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(-) Description

Title :  STRUCTURE OF RIBB COMPLEXED WITH SUBSTRATE (RU5P) AND METAL IONS
 
Authors :  Z. Islam, A. Kumar, S. Singh, L. Salmon, S. Karthikeyan
Date :  31 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, Zn, 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  (3, 20)

Asymmetric/Biological Unit (3, 20)
No.NameCountTypeFull Name
15RP2Ligand/IonRIBULOSE-5-PHOSPHATE
2EDO8Ligand/Ion1,2-ETHANEDIOL
3ZN10Ligand/IonZINC ION

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG 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 , LEU A:173 , GLU A:175 , ZN A:302 , ZN A:303 , HOH A:436 , HOH A:445 , HOH A:454 , HOH A:463 , HIS B:137binding site for residue 5RP A 301
02AC2SOFTWAREGLU A:39 , HIS A:154 , 5RP A:301 , ZN A:303 , HOH A:437binding site for residue ZN A 302
03AC3SOFTWAREGLU A:39 , 5RP A:301 , ZN A:302 , HOH A:445 , HOH A:454 , HOH A:463binding site for residue ZN A 303
04AC4SOFTWAREASP A:180 , HOH A:476 , THR B:53 , ALA B:54 , EDO B:310binding site for residue EDO A 304
05AC5SOFTWAREPRO A:125 , GLN A:126 , GLN A:168 , GLN B:168 , PRO B:169binding site for residue EDO A 305
06AC6SOFTWAREHIS A:137 , HOH A:460 , 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 , LEU B:173 , GLU B:175 , ZN B:302 , ZN B:303 , HOH B:445 , HOH B:446 , HOH B:447 , HOH B:532binding site for residue 5RP B 301
07AC7SOFTWAREGLU B:39 , HIS B:154 , 5RP B:301 , ZN B:303 , HOH B:447binding site for residue ZN B 302
08AC8SOFTWAREHOH A:460 , GLU B:39 , 5RP B:301 , ZN B:302 , HOH B:446 , HOH B:532binding site for residue ZN B 303
09AC9SOFTWAREGLU B:18 , GLU B:36 , THR B:186 , ZN B:308 , ZN B:309binding site for residue ZN B 304
10AD1SOFTWAREHIS B:0 , ASP B:214binding site for residue ZN B 305
11AD2SOFTWAREHIS B:104 , GLU B:191 , HOH B:401 , HOH B:441binding site for residue ZN B 306
12AD3SOFTWAREGLU B:62 , GLU B:130 , PHE B:192 , HIS B:196 , HOH B:430binding site for residue ZN B 307
13AD4SOFTWAREGLN B:3 , GLU B:18 , THR B:186 , ZN B:304binding site for residue ZN B 308
14AD5SOFTWAREGLU B:18 , ASN B:40 , LYS B:185 , THR B:186 , ZN B:304binding site for residue ZN B 309
15AD6SOFTWAREASP A:180 , GLY A:181 , SER A:182 , EDO A:304 , THR B:53 , SER B:111 , ALA B:112 , GLN B:113binding site for residue EDO B 310
16AD7SOFTWAREGLU B:9 , THR B:15 , ASN B:19 , ASP B:37binding site for residue EDO B 311
17AD8SOFTWAREHIS A:104 , GLY A:105 , VAL A:106 , HOH A:424 , ALA B:8 , GLU B:9 , HOH B:418binding site for residue EDO B 312
18AD9SOFTWAREALA B:80 , ARG B:134 , HOH B:423binding site for residue EDO B 313
19AE1SOFTWAREGLU B:9binding site for residue EDO B 314
20AE2SOFTWAREASP A:214 , LYS A:216 , ASP B:214 , LEU B:215binding site for residue EDO B 315

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P8E)

(-) 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 4P8E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P8E)

(-) Exons   (0, 0)

(no "Exon" information available for 4P8E)

(-) 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:216
                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhh...eeee........eeeeee.hhhhhhhhhhhhhhh....eeeehhhhhhhh....................eee........hhhhhhhhhhhhhh...hhh.eeeeeeeeeee...hhhhh..hhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhhh...eeehhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4p8e A   2 NQSSLLAEFGDPITRVENALQALREGRGVLLLDDEDRENEGDIIYAVESLTTAQMALMIRECSGIVCLCLTEAQADRLALPPMVVNNNSANQTAFTVSIEAKHGVTTGVSAQDRVTTIKTAANPQAKPEDLARPGHVFPLRARAGGVLARRGHTEGTVDLMQMAGLQPAGVLCELTNPDGSMAKTPEIIEFGKLHNMPVLTIEDMVQYRIQFDLKL 217
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      


Chain B from PDB  Type:PROTEIN  Length:217
                                                                                                                                                                                                                                                         
               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..hhhhhhhhhhhhhh....eeeee.........hhhhhhhhhhhhh..eeehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p8e B  -1 SHMNQSSLLAEFGDPITRVENALQALREGRGVLLLDDEDRENEGDIIYAVESLTTAQMALMIRECSGIVCLCLTEAQADRLALPPMVVNNNSANQTAFTVSIEAKHGVTTGVSAQDRVTTIKTAANPQAKPEDLARPGHVFPLRARAGGVLARRGHTEGTVDLMQMAGLQPAGVLCELTNPDGSMAKTPEIIEFGKLHNMPVLTIEDMVQYRIQFDL 215
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208
   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 4P8E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P8E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P8E)

(-) 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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        RIBB_VIBCH | Q9KKP2: 4p6c 4p6d 4p6p 4p77 4p8j

(-) Related Entries Specified in the PDB File

4p6c 4p6d 4p8j