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(-) Description

Title :  CRYSTAL STRUCTURE OF THE RIBOFLAVIN KINASE MODULE OF FAD SYNTHETASE FROM CORYNEBACTERIUM AMMONIAGENES IN COMPLEX WITH FMN AND ADP (P 21 21 21)
 
Authors :  B. Herguedas, M. Martinez-Julvez, J. A. Hermoso, M. Medina
Date :  13 Jul 15  (Deposition) - 09 Dec 15  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (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
    EC Number: 2.7.1.26
    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, RESIDUES 183-338
    Organism Scientific: CORYNEBACTERIUM AMMONIAGENES
    Organism Taxid: 1697
    Other Details: KINASE DOMAIN OF FAD SYNTHETASE (A BIFUNCTIONAL ENZYME)

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 12)

Asymmetric Unit (6, 12)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
3FMN2Ligand/IonFLAVIN MONONUCLEOTIDE
4GOL3Ligand/IonGLYCEROL
5MG2Ligand/IonMAGNESIUM ION
6ZN2Ligand/IonZINC ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
4GOL-1Ligand/IonGLYCEROL
5MG-1Ligand/IonMAGNESIUM ION
6ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1ACY-1Ligand/IonACETIC ACID
2ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
3FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
4GOL3Ligand/IonGLYCEROL
5MG-1Ligand/IonMAGNESIUM ION
6ZN-1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:208 , ASN A:210 , FMN A:339 , ADP A:501BINDING SITE FOR RESIDUE MG A 341
02AC2SOFTWAREHIS A:186 , ASP A:321 , HIS A:325 , HOH A:2004BINDING SITE FOR RESIDUE ZN A 343
03AC3SOFTWAREVAL A:193 , ARG A:195 , GLY A:196 , ALA A:197 , GLY A:198 , GLY A:200 , GLY A:201 , 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 , FMN A:339 , MG A:341 , HOH A:2016 , HOH A:2024 , HOH A:2030 , HOH A:2124 , HOH A:2131 , HOH A:2182BINDING SITE FOR RESIDUE ADP A 501
04AC4SOFTWAREALA B:197 , GLY B:198 , ARG B:199 , GLY B:200 , THR B:208 , ASN B:210 , VAL B:224 , ALA B:251 , SER B:253 , ASN B:257 , PRO B:258 , THR B:259 , PHE B:260 , GLU B:268 , ARG B:292 , MET B:294 , GLU B:295 , PHE B:297 , LEU B:303 , ASP B:310 , ADP B:340 , MG B:341 , HOH B:2019 , HOH B:2029BINDING SITE FOR RESIDUE FMN B 339
05AC5SOFTWAREVAL B:193 , ARG B:195 , GLY B:196 , ALA B:197 , GLY B:198 , GLY B:200 , GLY B:201 , 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 , ASP B:277 , LEU B:278 , TYR B:279 , FMN B:339 , MG B:341 , HOH B:2014 , HOH B:2017 , HOH B:2021 , HOH B:2118 , HOH B:2199BINDING SITE FOR RESIDUE ADP B 340
06AC6SOFTWARETHR B:208 , ASN B:210 , FMN B:339 , ADP B:340BINDING SITE FOR RESIDUE MG B 341
07AC7SOFTWAREHIS B:186 , ASP B:321 , HIS B:325 , HOH B:2004BINDING SITE FOR RESIDUE ZN B 343
08AC8SOFTWAREGLY A:196 , ALA A:197 , GLY A:198 , ARG A:199 , GLY A:200 , THR A:208 , ASN A:210 , VAL A:224 , ALA A:251 , SER A:253 , ASN A:257 , PRO A:258 , THR A:259 , PHE A:260 , GLU A:268 , ARG A:292 , MET A:294 , GLU A:295 , PHE A:297 , LEU A:303 , MET A:307 , ASP A:310 , MG A:341 , ADP A:501 , HOH A:2026 , HOH A:2034BINDING SITE FOR RESIDUE FMN A 339
09AC9SOFTWAREARG A:274 , HOH A:2082 , HOH B:2062 , HOH B:2064BINDING SITE FOR RESIDUE ACY A1337
10BC1SOFTWAREHIS A:290 , HOH A:2056 , HIS B:214 , ASP B:215 , VAL B:217 , LEU B:219 , GOL B:1340 , HOH B:2035 , HOH B:2045 , HOH B:2200BINDING SITE FOR RESIDUE GOL B1339
11BC2SOFTWAREHOH A:2050 , HOH A:2052 , ALA B:221 , ASP B:222 , ARG B:265 , GOL B:1339BINDING SITE FOR RESIDUE GOL B1340
12BC3SOFTWARELYS B:309 , GLN B:312 , TYR B:332 , PHE B:333 , LEU B:334 , HOH B:2171 , HOH B:2183BINDING SITE FOR RESIDUE GOL B1341

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5A89)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5A89)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5A89)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5A89)

(-) Exons   (0, 0)

(no "Exon" information available for 5A89)

(-) 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:151
                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......hhhhhhh...eeee..........eeeeeeeee...............eeeeeeeee..........eeeeee..........eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhh..hhh.ee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a89 A 186 HFYVTGPVVRGAGRGGKELGFPTANQYFHDTVALPADGVYAGWLTILPTEAPVSGNMEPEVAYAAAISVGTNPTFGDEQRSVESFVLDRDADLYGHDVKVEFVDHVRAMEKFDSVEQLLEVMAKDVQKTRTLLAQDVQAHKMAPETYFLQA 336
                                   195       205       215       225       235       245       255       265       275       285       295       305       315       325       335 


Chain B from PDB  Type:PROTEIN  Length:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......hhhhhhh...eee...........eeeeeeeee.......ee......eeeeeeeee..........eeeeee....ee....eeeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhh.ee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5a89 B 186 HFYVTGPVVRGAGRGGKELGFPTANQYFHDTVALPADGVYAGWLTILPTEAPVSGNMEPEVAYAAAISVGTNPTFGDEQRSVESFVLDRDADLYGHDVKVEFVDHVRAMEKFDSVEQLLEVMAKDVQKTRTLLAQDVQAHKMAPETYFLQAES 338
                                   195       205       215       225       235       245       255       265       275       285       295       305       315       325       335
   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 5A89)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5A89)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5A89)

(-) Gene Ontology  (13, 13)

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

(-) Related Entries Specified in the PDB File

5a88 CRYSTAL STRUCTURE OF THE RFK MODULE OF FAD SYNTHETASE FROM CORYNEBACTERIUM AMMONIAGENES IN COMPLEX WITH ADP
5a8a CRYSTAL STRUCTURE OF THE RFK MODULE OF FAD SYNTHETASE FROM CORYNEBACTERIUM AMMONIAGENES IN COMPLEX WITH FMN AND ADP (P3221)