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(-) Description

Title :  STRUCTURE OF VITAMIN B12 TRANSPORTER BTUCD IN A NUCLEOTIDE-BOUND OUTWARD FACING STATE
 
Authors :  V. M. Korkhov, S. A. Mireku, D. B. Veprintsev, K. P. Locher
Date :  08 Sep 14  (Deposition) - 19 Nov 14  (Release) - 17 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.79
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Nucleotide, Amppnp, Atp Binding Cassette, Membrane Protein, Abc Transporter, Btuf, Inner Membrane, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. M. Korkhov, S. A. Mireku, D. B. Veprintsev, K. P. Locher
Structure Of Amp-Pnp-Bound Btucd And Mechanism Of Atp-Powered Vitamin B12 Transport By Btucd-F.
Nat. Struct. Mol. Biol. V. 21 1097 2014
PubMed-ID: 25402482  |  Reference-DOI: 10.1038/NSMB.2918

(-) Compounds

Molecule 1 - VITAMIN B12 IMPORT SYSTEM PERMEASE PROTEIN BTUC
    Chains: A, B
    EC Number: 3.6.3.33
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BTUC, B1711, JW1701
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
 
Molecule 2 - VITAMIN B12 IMPORT ATP-BINDING PROTEIN BTUD
    Chains: C, D
    EC Number: 3.6.3.33
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: BTUD, B1709, JW1699
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: VITAMIN B12-TRANSPORTING ATPASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
2LDA4Ligand/IonLAURYL DIMETHYLAMINE-N-OXIDE
3MG2Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:115 , ARG A:189 , TRP A:192BINDING SITE FOR RESIDUE LDA A 501
2AC2SOFTWARETRP A:188BINDING SITE FOR RESIDUE LDA A 502
3AC3SOFTWARETRP B:192BINDING SITE FOR RESIDUE LDA B 501
4AC4SOFTWARETRP B:188BINDING SITE FOR RESIDUE LDA B 502
5AC5SOFTWAREARG C:15 , ASN C:35 , GLY C:36 , GLY C:38 , LYS C:39 , SER C:40 , THR C:41 , GLN C:80 , GLN C:159 , HIS C:191 , MG C:302 , ARG D:122 , GLN D:126 , SER D:128 , GLY D:129 , GLY D:130 , GLU D:131 , SER D:163BINDING SITE FOR RESIDUE ANP C 301
6AC6SOFTWARESER C:40 , GLN C:80 , ANP C:301BINDING SITE FOR RESIDUE MG C 302
7AC7SOFTWAREARG C:122 , SER C:128 , GLY C:129 , GLY C:130 , GLU C:131 , SER C:163 , ARG D:15 , ASN D:35 , GLY D:36 , GLY D:38 , LYS D:39 , SER D:40 , THR D:41 , GLN D:80 , HIS D:191 , MG D:302BINDING SITE FOR RESIDUE ANP D 301
8AC8SOFTWARESER D:40 , GLN D:80 , ANP D:301BINDING SITE FOR RESIDUE MG D 302

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1C:162 -D:162

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Met B:1 -Leu B:2

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4R9U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4R9U)

(-) Exons   (0, 0)

(no "Exon" information available for 4R9U)

(-) 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:324
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4r9u A   1 MLTLARQQQRQNIRWLLSLSVLMLLALLLSLSAGEQWISPGDWFTPRGELFVWQIRLPRTLAVLLVGAALAISGAVMQALFENPLAEPGLLGVSNGAGVGLIAAVLLGQGQLPNWALGLSAIAGALIITLILLRFARRHLSTSRLLLAGVALGIISSALMTWAIYFSTSVDLRQLMYWMMGGFGGVDWRQSWLMLALIPVLLWISSQSRPMNMLALGEISARQLGLPLWFWRNVLVAATGWMVGVSVALAGAIGFIGLVIPHILRLSGLTDHRVLLPGCALAGASALLLADIVARLALAAAELPIGVVTATLGAPVFIWLLLKA 324
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320    


Chain B from PDB  Type:PROTEIN  Length:324
                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4r9u B   1 MLTLARQQQRQNIRWLLSLSVLMLLALLLSLSAGEQWISPGDWFTPRGELFVWQIRLPRTLAVLLVGAALAISGAVMQALFENPLAEPGLLGVSNGAGVGLIAAVLLGQGQLPNWALGLSAIAGALIITLILLRFARRHLSTSRLLLAGVALGIISSALMTWAIYFSTSVDLRQLMYWMMGGFGGVDWRQSWLMLALIPVLLWISSQSRPMNMLALGEISARQLGLPLWFWRNVLVAATGWMVGVSVALAGAIGFIGLVIPHILRLSGLTDHRVLLPGCALAGASALLLADIVARLALAAAELPIGVVTATLGAPVFIWLLLKA 324
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320    


Chain C from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee...eeeeeeee....eeeee.....hhhhhhhhhh.......eeee..ee....hhhhhhhhh.ee..........hhhhhhhh.......hhhhhhhhhhh.............hhhhhhhhhhhhhhhhhh..........ee.......hhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhh.eeeeee..eeeeeeehhhhhhhhhhhhhh...eeee......eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r9u C   2 SIVMQLQDVAESTRLGPLSGEVRAGEILHLVGPNGAGKSTLLARMAGMTSGKGSIQFAGQPLEAWSATKLALHRAYLSQQQTPPFATPVWHYLTLHQHDKTRTELLNDVAGALALDDKLGRSTNQLSGGEWQRVRLAAVVLQITPQANPAGQLLLLDQPMCSLDVAQQSALDKILSALSQQGLAIVMSSHDLNHTLRHAHRAWLLKGGKMLASGRREEVLTPPNLAQAYGMNFRRLDIEGHRMLISTI 249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241        


Chain D from PDB  Type:PROTEIN  Length:248
                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.eee...eeee..eee...eeeee.....hhhhhhhhhhh......eeee..ee.hhhhhhhhhhheeee..........hhhhhhhh.......hhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh........eeee.......hhhhhhhhhhhhhhhhhh...eeee..hhhhhhhhh.eeeeee..eeeeeeehhhhhhhhhhhhhhh..eeee......eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4r9u D   2 SIVMQLQDVAESTRLGPLSGEVRAGEILHLVGPNGAGKSTLLARMAGMTSGKGSIQFAGQPLEAWSATKLALHRAYLSQQQTPPFATPVWHYLTLHQHDKTRTELLNDVAGALALDDKLGRSTNQLSGGEWQRVRLAAVVLQITPQANPAGQLLLLDQPMCSLDVAQQSALDKILSALSQQGLAIVMSSHDLNHTLRHAHRAWLLKGGKMLASGRREEVLTPPNLAQAYGMNFRRLDIEGHRMLISTI 249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241
   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 4R9U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4R9U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4R9U)

(-) Gene Ontology  (19, 27)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        BTUC_ECOLI | P06609: 1l7v 2qi9 4dbl 4fi3
        BTUD_ECOLI | P06611: 1l7v 2qi9 4dbl 4fi3

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4R9U)