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(-) Description

Title :  CRYSTAL STRUCTURE OF MTB-RIBA2 (RV1415)
 
Authors :  M. Singh, P. Kumar, S. Yadav, R. Gautam, N. Sharma, S. Karthikeyan
Date :  20 Nov 12  (Deposition) - 28 Aug 13  (Release) - 19 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dhbps, Gchii, Riba2, Gtp, Riboflavin, Antimicrobial, Hydrolase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Singh, P. Kumar, S. Yadav, R. Gautam, N. Sharma, S. Karthikeyan
The Crystal Structure Reveals The Molecular Mechanism Of Bifunctional 3, 4-Dihydroxy-2-Butanone 4-Phosphate Synthase/Gtp Cyclohydrolase Ii (Rv1415) From Mycobacterium Tuberculosis
Acta Crystallogr. , Sect. D V. 69 1633 2013
PubMed-ID: 23999287  |  Reference-DOI: 10.1107/S0907444913011402

(-) Compounds

Molecule 1 - RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBBA
    Chains: A, B
    EC Number: 4.1.99.12, 3.5.4.25
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28C
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MRA_1424, RIBBA, RV1415
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS
    Organism Taxid: 419947
    Strain: H37RA
    Synonym: 3,4-DIHYDROXY-2-BUTANONE 4-PHOSPHATE SYNTHASE, DHBP SYNTHASE, GTP CYCLOHYDROLASE-2, GTP CYCLOHYDROLASE II

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:264 , CYS A:275 , CYS A:277 , HOH A:601BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWAREARG A:141 , GLY A:143 , HIS A:144 , THR A:145 , GLU A:146BINDING SITE FOR RESIDUE SO4 A 502
3AC3SOFTWARECYS B:264 , CYS B:275 , CYS B:277 , HOH B:601BINDING SITE FOR RESIDUE ZN B 501
4AC4SOFTWAREARG B:141 , GLY B:143 , HIS B:144 , THR B:145BINDING SITE FOR RESIDUE SO4 B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I14)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:124 -Pro A:125
2Arg B:124 -Pro B:125

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I14)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I14)

(-) Exons   (0, 0)

(no "Exon" information available for 4I14)

(-) 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:325
                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh...eeee.........eeeee.hhhhhhhhhhhhhhh....eeeeehhhhhhh...........eee........hhhhhhhhhhhhhh...hhh.eeeeeeeeeeee..hhhhh..hhhhhhhhhhhhh.....eeeee...........hhhhhhhhhhhh..eeeehhhhhhhhhhhh..eeeeeeeeeee..eeeeeeeeee.....eeeeeee.........eeeeeee.hhhhhh......hhhhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhh...eeee..........ee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i14 A   1 MTRLDSVERAVADIAAGKAVIVIDDEDRENEGDLIFAAEKATPEMVAFMVRYTSGYLCVPLDGAICDRLGLLPMYAYTVTVDARNGIGTGISASDRATTMRLLADPTSVADDFTRPGHVVPLRAKDGGVLRRPGHTEAAVDLARMAGLQPAGAICEIVSQKDEGSMAHTDELRVFADEHGLALITIADLIEWRRKHEKHIERVAEARIPTRHGEFRAIGYTSIYEDVEHVALVRGEIAGDGDDVLVRVHSECLTGDVFGSRRCDCGPQLDAALAMVAREGRGVVLYMRYGIGAQILVDLGVRSMRLLTNNPDGYGLHIIERVPLP 383
                                    10        20        30        40        50        60        70    ||  89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       252       262       272       282       292       342       352       362||     378     
                                                                                                     75|                                                                                                                                                                248|                                             300|                   363|             
                                                                                                      85                                                                                                                                                                 252                                              341                    370             


Chain B from PDB  Type:PROTEIN  Length:320
                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhhh...eeee.........eeeee.hhhhhhhhhhhhhhh....eeeehhhhhhhhh........eee........hhhhhhhhhhhhhh...hhh.eeeeeeeeeee...hhhhh..hhhhhhhhhhhhh.....eeeee...........hhhhhhhhhhhhh.eeeehhhhhhhhhh....eeeeeeeeeee..eeeeeeeeee.....eeeeeee......eeeeeee.hhhhhh......hhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhh..eeeee..........eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i14 B   1 MTRLDSVERAVADIAAGKAVIVIDDEDRENEGDLIFAAEKATPEMVAFMVRYTSGYLCVPLDGAICDRLGLLPMYTVTVDARNGIGTGISASDRATTMRLLADPTSVADDFTRPGHVVPLRAKDGGVLRRPGHTEAAVDLARMAGLQPAGAICEIVSQKDEGSMAHTDELRVFADEHGLALITIADLIEWRRKHEKHIERVAEARIPTRHGEFRAIGYTSIYEDVEHVALVRGEIGDDVLVRVHSECLTGDVFGSRRCDCGPQLDAALAMVAREGRGVVLYMRYGIGAQILVDLGVRSMRLLTNNPADGYGLHIIERVPL 382
                                    10        20        30        40        50        60        70   ||   91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241    || 257       267       277       287       297  ||   347       357      |372       382
                                                                                                    74|                                                                                                                                                             246|                                            300|                    364|            
                                                                                                     86                                                                                                                                                              253                                             341                     370
   Legend:   → Mismatch (orange background)
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  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 4I14)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I14)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I14)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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  4i14
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  RIBBA_MYCTA | A5U2B7
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 Related Entries

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

UniProtKB/Swiss-Prot
        RIBBA_MYCTA | A5U2B7: 3mgz 3mio 3mk5

(-) Related Entries Specified in the PDB File

3mio DHBPS DOMAIN OF MTB-RIBA2