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(-) Description

Title :  STRUCTURE OF COBINAMIDE-BOUND BTUF MUTANT W66F, 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 :  13 Oct 16  (Deposition) - 01 Mar 17  (Release) - 01 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
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 - OUTER MEMBRANE PROTEIN A,VITAMIN B12-BINDING PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: OMPA, CON, TOLG, TUT, B0957, JW0940, BTUF, YADT, B0158, JW0154
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: OMPA-NCOI-BTUF-BAMHI-3C-BAMHI-HIS6
    Synonym: OUTER MEMBRANE PROTEIN II*

 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, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1CBY2Ligand/IonCOB(II)INAMIDE
2CYN2Ligand/IonCYANIDE ION
3GOL3Ligand/IonGLYCEROL
Biological Unit 1 (3, 4)
No.NameCountTypeFull Name
1CBY1Ligand/IonCOB(II)INAMIDE
2CYN1Ligand/IonCYANIDE ION
3GOL2Ligand/IonGLYCEROL
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1CBY1Ligand/IonCOB(II)INAMIDE
2CYN1Ligand/IonCYANIDE ION
3GOL1Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:31 , ALA A:32 , TYR A:50 , PHE A:66 , TRP A:85 , GLY A:87 , PHE A:162 , PHE A:168 , TRP A:196 , SER A:241 , ASP A:242 , GLU A:245 , ARG A:246 , CYN A:302 , HOH A:410 , HOH A:413 , HOH A:415 , HOH A:457 , HOH A:463 , HOH A:550binding site for residue CBY A 301
2AC2SOFTWAREGLU A:245 , CBY A:301 , HOH A:415 , HOH A:530binding site for residue CYN A 302
3AC3SOFTWAREMET A:105 , TRP A:106 , HOH A:437 , VAL B:104 , TRP B:106 , GOL B:303binding site for residue GOL A 303
4AC4SOFTWAREARG A:25 , VAL A:45binding site for residue GOL A 304
5AC5SOFTWAREPRO B:31 , ALA B:32 , TYR B:50 , PHE B:66 , GLN B:67 , TRP B:85 , GLY B:87 , PHE B:162 , PHE B:168 , ASP B:242 , GLU B:245 , ARG B:246 , CYN B:302 , HOH B:406 , HOH B:422 , HOH B:467 , HOH B:471 , HOH B:510 , HOH B:529binding site for residue CBY B 301
6AC6SOFTWAREGLU B:245 , CBY B:301binding site for residue CYN B 302
7AC7SOFTWAREARG A:86 , TRP A:106 , GOL A:303 , TRP B:106 , VAL B:107 , ASP B:108 , ALA B:109 , ALA B:118 , HOH B:478 , HOH B:501binding site for residue GOL B 303

(-) SS Bonds  (2, 2)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Tyr A:53 -Pro A:54
2Asn A:165 -Pro A:166
3Tyr B:53 -Pro B:54

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5M2Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M2Q)

(-) Exons   (0, 0)

(no "Exon" information available for 5M2Q)

(-) 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.eee.....hhhhhhhh...eeee.....hhhhhhhhhhh...eee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh....eeeeeee...........hhhhhhhhhh.eee............hhhhhhhh...eeeee....eee.hhhhhh....hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5m2q A  23 APRVITLSPANTELAFAAGITPVGVSSYSDYPPQAQKIEQVSTFQGMNLERIVALKPDLVIAWRGGNAERQVDQLASLGIKVMWVDATSIEQIANALRQLAPWSPQPDKAEQAAQSLLDQYAQLKAQYADKPKKRVFLQFGINPPFTSGKESIQNQVLEVCGGENIFKDSRVPWPQVSREQVLARSPQAIVITGKIPVIPLTSDWFERASPRIILAAQQLCNALSQVD 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:228
                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eee.hhhhhhhhhhh......ee.....hhhhhhh.eee.....hhhhhhhh...eeee.....hhhhhhhhhhh...eee....hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.....eeeee.............hhhhhhhhhh.eee............hhhhhhhh...eeee....eee.hhhhhhh...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5m2q B  21 MAAPRVITLSPANTELAFAAGITPVGVSSYSDYPPQAQKIEQVSTFQGMNLERIVALKPDLVIAWRGGNAERQVDQLASLGIKVMWVDATSIEQIANALRQLAPWSPQPDKAEQAAQSLLDQYAQLKAQYADKPKKRVFLQFGINPPFTSGKESIQNQVLEVCGGENIFKDSRVPWPQVSREQVLARSPQAIVITKIPVIPLTSDWFERASPRIILAAQQLCNALSQV 265
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    || 237       247       257        
                                                                                                                                                                                                                            215|                                
                                                                                                                                                                                                                             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 5M2Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M2Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M2Q)

(-) Gene Ontology  (19, 20)

Asymmetric Unit(hide GO term definitions)

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  5m2q
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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 5m34 5m3b
        OMPA_ECOLI | P0A910: 1bxw 1g90 1qjp 2ge4 2jmm 3jbu 3nb3

(-) Related Entries Specified in the PDB File

1n2z B12-BOUND BTUF
1n4a B12-BOUND BTUF
1n4d LIGAND-FREE BTUF
5m29 BTUFCBI WT