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(-) Description

Title :  CRYSTAL STRUCTURE OF MODULAR FAD SYNTHETASE FROM CORYNEBACTERIUM AMMONIAGENES
 
Authors :  B. Herguedas, J. A. Hermoso, M. Martinez-Julvez, M. Medina, S. Frago
Date :  15 Dec 09  (Deposition) - 26 May 10  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Riboflavin Kinase, Nucleotide-Binding, Transferase, Atp-Binding, Multifunctional Enzyme, Nucleotidyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Herguedas, M. Martinez-Julvez, S. Frago, M. Medina, J. A. Hermoso
Oligomeric State In The Crystal Structure Of Modular Fad Synthetase Provides Insights Into Its Sequential Catalysis In Prokaryotes
J. Mol. Biol. V. 400 218 2010
PubMed-ID: 20471397  |  Reference-DOI: 10.1016/J.JMB.2010.05.018

(-) Compounds

Molecule 1 - RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF
    Atcc: 6872
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Organism Scientific: CORYNEBACTERIUM AMMONIAGENES
    Organism Taxid: 1697

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB
Biological Unit 2 (1x): A 
Biological Unit 3 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1PPV2Ligand/IonPYROPHOSPHATE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1PPV6Ligand/IonPYROPHOSPHATE
2SO46Ligand/IonSULFATE ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1PPV1Ligand/IonPYROPHOSPHATE
2SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1PPV1Ligand/IonPYROPHOSPHATE
2SO41Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:195 , TYR A:279 , THR B:1073 , LEU B:1074 , HOH B:2198 , HOH B:2199BINDING SITE FOR RESIDUE SO4 B2339
2AC2SOFTWARETHR A:73 , LEU A:74 , ARG B:1195 , TYR B:1279BINDING SITE FOR RESIDUE SO4 A1339
3AC3SOFTWAREVAL A:23 , PHE A:24 , HIS A:28 , HIS A:31 , ASN A:125 , SER A:163 , SER A:164 , HOH A:2163 , HOH A:2316 , HOH A:2317 , HOH A:2318 , HOH A:2319 , HOH A:2320BINDING SITE FOR RESIDUE PPV A1340
4AC4SOFTWAREGLY B:1022 , VAL B:1023 , PHE B:1024 , HIS B:1028 , HIS B:1031 , ASN B:1125 , SER B:1163 , SER B:1164 , HOH B:2103 , HOH B:2200 , HOH B:2201 , HOH B:2202BINDING SITE FOR RESIDUE PPV B2340

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X0K)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Asp A:55 -Pro A:56
2Asp B:1055 -Pro B:1056

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X0K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2X0K)

(-) Exons   (0, 0)

(no "Exon" information available for 2X0K)

(-) 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:338
 aligned with RIBF_CORAM | Q59263 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:338
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330        
          RIBF_CORAM      1 MDIWYGTAAVPKDLDNSAVTIGVFDGVHRGHQKLINATVEKAREVGAKAIMVTFDPHPVSVFLPRRAPLGITTLAERFALAESFGIDGVLVIDFTRELSGTSPEKYVEFLLEDTLHASHVVVGANFTFGENAAGTADSLRQICQSRLTVDVIDLLDDEGVRISSTTVREFLSEGDVARANWALGRHFYVTGPVVRGAGRGGKELGFPTANQYFHDTVALPADGVYAGWLTILPTEAPVSGNMEPEVAYAAAISVGTNPTFGDEQRSVESFVLDRDADLYGHDVKVEFVDHVRAMEKFDSVEQLLEVMAKDVQKTRTLLAQDVQAHKMAPETYFLQAES  338
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2x0kA01 A:1-186 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                     -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.hhhh......eeeee......hhhhhhhhhhhhhhhhhhh.eeeeeee..hhhhhhh.........hhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhh.eeeeeee...eehhhhheehhhhhhhh....eeeee...ee..ee.hhhhhhhhhhh.hhhhhhhhhh...eeeee................eeeee.........eeeeeeeee.......ee......eeeeeeeeeee......eeeeeeee....ee....eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh.......ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2x0k A    1 MDIWYGTAAVPKDLDNSAVTIGVFDGVHRGHQKLINATVEKAREVGAKAIMVTFDPHPVSVFLPRRAPLGITTLAERFALAESFGIDGVLVIDFTRELSGTSPEKYVEFLLEDTLHASHVVVGANFTFGENAAGTADSLRQICQSRLTVDVIDLLDDEGVRISSTTVREFLSEGDVARANWALGRHFYVTGPVVRGAGRGGKELGFPTANQYFHDTVALPADGVYAGWLTILPTEAPVSGNMEPEVAYAAAISVGTNPTFGDEQRSVESFVLDRDADLYGHDVKVEFVDHVRAMEKFDSVEQLLEVMAKDVQKTRTLLAQDVQAHKMAPETYFLQAES  338
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330        


Chain B from PDB  Type:PROTEIN  Length:338
 aligned with RIBF_CORAM | Q59263 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:338
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330        
          RIBF_CORAM      1 MDIWYGTAAVPKDLDNSAVTIGVFDGVHRGHQKLINATVEKAREVGAKAIMVTFDPHPVSVFLPRRAPLGITTLAERFALAESFGIDGVLVIDFTRELSGTSPEKYVEFLLEDTLHASHVVVGANFTFGENAAGTADSLRQICQSRLTVDVIDLLDDEGVRISSTTVREFLSEGDVARANWALGRHFYVTGPVVRGAGRGGKELGFPTANQYFHDTVALPADGVYAGWLTILPTEAPVSGNMEPEVAYAAAISVGTNPTFGDEQRSVESFVLDRDADLYGHDVKVEFVDHVRAMEKFDSVEQLLEVMAKDVQKTRTLLAQDVQAHKMAPETYFLQAES  338
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2x0kB01 B:1001-1186 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                                                 -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------FAD_syn-2x0kB01 B:1010-1166                                                                                                                                  ---------------Flavokinase-2x0kB03 B:1182-1319                                                                                                           ------------------- Pfam domains (1)
           Pfam domains (2) ---------FAD_syn-2x0kB02 B:1010-1166                                                                                                                                  ---------------Flavokinase-2x0kB04 B:1182-1319                                                                                                           ------------------- Pfam domains (2)
         Sec.struct. author .eeee.hhhh......eeeee......hhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhh.........hhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhh.eeeeeee...eehhhhheehhhhhhhh....eeeee...ee..ee.hhhhhhhhhhh.hhhhhhhhhh..eeeeee................eeeee.........eeeeeeeee.......ee......eeeeeeeeee........eeeeeee....ee....eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                2x0k B 1001 MDIWYGTAAVPKDLDNSAVTIGVFDGVHRGHQKLINATVEKAREVGAKAIMVTFDPHPVSVFLPRRAPLGITTLAERFALAESFGIDGVLVIDFTRELSGTSPEKYVEFLLEDTLHASHVVVGANFTFGENAAGTADSLRQICQSRLTVDVIDLLDDEGVRISSTTVREFLSEGDVARANWALGRHFYVTGPVVRGAGRGGKELGFPTANQYFHDTVALPADGVYAGWLTILPTEAPVSGNMEPEVAYAAAISVGTNPTFGDEQRSVESFVLDRDADLYGHDVKVEFVDHVRAMEKFDSVEQLLEVMAKDVQKTRTLLAQDVQAHKMAPETYFLQAES 1338
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310      1320      1330
   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  (0, 0)

(no "SCOP Domain" information available for 2X0K)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (2, 4)

Asymmetric Unit
(-)
Clan: HUP (230)
(-)
Clan: no clan defined [family: Flavokinase] (12)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RIBF_CORAM | Q59263)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003919    FMN adenylyltransferase activity    Catalysis of the reaction: ATP + FMN = diphosphate + FAD.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    GO:0016779    nucleotidyltransferase activity    Catalysis of the transfer of a nucleotidyl group to a reactant.
    GO:0008531    riboflavin kinase activity    Catalysis of the reaction: ATP + riboflavin = ADP + FMN + 2 H(+).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0006747    FAD biosynthetic process    The chemical reactions and pathways resulting in the formation of FAD, the oxidized form of flavin-adenine dinucleotide.
    GO:0009398    FMN biosynthetic process    The chemical reactions and pathways resulting in the formation of FMN, the oxidized form of flavin mononucleotide (riboflavin 5'-(dihydrogen phosphate)), which acts as a coenzyme for a number of oxidative enzymes including NADH dehydrogenase.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0009231    riboflavin biosynthetic process    The chemical reactions and pathways resulting in the formation of riboflavin (vitamin B2), the precursor for the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD).

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 Related Entries

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

UniProtKB/Swiss-Prot
        RIBF_CORAM | Q59263: 3zug 4uze 4uzf 5a88 5a89 5a8a 5fnz 5fo0 5fo1

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