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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RIBOFLAVIN KINASE MODULE OF FAD SYNTHETASE FROM CORYNEBACTERIUM AMMONIAGENES IN COMPLEX WITH ADP
 
Authors :  B. Herguedas, M. Martinez-Julvez, J. A. Hermoso, M. Medina
Date :  13 Jul 15  (Deposition) - 09 Dec 15  (Release) - 02 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.08
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  C  (1x)
Biol. Unit 3:  B  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Transferase, Riboflavin Kinase Domain, Atp-Binding, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Herguedas, I. Lans, M. Sebastian, J. A. Hermoso, M. Martinez-Julvez, M. Medina
Structural Insights Into The Synthesis Of Fmn In Prokaryotic Organisms.
Acta Crystallogr. , Sect. D V. 71 2526 2015
PubMed-ID: 26627660  |  Reference-DOI: 10.1107/S1399004715019641

(-) Compounds

Molecule 1 - RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF
    Atcc: 6872
    Chains: A, B, C, D
    EC Number: 2.7.1.26, 2.7.7.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: RIBOFLAVIN KINASE DOMAIN, UNP RESIDUES 183-338
    Organism Scientific: CORYNEBACTERIUM AMMONIAGENES
    Organism Taxid: 1697
    Other Details: KINASE DOMAIN OF FAD SYNTHETASE (A BIFUNCTIONAL ENZYME)
    Synonym: RIBOFLAVIN KINASE, FLAVOKINASE, FMN ADENYLYLTRANSFERASE, FAD PYROPHOSPHORYLASE, FAD SYNTHASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):   C 
Biological Unit 3 (1x):  B  
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1ADP4Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CA4Ligand/IonCALCIUM ION
3GOL6Ligand/IonGLYCEROL
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
3GOL2Ligand/IonGLYCEROL
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
3GOL2Ligand/IonGLYCEROL
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
3GOL1Ligand/IonGLYCEROL
Biological Unit 4 (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CA-1Ligand/IonCALCIUM ION
3GOL1Ligand/IonGLYCEROL

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:193 , GLY A:196 , ALA A:197 , GLY A:198 , GLY A:201 , LYS A:202 , PRO A:207 , THR A:208 , ALA A:209 , ASN A:210 , SER A:269 , VAL A:271 , ARG A:274 , ASP A:275 , ALA A:276 , LEU A:278 , TYR A:279 , GOL A:1338 , CA A:1340 , HOH A:2009 , HOH A:2015 , HOH A:2020 , HOH A:2099BINDING SITE FOR RESIDUE ADP A 501
02AC2SOFTWAREGLY A:196 , ALA A:197 , ARG A:199 , THR A:208 , ASN A:210 , ADP A:501 , CA A:1340 , HOH A:2017BINDING SITE FOR RESIDUE GOL A1338
03AC3SOFTWAREVAL A:238 , GLY A:240 , MET A:242 , GLU A:243 , HOH A:2046 , HOH A:2047 , VAL C:238 , GLY C:240 , ASN C:241 , MET C:242 , GLU C:243BINDING SITE FOR RESIDUE GOL A1339
04AC4SOFTWAREVAL B:193 , GLY B:196 , ALA B:197 , GLY B:198 , PRO B:207 , THR B:208 , ALA B:209 , ASN B:210 , SER B:269 , VAL B:271 , ARG B:274 , ASP B:275 , ALA B:276 , LEU B:278 , TYR B:279 , GOL B:1337 , CA B:1338 , HOH B:2006 , HOH B:2008 , HOH B:2046 , HOH B:2070BINDING SITE FOR RESIDUE ADP B 501
05AC5SOFTWAREGLY B:196 , ALA B:197 , THR B:208 , ASN B:210 , GLU B:268 , ADP B:501 , CA B:1338 , HOH B:2013BINDING SITE FOR RESIDUE GOL B1337
06AC6SOFTWAREVAL C:193 , ARG C:195 , GLY C:196 , GLY C:198 , LYS C:202 , PRO C:207 , THR C:208 , ASN C:210 , SER C:269 , VAL C:271 , ARG C:274 , ASP C:275 , ALA C:276 , LEU C:278 , TYR C:279 , GOL C:1338 , CA C:1340 , HOH C:2010 , HOH C:2072BINDING SITE FOR RESIDUE ADP C 501
07AC7SOFTWAREALA C:197 , THR C:208 , ASN C:210 , GLU C:268 , ADP C:501 , GOL C:1339 , CA C:1340BINDING SITE FOR RESIDUE GOL C1338
08AC8SOFTWAREVAL A:300 , GLY C:200 , GLY C:201 , PHE C:206 , THR C:208 , GLU C:268 , MET C:307 , GOL C:1338BINDING SITE FOR RESIDUE GOL C1339
09AC9SOFTWAREVAL D:193 , ARG D:195 , GLY D:196 , PRO D:207 , THR D:208 , ALA D:209 , ASN D:210 , SER D:269 , VAL D:271 , ARG D:274 , ASP D:275 , ALA D:276 , LEU D:278 , TYR D:279 , GOL D:1337 , CA D:1338 , HOH D:2005 , HOH D:2006 , HOH D:2052 , HOH D:2053BINDING SITE FOR RESIDUE ADP D 501
10BC1SOFTWAREGLY D:196 , THR D:208 , ASN D:210 , ADP D:501 , CA D:1338 , HOH D:2007BINDING SITE FOR RESIDUE GOL D1337
11BC2SOFTWARETHR A:208 , ASN A:210 , ADP A:501 , GOL A:1338BINDING SITE FOR RESIDUE CA A1340
12BC3SOFTWARETHR B:208 , ASN B:210 , ADP B:501 , GOL B:1337BINDING SITE FOR RESIDUE CA B1338
13BC4SOFTWARETHR C:208 , ASN C:210 , ADP C:501 , GOL C:1338BINDING SITE FOR RESIDUE CA C1340
14BC5SOFTWARETHR D:208 , ASN D:210 , ADP D:501 , GOL D:1337BINDING SITE FOR RESIDUE CA D1338

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A88)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Arg C:199 -Gly C:200

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A88)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A88)

(-) Exons   (0, 0)

(no "Exon" information available for 5A88)

(-) Sequences/Alignments

Asymmetric 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:147
                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee........hhhhh...eeeee.........eeeeeeeee.......ee......eeeeeeeeee..eeeeeee....ee....eeeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh...hhh.ee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a88 A 185 RHFYVTGPVVRGAGRGGKELGFPTANQYFHDTVALPADGVYAGWLTILPTEAPVSGNMEPEVAYAAAISVGTNQRSVESFVLDRDADLYGHDVKVEFVDHVRAMEKFDSVEQLLEVMAKDVQKTRTLLAQDVQAHKMAPETYFLQAE 337
                                   194       204       214       224       234       244       254  ||   270       280       290       300       310       320       330       
                                                                                                  257|                                                                         
                                                                                                   264                                                                         


Chain B from PDB  Type:PROTEIN  Length:133
                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...........eeeee.........eeeeeeeee.......ee......eeeeeeeee..eeeeeee....ee....eeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh...ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a88 B 186 HFYVTGPVVRGAGLGFPTANQYFHDTVALPADGVYAGWLTILPTEAPVSGNMEPEVAYAAAISVGTQRSVESFVLDRDADLYGHDVKVEFVDHVRAMEKFSVEQLLEVMAKDVQKTRTLLAQDVQAETYFLQA 336
                                   195  ||   210       220       230       240       250     ||267       277       287       297|      308       318     ||333   
                                      198|                                                 256|                              297|                      324|      
                                       204                                                  264                               299                       330      


Chain C from PDB  Type:PROTEIN  Length:138
                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee........hhhhh...eeeee.........eeeeeeeee...............eeeeeeeeee..eeeeeee..........eeeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhh.ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5a88 C 186 HFYVTGPVVRGAGRGGKELGFPTANQYFHDTVALPADGVYAGWLTILPTEAPVSGNMEPEVAYAAAISVGTNQRSVESFVLDRDADLYGHDVKVEFVDHVRAMEKFDSVEQLLEVMAKDVQKTRTLLAQDVTYFLQAE 337
                                   195       205       215       225       235       245       255 ||    271       281       291       301       311       321||      
                                                                                                 257|                                                       322|      
                                                                                                  264                                                        331      


Chain D from PDB  Type:PROTEIN  Length:137
                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........eeeee.........eeeeeeeee...............eeeeeeeeee..eeeeeee..........eeeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh......ee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a88 D 186 HFYVTGPVVRGGFPTANQYFHDTVALPADGVYAGWLTILPTEAPVSGNMEPEVAYAAAISVGTNQRSVESFVLDRDADLYGHDVKVEFVDHVRAMEKFDSVEQLLEVMAKDVQKTRTLLAQDVQAHKMAPETYFLQA 336
                                   195||     213       223       233       243       253   ||  269       279       289       299       309       319       329       
                                    196|                                                 257|                                                                        
                                     205                                                  264
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 5A88)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A88)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A88)

(-) Gene Ontology  (13, 13)

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  5a88
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  2.7.1.26
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        RIBF_CORAM | Q59263: 2x0k 3zug 4uze 4uzf 5a89 5a8a 5fnz 5fo0 5fo1

(-) Related Entries Specified in the PDB File

5a89 CRYSTAL STRUCTURE OF THE RFK MODULE OF FAD SYNTHETASE FROM CORYNEBACTERIUM AMMONIAGENES IN COMPLEX WITH FMN AND ADP(P212121)
5a8a CRYSTAL STRUCTURE OF THE RFK MODULE OF FAD SYNTHETASE FROM CORYNEBACTERIUM AMMONIAGENES IN COMPLEX WITH FMN AND ADP (P3221)