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(-) Description

Title :  COMPLEX STRUCTURE OF BACILLUS SUBTILIS RIBG: THE DEAMINATION PROCESS IN RIBOFLAVIN BIOSYNTHESIS
 
Authors :  S. C. Chen, C. Y. Shen, T. M. Yen, H. C. Yu, T. H. Chang, W. L. Lai, S. H. Liaw
Date :  15 Jul 12  (Deposition) - 20 Feb 13  (Release) - 20 Feb 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.56
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Alpha/Beta/Alpha, Deaminase Domain, Reductase Domain, Hydrolase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. C. Chen, C. Y. Shen, T. M. Yen, H. C. Yu, T. H. Chang, W. L. Lai, S. H. Liaw
Evolution Of Vitamin B(2) Biosynthesis: Eubacterial Ribg An Fungal Rib2 Deaminases.
Acta Crystallogr. , Sect. D V. 69 227 2013
PubMed-ID: 23385458  |  Reference-DOI: 10.1107/S0907444912044903

(-) Compounds

Molecule 1 - RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBD
    Chains: A, B, C, D
    EC Number: 3.5.4.26, 1.1.1.193
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-30
    Expression System Strain: BL21 PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BSU23280, RIBD, RIBG
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 224308
    Strain: 168
    Synonym: DIAMINOHYDROXYPHOSPHORIBOSYLAMINOPYRIMIDINE DEAMINASE, DRAP DEAMINASE, RIBOFLAVIN-SPECIFIC DEAMINASE, 5-AMINO-6-(5- PHOSPHORIBOSYLAMINO)URACIL REDUCTASE, HTP REDUCTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 11)

Asymmetric/Biological Unit (3, 11)
No.NameCountTypeFull Name
1AI94Ligand/Ion[(2R,3S,4S,5E)-5-[[5-AZANYL-2,4-BIS(OXIDANYLIDENE)-1H-PYRIMIDIN-6-YL]IMINO]-2,3,4-TRIS(OXIDANYL)PENTYL]DIHYDROGEN PHOSPHATE
2AOF3Ligand/IonN-(5-AMINO-2,6-DIOXO-1,2,3,6-TETRAHYDROPYRIMIDIN-4-YL)-5-O-PHOSPHONO-BETA-D-RIBOFURANOSYLAMINE
3ZN4Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:49 , GLU A:51 , CYS A:74 , CYS A:83BINDING SITE FOR RESIDUE ZN A 401
02AC2SOFTWARELYS A:151 , ALA A:153 , SER A:167 , ILE A:170 , THR A:171 , ARG A:176 , ARG A:183 , ASP A:199 , PRO A:201 , SER A:202 , LEU A:203 , THR A:204 , ARG A:206 , GLU A:290 , HOH A:511 , HOH A:546 , HOH A:603BINDING SITE FOR RESIDUE AI9 A 402
03AC3SOFTWAREHIS B:49 , CYS B:74 , CYS B:83 , AOF B:402BINDING SITE FOR RESIDUE ZN B 401
04AC4SOFTWAREASN B:23 , VAL B:26 , HIS B:42 , HIS B:49 , ALA B:50 , GLU B:51 , CYS B:74 , HIS B:76 , LYS B:79 , THR B:80 , CYS B:83 , ASP B:101 , ASN B:103 , PHE B:137 , ZN B:401 , HOH B:503 , HOH B:533BINDING SITE FOR RESIDUE AOF B 402
05AC5SOFTWARELYS B:151 , ALA B:153 , SER B:167 , ILE B:170 , THR B:171 , ARG B:176 , ARG B:183 , ASP B:199 , PRO B:201 , SER B:202 , LEU B:203 , ARG B:206 , HOH B:568BINDING SITE FOR RESIDUE AI9 B 403
06AC6SOFTWAREHIS C:49 , CYS C:74 , CYS C:83 , AOF C:402BINDING SITE FOR RESIDUE ZN C 401
07AC7SOFTWAREASN C:23 , PRO C:24 , VAL C:26 , HIS C:42 , HIS C:49 , ALA C:50 , GLU C:51 , CYS C:74 , GLY C:78 , LYS C:79 , THR C:80 , ASP C:101 , PHE C:137 , ZN C:401 , HOH C:550 , HOH C:561BINDING SITE FOR RESIDUE AOF C 402
08AC8SOFTWARELYS C:151 , ALA C:153 , SER C:167 , TRP C:169 , ILE C:170 , THR C:171 , ARG C:176 , ARG C:183 , ASP C:199 , PRO C:201 , SER C:202 , LEU C:203 , ARG C:206 , GLU C:290 , HOH C:506 , HOH C:549BINDING SITE FOR RESIDUE AI9 C 403
09AC9SOFTWAREHIS D:49 , CYS D:74 , CYS D:83 , AOF D:402BINDING SITE FOR RESIDUE ZN D 401
10BC1SOFTWAREASN D:23 , PRO D:24 , VAL D:26 , HIS D:42 , HIS D:49 , ALA D:50 , GLU D:51 , CYS D:74 , HIS D:76 , GLY D:78 , LYS D:79 , THR D:80 , CYS D:83 , ASP D:101 , PHE D:137 , ZN D:401 , HOH D:530 , HOH D:549BINDING SITE FOR RESIDUE AOF D 402
11BC2SOFTWARELYS D:151 , ALA D:153 , ILE D:170 , THR D:171 , ARG D:176 , ARG D:183 , ASP D:199 , PRO D:201 , SER D:202 , LEU D:203 , ARG D:206 , GLU D:290BINDING SITE FOR RESIDUE AI9 D 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4G3M)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4G3M)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G3M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G3M)

(-) Exons   (0, 0)

(no "Exon" information available for 4G3M)

(-) 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:361
                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4g3ma1 A:0-145 Riboflavin biosynthesis protein RibD                                                                                              d4g3ma2 A:146-360 Riboflavin biosynthesis protein RibD                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...........eeeeee..eeeeeee.......hhhhhhhhhhhhhhh..eeeeee..........hhhhhhhhhh..eeeeee........hhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhhh..eeeeeeeee................hhhhhhhhhhhhhhh.eeeeehhhhhhhh..............eeeee.........hhhhhh....eeeee....hhhhhhhhhhh..eeee......hhhhhhhhhhhh...eeee..hhhhhhhhhhh....eeeeeee..........................eeeeeeeee..eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g3m A   0 SMEEYYMKLALDLAKQGEGQTESNPLVGAVVVKDGQIVGMGAHLKYGEAHAEVHAIHMAGAHAEGADIYVTLEPCSHYGKTPPCAELIINSGIKRVFVAMRDPNPLVAGRGISMMKEAGIEVREGILADQAERLNEKFLHFMRTGLPYVTLKAAASLDGKIATSTGDSKWITSEAARQDAQQYRKTHQSILVGVGTVKADNPSLTCRLPNVTKQPVRVILDTVLSIPEDAKVICDQIAPTWIFTTARADEEKKKRLSAFGVNIFTLETERIQIPDVLKILAEEGIMSVYVEGGSAVHGSFVKEGCFQEIIFYFAPKLIGGTHAPSLISGEGFQSMKDVPLLQFTDITQIGRDIKLTAKPTK 360
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359 


Chain B from PDB  Type:PROTEIN  Length:361
                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4g3mb1 B:-1-145 Riboflavin biosynthesis protein RibD                                                                                              d4g3mb2 B:146-359 Riboflavin biosynthesis protein RibD                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh...........eeeeee..eeeeeee.......hhhhhhhhhhhhhhh..eeee............hhhhhhhhh...eeee..........hhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhhh..eeeeeeeee................hhhhhhhhhhhhhhh.eeeeehhhhhhhh..............eeeee.........hhhhhh....eeeeee...hhhhhhhhhh...eeeee.....hhhhhhhhhhhhh..eeeeeehhhhhhhhhhh....eeeeeee...................hhhhh..eeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g3m B  -1 GSMEEYYMKLALDLAKQGEGQTESNPLVGAVVVKDGQIVGMGAHLKYGEAHAEVHAIHMAGAHAEGADIYVTLEPCSHYGKTPPCAELIINSGIKRVFVAMRDPNPLVAGRGISMMKEAGIEVREGILADQAERLNEKFLHFMRTGLPYVTLKAAASLDGKIATSTGDSKWITSEAARQDAQQYRKTHQSILVGVGTVKADNPSLTCRLPNVTKQPVRVILDTVLSIPEDAKVICDQIAPTWIFTTARADEEKKKRLSAFGVNIFTLETERIQIPDVLKILAEEGIMSVYVEGGSAVHGSFVKEGCFQEIIFYFAPKLIGGTHAPSLISGEGFQSMKDVPLLQFTDITQIGRDIKLTAKPT 359
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358 


Chain C from PDB  Type:PROTEIN  Length:361
                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4g3mc1 C:-1-145 Riboflavin biosynthesis protein RibD                                                                                              d4g3mc2 C:146-359 Riboflavin biosynthesis protein RibD                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh...........eeeeee..eeeeeee.......hhhhhhhhhhhhhhh..eeee............hhhhhhhhh...eeee..........hhhhhhhhh...eeee..hhhhhhhhhhhhhhhhhhh..eeeeeeeee................hhhhhhhhhhhhhhh.eeeeehhhhh.................eeeee.........hhhhhh....eeeee....hhhhhhhhhh...eeee......hhhhhhhhhhhh...eeee..hhhhhhhhhhhh...eeeeeee..........................eeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g3m C  -1 GSMEEYYMKLALDLAKQGEGQTESNPLVGAVVVKDGQIVGMGAHLKYGEAHAEVHAIHMAGAHAEGADIYVTLEPCSHYGKTPPCAELIINSGIKRVFVAMRDPNPLVAGRGISMMKEAGIEVREGILADQAERLNEKFLHFMRTGLPYVTLKAAASLDGKIATSTGDSKWITSEAARQDAQQYRKTHQSILVGVGTVKADNPSLTCRLPNVTKQPVRVILDTVLSIPEDAKVICDQIAPTWIFTTARADEEKKKRLSAFGVNIFTLETERIQIPDVLKILAEEGIMSVYVEGGSAVHGSFVKEGCFQEIIFYFAPKLIGGTHAPSLISGEGFQSMKDVPLLQFTDITQIGRDIKLTAKPT 359
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358 


Chain D from PDB  Type:PROTEIN  Length:361
                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4g3md1 D:-1-145 Riboflavin biosynthesis protein RibD                                                                                              d4g3md2 D:146-359 Riboflavin biosynthesis protein RibD                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh...........eeeeee..eeeeeee.......hhhhhhhhhhhhhhh..eeeeee..........hhhhhhhhhh..eeeeee........hhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhh..eeeeeeeee................hhhhhhhhhhhhhhh.eeeeehhhhhhhh..............eeeee.........hhhhh.....eeeeee................eeeee.....hhhhhhhhhhhh...eeee..hhhhhhhhhhhh...eeeeeee...................hhhhh..eeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g3m D  -1 GSMEEYYMKLALDLAKQGEGQTESNPLVGAVVVKDGQIVGMGAHLKYGEAHAEVHAIHMAGAHAEGADIYVTLEPCSHYGKTPPCAELIINSGIKRVFVAMRDPNPLVAGRGISMMKEAGIEVREGILADQAERLNEKFLHFMRTGLPYVTLKAAASLDGKIATSTGDSKWITSEAARQDAQQYRKTHQSILVGVGTVKADNPSLTCRLPNVTKQPVRVILDTVLSIPEDAKVICDQIAPTWIFTTARADEEKKKRLSAFGVNIFTLETERIQIPDVLKILAEEGIMSVYVEGGSAVHGSFVKEGCFQEIIFYFAPKLIGGTHAPSLISGEGFQSMKDVPLLQFTDITQIGRDIKLTAKPT 359
                                     8        18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358
   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  (2, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G3M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G3M)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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        RIBD_BACSU | P17618: 2b3z 2d5n 3ex8

(-) Related Entries Specified in the PDB File

2b3z 3ex8