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(-) Description

Title :  STRUCTURE OF RIBB COMPLEXED WITH SUBSTRATE RU5P
 
Authors :  Z. Islam, A. Kumar, S. Singh, L. Salmon, S. Karthikeyan
Date :  26 Mar 14  (Deposition) - 25 Mar 15  (Release) - 13 May 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.04
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ribb, Riboflvain, Ligand, Complex, Crystal, Ru5P, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Islam, A. Kumar, S. Singh, L. Salmon, S. Karthikeyan
Structural Basis For Competitive Inhibition Of 3, 4-Dihydroxy-2-Butanone-4-Phosphate Synthase From Vibrio Cholerae.
J. Biol. Chem. V. 290 11293 2015
PubMed-ID: 25792735  |  Reference-DOI: 10.1074/JBC.M114.611830

(-) Compounds

Molecule 1 - 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE
    Chains: A, B
    EC Number: 4.1.99.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: RIBB, VC_A1060
    Organism Scientific: VIBRIO CHOLERAE SEROTYPE O1
    Organism Taxid: 243277
    Strain: ATCC 39315 / EL TOR INABA N16961
    Synonym: DHBP SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
15RP2Ligand/IonRIBULOSE-5-PHOSPHATE
2GOL1Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:38 , GLU A:39 , ASP A:43 , CYS A:68 , THR A:94 , PHE A:96 , ARG A:151 , GLY A:153 , HIS A:154 , THR A:155 , GLU A:175 , HOH A:430 , HOH A:431 , HIS B:137binding site for residue 5RP A 301
2AC2SOFTWARETHR A:107 , GLN A:113 , ASP A:114 , HOH A:401 , HOH A:403 , SER B:4 , ASP B:12 , PRO B:13 , ARG B:16binding site for residue GOL A 302
3AC3SOFTWAREHIS A:137 , HOH A:434 , ARG B:38 , GLU B:39 , ASP B:43 , CYS B:68 , THR B:94 , PHE B:96 , ARG B:151 , GLY B:153 , HIS B:154 , THR B:155 , GLU B:175 , HOH B:643 , HOH B:644 , HOH B:682binding site for residue 5RP B 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P77)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:134 -Pro A:135
2Arg B:134 -Pro B:135

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P77)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P77)

(-) Exons   (0, 0)

(no "Exon" information available for 4P77)

(-) 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:214
                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh...eeee........eeeeee....hhhhhhhhhhhh....eeeehhhhhhhh..................eee........hhhhhhhhhhhhhh...hhh.eeeeeeeeeee...hhhhh..hhhhhhhhhhhhh.....eeeee.........hhhhhhhhhhhhh..eeehhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p77 A   2 NQSSLLAEFGDPITRVENALQALREGRGVLLLDDEDRENEGDIIYAVESLTTAQMALMIRECSGIVCLCLTEAQADRLALPPMVVNNNNQTAFTVSIEAKHGVTTGVSAQDRVTTIKTAANPQAKPEDLARPGHVFPLRARAGGVLARRGHTEGTVDLMQMAGLQPAGVLCELTNPDGSMAKTPEIIEFGKLHNMPVLTIEDMVQYRIQFDLKL 217
                                    11        21        31        41        51        61        71        81       |93       103       113       123       133       143       153       163       173       183       193       203       213    
                                                                                                                  89|                                                                                                                             
                                                                                                                   92                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:209
                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh...eeee........eeeeee.hhhhhhhhhhhhhhh....eeeeehhhhhhh.............eee........hhhhhhhhhhhhhh...hhh.eeeeeeeeeeee..hhhhh..hhhhhhhhhhhhh.....eeeee.........hhhhhhhhhhhhh..eeehhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p77 B   2 NQSSLLAEFGDPITRVENALQALREGRGVLLLDDEDRENEGDIIYAVESLTTAQMALMIRECSGIVCLCLTEAQADRLALPPMVVTAFTVSIEAKHGVTTGVSAQDRVTTIKTAANPQAKPEDLARPGHVFPLRARAGGVLARRGHTEGTVDLMQMAGLQPAGVLCELTNPDGSMAKTPEIIEFGKLHNMPVLTIEDMVQYRIQFDLKL 217
                                    11        21        31        41        51        61        71        81    ||  98       108       118       128       138       148       158       168       178       188       198       208         
                                                                                                               86|                                                                                                                           
                                                                                                                94
   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 4P77)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P77)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P77)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Arg A:134 - Pro A:135   [ RasMol ]  
    Arg B:134 - Pro B:135   [ RasMol ]  
 

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  4p77
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  4.1.99.12
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 Related Entries

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

UniProtKB/Swiss-Prot
        RIBB_VIBCH | Q9KKP2: 4p6c 4p6d 4p6p 4p8e 4p8j

(-) Related Entries Specified in the PDB File

4p6c 4p6d 4p6p