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(-) Description

Title :  STRUCTURE OF COBINAMIDE-BOUND BTUF MUTANT W66L, THE PERIPLASMIC VITAMIN B12 BINDING PROTEIN IN E.COLI
 
Authors :  S. A. Mireku, M. Ruetz, T. Zhou, V. M. Korkhov, B. Kraeutler, K. P. Locher
Date :  14 Oct 16  (Deposition) - 01 Mar 17  (Release) - 01 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Btuf, Cobinamide, Periplasmic Binding Protein, Abc Transporter, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. A. Mireku, M. Ruetz, T. Zhou, V. M. Korkhov, B. Krautler, K. P. Locher
Conformational Change Of A Tryptophan Residue In Btuf Facilitates Binding And Transport Of Cobinamide By The Vitamin B12 Transporter Btucd-F.
Sci Rep V. 7 41575 2017
PubMed-ID: 28128319  |  Reference-DOI: 10.1038/SREP41575

(-) Compounds

Molecule 1 - VITAMIN B12-BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BTUF, YADT, B0158, JW0154
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Other Details: OMPA-NCOI-BTUF-BAMHI-3C-BAMHI-HIS6
    Strain: K12

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1CBY2Ligand/IonCOB(II)INAMIDE
2CYN3Ligand/IonCYANIDE ION
3GOL3Ligand/IonGLYCEROL
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1CBY1Ligand/IonCOB(II)INAMIDE
2CYN2Ligand/IonCYANIDE ION
3GOL1Ligand/IonGLYCEROL
Biological Unit 2 (3, 4)
No.NameCountTypeFull Name
1CBY1Ligand/IonCOB(II)INAMIDE
2CYN1Ligand/IonCYANIDE ION
3GOL2Ligand/IonGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:245 , CBY A:302 , CYN A:303 , HOH A:414 , HOH A:553binding site for residue CYN A 301
2AC2SOFTWAREPRO A:31 , ALA A:32 , TYR A:50 , LEU A:66 , TRP A:85 , GLY A:87 , PHE A:162 , PHE A:168 , TRP A:196 , ASP A:242 , GLU A:245 , ARG A:246 , CYN A:301 , CYN A:303 , GOL A:304 , HOH A:402 , HOH A:417 , HOH A:427 , HOH A:434 , HOH A:454 , HOH A:506 , HOH A:548 , HOH A:561 , HOH A:571binding site for residue CBY A 302
3AC3SOFTWARETRP A:85 , CYN A:301 , CBY A:302 , GOL A:304binding site for residue CYN A 303
4AC4SOFTWARESER A:49 , LEU A:66 , CBY A:302 , CYN A:303binding site for residue GOL A 304
5AC5SOFTWAREPRO B:31 , ALA B:32 , TYR B:50 , LEU B:66 , TRP B:85 , GLY B:87 , PHE B:162 , PHE B:168 , TRP B:196 , ASP B:242 , GLU B:245 , ARG B:246 , CYN B:302 , GOL B:303 , HOH B:408 , HOH B:412 , HOH B:423 , HOH B:430 , HOH B:441 , HOH B:484 , HOH B:494 , HOH B:531 , HOH B:575 , HOH B:576binding site for residue CBY B 301
6AC6SOFTWAREGLU B:245 , CBY B:301binding site for residue CYN B 302
7AC7SOFTWARELEU B:29 , SER B:48 , SER B:49 , TYR B:50 , LEU B:66 , TRP B:85 , CBY B:301 , HOH B:406binding site for residue GOL B 303
8AC8SOFTWARESER B:49 , TYR B:50 , GLN B:62 , HOH B:415 , HOH B:422 , HOH B:486binding site for residue GOL B 304

(-) SS Bonds  (2, 2)

Asymmetric Unit
No.Residues
1A:183 -A:259
2B:183 -B:259

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:53 -Pro A:54
2Tyr B:53 -Pro B:54

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5M3B)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M3B)

(-) Exons   (0, 0)

(no "Exon" information available for 5M3B)

(-) Sequences/Alignments

Asymmetric 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:228
                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eee.hhhhhhhhhhh......ee.....hhhhhhh.eeee..eehhhhhhhh...eeee.....hhhhhhhhhhh...eee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee...........hhhhhhhhhh.eee............hhhhhhhh...eeeee....eee.hhhhhh....hhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5m3b A  23 APRVITLSPANTELAFAAGITPVGVSSYSDYPPQAQKIEQVSTLQGMNLERIVALKPDLVIAWRGGNAERQVDQLASLGIKVMWVDATSIEQIANALRQLAPWSPQPDKAEQAAQSLLDQYAQLKAQYADKPKKRVFLQFGINPPFTSGKESIQNQVLEVCGGENIFKDSRVPWPQVSREQVLARSPQAIVITGKIPVIPLTSDWFERASPRIILAAQQLCNALSQVD 266
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212   ||  238       248       258        
                                                                                                                                                                                                                           216|                                 
                                                                                                                                                                                                                            233                                 


Chain B from PDB  Type:PROTEIN  Length:230
                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee.hhhhhhhhhhh......ee.....hhhhhhh.eeee..eehhhhhhhh...eeee.....hhhhhhhhhhh...eee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....eeeee.............hhhhhhhhhh.eee............hhhhhhhh...eeeee....eeeehhhhhhh...hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m3b B  21 MAAPRVITLSPANTELAFAAGITPVGVSSYSDYPPQAQKIEQVSTLQGMNLERIVALKPDLVIAWRGGNAERQVDQLASLGIKVMWVDATSIEQIANALRQLAPWSPQPDKAEQAAQSLLDQYAQLKAQYADKPKKRVFLQFGINPPFTSGKESIQNQVLEVCGGENIFKDSRVPWPQVSREQVLARSPQAIVITGKIPVIPLTSDWFERASPRIILAAQQLCNALSQVD 266
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210     ||236       246       256       266
                                                                                                                                                                                                                             216|                                 
                                                                                                                                                                                                                              233
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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 5M3B)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M3B)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M3B)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        BTUF_ECOLI | P37028: 1n2z 1n4a 1n4d 2qi9 4dbl 4fi3 5m29 5m2q 5m34

(-) Related Entries Specified in the PDB File

1n2z B12-BOUND BTUF
1n4a B12-BOUND BTUF
1n4d LIGAND-FREE BTUF
5m29 CBI-BOUND BTUF WT
5m2q CBI-BOUND BTUF W66F
5m34 CBI-BOUND BTUF W66Y