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(-) Description

Title :  CRYSTAL STRUCTURE OF A PROBABLE RIBOFLAVIN SYNTHASE, BETA CHAIN RIBH (6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE, DMRL SYNTHASE, LUMAZINE SYNTHASE) FROM MYCOBACTERIUM LEPRAE
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  30 Jan 13  (Deposition) - 06 Mar 13  (Release) - 06 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Ssgcid, Mycobacterium Leprae, 6, 7-Dimethyl-8-Ribityllumazine Synthase, Dmrl Synthase, Lumazine Synthase, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Seattle Structural Genomics Center For Infectious Disease (Ssgcid), J. Abendroth, D. Lorimer, T. E. Edwards
Crystal Structure Of A Probable Riboflavin Synthase, Beta Chain Ribh (6, 7-Dimethyl-8-Ribityllumazine Synthase, Dmrl Synthase, Lumazine Synthase) From Mycobacterium Leprae
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - 6,7-DIMETHYL-8-RIBITYLLUMAZINE SYNTHASE
    Chains: A, B, C, D, E
    EC Number: 2.5.1.78
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: MYLEA.00730.A.A1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: MYLEA.00730.A.A1
    Gene: MLBR00560, RIBH
    Organism Scientific: MYCOBACTERIUM LEPRAE
    Organism Taxid: 561304
    Strain: BR4923
    Synonym: DMRL SYNTHASE, LS, LUMAZINE SYNTHASE

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 11)

Asymmetric/Biological Unit (2, 11)
No.NameCountTypeFull Name
1NA5Ligand/IonSODIUM ION
2SO46Ligand/IonSULFATE ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:70 , HIS A:73 , THR A:110 , HOH A:327 , HOH A:363 , HOH A:375BINDING SITE FOR RESIDUE NA A 201
02AC2SOFTWAREGLY A:85 , ASP A:86 , THR A:87 , HOH A:309 , HOH A:340 , ARG B:128 , LYS D:123BINDING SITE FOR RESIDUE SO4 A 202
03AC3SOFTWAREALA B:70 , HIS B:73 , THR B:110 , HOH B:344 , HOH B:353 , HOH B:366BINDING SITE FOR RESIDUE NA B 201
04AC4SOFTWAREASP B:86 , THR B:87 , HOH B:345 , LYS C:123 , ARG E:128 , HOH E:327BINDING SITE FOR RESIDUE SO4 B 202
05AC5SOFTWAREALA C:70 , HIS C:73 , THR C:110 , HOH C:309 , HOH C:328 , HOH C:393BINDING SITE FOR RESIDUE NA C 201
06AC6SOFTWARELYS B:123 , GLY C:85 , ASP C:86 , THR C:87 , HOH C:347 , HOH C:369 , ARG D:128 , HOH D:384BINDING SITE FOR RESIDUE SO4 C 202
07AC7SOFTWARELYS A:123 , ARG A:128 , ASP D:86 , THR D:87 , HOH D:357 , HOH D:370BINDING SITE FOR RESIDUE SO4 D 201
08AC8SOFTWAREASN A:95 , GLN A:99 , ASN B:95 , ASN C:95 , GLN C:99 , ASN D:95 , GLN D:99 , ASN E:95 , GLN E:99BINDING SITE FOR RESIDUE SO4 D 202
09AC9SOFTWAREALA D:70 , HIS D:73 , THR D:110 , HOH D:326 , HOH D:329 , HOH D:334BINDING SITE FOR RESIDUE NA D 203
10BC1SOFTWAREARG C:128 , GLY E:85 , ASP E:86 , THR E:87 , LYS E:123 , HOH E:324 , HOH E:343BINDING SITE FOR RESIDUE SO4 E 201
11BC2SOFTWAREALA E:70 , HIS E:73 , THR E:110 , HOH E:316 , HOH E:328 , HOH E:369BINDING SITE FOR RESIDUE NA E 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4J07)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4J07)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J07)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J07)

(-) Exons   (0, 0)

(no "Exon" information available for 4J07)

(-) 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:152
                                                                                                                                                                                        
               SCOP domains d4j07a_ A: automated matches                                                                                                                             SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeee...hhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j07 A   8 PEVPGIDASGLRLGIVASTWHSRICDALLAGARKVAADSGIDGPTVVRVLGAIEIPVVVQELARHHDAVVALGVVIRGDTPHFDYVCNSVTQGLTRIALDTSTPVGNGVLTTNTEKQALDRAGLPTSAEDKGAQAAAAALTTALTLLNLRSR 159
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157  


Chain B from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               SCOP domains d4j07b_ B: automated matches                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeee...hhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j07 B  12 GIDASGLRLGIVASTWHSRICDALLAGARKVAADSGIDGPTVVRVLGAIEIPVVVQELARHHDAVVALGVVIRGDTPHFDYVCNSVTQGLTRIALDTSTPVGNGVLTTNTEKQALDRAGLPTSAEDKGAQAAAAALTTALTLLNLRSR 159
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151        


Chain C from PDB  Type:PROTEIN  Length:149
                                                                                                                                                                                     
               SCOP domains d4j07c_ C: automated matches                                                                                                                          SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeee..hhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j07 C  12 GIDASGLRLGIVASTWHSRICDALLAGARKVAADSGIDGPTVVRVLGAIEIPVVVQELARHHDAVVALGVVIRGDTPHFDYVCNSVTQGLTRIALDTSTPVGNGVLTTNTEKQALDRAGLPTSAEDKGAQAAAAALTTALTLLNLRSRI 160
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151         


Chain D from PDB  Type:PROTEIN  Length:146
                                                                                                                                                                                  
               SCOP domains d4j07d_ D: automated matches                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee...hhhhhhhhhhhhhhhhhhh.....eeee..hhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j07 D  13 IDASGLRLGIVASTWHSRICDALLAGARKVAADSGIDGPTVVRVLGAIEIPVVVQELARHHDAVVALGVVIRGDTPHFDYVCNSVTQGLTRIALDTSTPVGNGVLTTNTEKQALDRAGLPTSAEDKGAQAAAAALTTALTLLNLRS 158
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152      


Chain E from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               SCOP domains d4j07e_ E: automated matches                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeeee..hhhhhhhhhhhhhhhhhhh.....eeeee.hhhhhhhhhhhhhh...eeeeeeeee....hhhhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j07 E  13 IDASGLRLGIVASTWHSRICDALLAGARKVAADSGIDGPTVVRVLGAIEIPVVVQELARHHDAVVALGVVIRGDTPHFDYVCNSVTQGLTRIALDTSTPVGNGVLTTNTEKQALDRAGLPTSAEDKGAQAAAAALTTALTLLNLRSRI 160
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152
   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  (1, 5)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J07)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J07)

(-) Gene Ontology  (4, 4)

Asymmetric/Biological Unit(hide GO term definitions)

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