHQQYLQKDLPDLYVDLSTVGEGYAADHLARLMEQEGISRYLVSVGGALNSRGMNGEGLPWRVAIQKPTDKENAVQAVVDINGHGISTSGSYRNYYELDGKRLSHVIDPQTGRPIEHNLVSVTVIAPTALEADAWDTGLMVLGPEKAKEVVRREGLAVYMITKEGDSFKTWMSPQFKSFLVSE 349
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.....eeehhhhhhhhhhhhhhhhh........hhhhhhh....---------.hhhhhhhhhhhhhh.eeeee....eeeee........hhhhhhhhhhhhhhhhhhhh....eeeee..eeeee..........ee..---------..ee....eeeeee.............................eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeeee....eeeeehhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2o18 B  13 TEVTVLEGKTmGTFWRASIPGIDAKRSAELKEKIQTQLDADDQLLSTYKKDSALmRFNDSQSLSPWPVSEAmADIVTTSLRIGAKTDGAmDITVGPLVNLWGFG---------SQEQIDAmKAKTGLQHLTVINQSHQQYLQKDLPDLYVDLSTVGEGYAADHLARLmEQEGISRYLVSVGGALNSRGmNGEGLPWRVAIQ---------QAVVDINGHGISTSGSYRNYYELDGKRLSHVIDPQTGRPIEHNLVSVTVIAPTALEADAWDTGLmVLGPEKAKEVVRREGLAVYmITKEGDSFKTWmSPQFKSFLVSE 330
                                    22|       32        42        52        62    |   72        82 |      92       102       112   |     -   |   132|      142       152       162       172       182       192       202       212|        -|      232       242       252       262       272       282    |  292       302    |  312      |322        
                                     23-MSE                                      67-MSE           84-MSE           102-MSE       116       126      |                                            180-MSE              201-MSE     213       223                                                             287-MSE             307-MSE     319-MSE       
                                                                                                                                                  133-MSE                                                                                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:313
 aligned with APBE_ECOLI | P0AB85 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:318
                                    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        
           APBE_ECOLI    32 TEVTVLEGKTMGTFWRASIPGIDAKRSAELKEKIQTQLDADDQLLSTYKKDSALMRFNDSQSLSPWPVSEAMADIVTTSLRIGAKTDGAMDITVGPLVNLWGFGPEQQPVQIPSQEQIDAMKAKTGLQHLTVINQSHQQYLQKDLPDLYVDLSTVGEGYAADHLARLMEQEGISRYLVSVGGALNSRGMNGEGLPWRVAIQKPTDKENAVQAVVDINGHGISTSGSYRNYYELDGKRLSHVIDPQTGRPIEHNLVSVTVIAPTALEADAWDTGLMVLGPEKAKEVVRREGLAVYMITKEGDSFKTWMSPQFKSFLVSE 349
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee..eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.....eeehhhhhhhhhhhhhhhhhh.......hhhhhh..................hhhhhhhhhhh.eeeee....eeeee........hhhhhhhhhhhhhhhhhhhh....eeeee..eeeee.................-----.........eeeeeee............................eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....eeeeehhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2o18 C  13 TEVTVLEGKTmGTFWRASIPGIDAKRSAELKEKIQTQLDADDQLLSTYKKDSALmRFNDSQSLSPWPVSEAmADIVTTSLRIGAKTDGAmDITVGPLVNLWGFGPEQQPVQIPSQEQIDAmKAKTGLQHLTVINQSHQQYLQKDLPDLYVDLSTVGEGYAADHLARLmEQEGISRYLVSVGGALNSRGmNGEGLPWRVAIQKPT-----VQAVVDINGHGISTSGSYRNYYELDGKRLSHVIDPQTGRPIEHNLVSVTVIAPTALEADAWDTGLmVLGPEKAKEVVRREGLAVYmITKEGDSFKTWmSPQFKSFLVSE 330
                                    22|       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        
                                     23-MSE                                      67-MSE           84-MSE           102-MSE                        133-MSE                                        180-MSE              201-MSE        216   222                                                              287-MSE             307-MSE     319-MSE       


Chain D from PDB  Type:PROTEIN  Length:306
 aligned with APBE_ECOLI | P0AB85 from UniProtKB/Swiss-Prot  Length:351

    Alignment length:319
                                    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         
           APBE_ECOLI    32 TEVTVLEGKTMGTFWRASIPGIDAKRSAELKEKIQTQLDADDQLLSTYKKDSALMRFNDSQSLSPWPVSEAMADIVTTSLRIGAKTDGAMDITVGPLVNLWGFGPEQQPVQIPSQEQIDAMKAKTGLQHLTVINQSHQQYLQKDLPDLYVDLSTVGEGYAADHLARLMEQEGISRYLVSVGGALNSRGMNGEGLPWRVAIQKPTDKENAVQAVVDINGHGISTSGSYRNYYELDGKRLSHVIDPQTGRPIEHNLVSVTVIAPTALEADAWDTGLMVLGPEKAKEVVRREGLAVYMITKEGDSFKTWMSPQFKSFLVSEK 350
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------------------ApbE-2o18D01 D:50-308                                                                                                                                                                                                                                              ----------------------- Pfam domains (1)
           Pfam domains (2) -------------------------------------ApbE-2o18D02 D:50-308                                                                                                                                                                                                                                              ----------------------- Pfam domains (2)
           Pfam domains (3) -------------------------------------ApbE-2o18D03 D:50-308                                                                                                                                                                                                                                              ----------------------- Pfam domains (3)
           Pfam domains (4) -------------------------------------ApbE-2o18D04 D:50-308                                                                                                                                                                                                                                              ----------------------- Pfam domains (4)
         Sec.struct. author ..eeeeeeee..eeeeeeee..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh.....eeehhhhhhhhhhhhhhhhh........hhhhhhhhh..-----......hhhhhhhhhhhhh.eeeee....eeeee...........hhhhhhhhhhhhhhhhh....eeeee..eeeee..........ee...--------..ee.....eeeeee............................eeeeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee....eeeeehhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o18 D  13 TEVTVLEGKTmGTFWRASIPGIDAKRSAELKEKIQTQLDADDQLLSTYKKDSALmRFNDSQSLSPWPVSEAmADIVTTSLRIGAKTDGAmDITVGPLVNLWGFG-----VQIPSQEQIDAmKAKTGLQHLTVINQSHQQYLQKDLPDLYVDLSTVGEGYAADHLARLmEQEGISRYLVSVGGALNSRGmNGEGLPWRVAIQK--------QAVVDINGHGISTSGSYRNYYELDGKRLSHVIDPQTGRPIEHNLVSVTVIAPTALEADAWDTGLmVLGPEKAKEVVRREGLAVYmITKEGDSFKTWmSPQFKSFLVSEK 331
                                    22|       32        42        52        62    |   72        82 |      92       102       112   |   122       132|      142       152       162       172       182       192       202       212 |       -|      232       242       252       262       272       282    |  292       302    |  312      |322         
                                     23-MSE                                      67-MSE           84-MSE           102-MSE       116   122        133-MSE                                        180-MSE              201-MSE      214      223                                                             287-MSE             307-MSE     319-MSE
   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 2O18)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2O18)

(-) Pfam Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: ApbE] (4)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (APBE_ECOLI | P0AB85)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0017013    protein flavinylation    The addition of a flavin group to a protein amino acid.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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  2o18
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 Related Entries

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

UniProtKB/Swiss-Prot
        APBE_ECOLI | P0AB85: 4xgv 4xgw 4xgx

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2O18)