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(-) Description

Title :  CRYSTAL STRUCTURE OF SCHIZOSACCHAROMYCES POMBE RIBOFLAVIN KINASE REVEALS A NOVEL ATP AND RIBOFLAVIN BINDING FOLD
 
Authors :  S. Bauer, K. Kemter, A. Bacher, R. Huber, M. Fischer, S. Steinbacher
Date :  11 Oct 02  (Deposition) - 25 Feb 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Kinase, Phosphoryl Transferases, Flavin Cofactors, Metal Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Bauer, K. Kemter, A. Bacher, R. Huber, M. Fischer, S. Steinbacher
Crystal Structure Of Schizosaccharomyces Pombe Riboflavin Kinase Reveals A Novel Atp And Riboflavin Binding Fold
J. Mol. Biol. V. 326 1463 2003
PubMed-ID: 12595258  |  Reference-DOI: 10.1016/S0022-2836(03)00059-7
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PUTATIVE RIBOFLAVIN KINASE
    Chains: A, B
    EC Number: 2.7.1.26
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNCO
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SPCC18.16.C
    Organism Common: FISSION YEAST
    Organism Scientific: SCHIZOSACCHAROMYCES POMBE
    Organism Taxid: 4896

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:30 , GLY A:33 , ARG A:36 , GLY A:37 , SER A:38 , LYS A:39 , PRO A:44 , THR A:45 , VAL A:97 , HIS A:98 , LEU A:99 , ASP A:106 , PHE A:107 , TYR A:108 , HOH A:205 , HOH A:211 , HOH A:233 , HOH A:235 , HOH A:242 , HOH A:289 , TYR B:88BINDING SITE FOR RESIDUE ADP A 201
2AC2SOFTWARETYR A:88 , VAL B:30 , GLY B:35 , ARG B:36 , GLY B:37 , SER B:38 , LYS B:39 , PRO B:44 , THR B:45 , ALA B:46 , VAL B:97 , HIS B:98 , LEU B:99 , ARG B:102 , ASP B:106 , PHE B:107 , TYR B:108 , HOH B:310 , HOH B:319 , HOH B:337 , HOH B:339 , HOH B:343 , HOH B:346 , HOH B:366BINDING SITE FOR RESIDUE ADP B 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1N06)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ser A:20 -Pro A:21
2Tyr A:22 -Pro A:23
3Ser B:20 -Pro B:21
4Tyr B:22 -Pro B:23

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1N06)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1N06)

(-) Exons   (0, 0)

(no "Exon" information available for 1N06)

(-) 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:154
 aligned with RIFK_SCHPO | O74866 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:154
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158    
           RIFK_SCHPO     9 RPEIVGPEKVQSPYPIRFEGKVVHGFGRGSKELGIPTANISEDAIQELLRYRDSGVYFGYAMVQKRVFPMVMSVGWNPYYKNKLRSAEVHLIERQGEDFYEEIMRVIVLGYIRPELNYAGLDKLIEDIHTDIRVALNSMDRPSYSSYKKDPFFK 162
               SCOP domains d1n06a_ A: Riboflavin kinase                                                                                                                               SCOP domains
               CATH domains 1n06A00 A:9-162 Riboflavin kinase-like                                                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeeee..............eee.hhhhhhhhh....eeeeeeeee..eeeeeeeeeee........eeeeeee...........eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n06 A   9 RPEIVGPEKVQSPYPIRFEGKVVHGFGRGSKELGIPTANISEDAIQELLRYRDSGVYFGYAMVQKRVFPMVMSVGWNPYYKNKLRSAEVHLIERQGEDFYEEIMRVIVLGYIRPELNYAGLDKLIEDIHTDIRVALNSMDRPSYSSYKKDPFFK 162
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158    


Chain B from PDB  Type:PROTEIN  Length:155
 aligned with RIFK_SCHPO | O74866 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:155
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157     
           RIFK_SCHPO     8 KRPEIVGPEKVQSPYPIRFEGKVVHGFGRGSKELGIPTANISEDAIQELLRYRDSGVYFGYAMVQKRVFPMVMSVGWNPYYKNKLRSAEVHLIERQGEDFYEEIMRVIVLGYIRPELNYAGLDKLIEDIHTDIRVALNSMDRPSYSSYKKDPFFK 162
               SCOP domains d1n06b_ B: Riboflavin kinase                                                                                                                                SCOP domains
               CATH domains 1n06B00 B:8-162 Riboflavin kinase-like                                                                                                                      CATH domains
           Pfam domains (1) -----------Flavokinase-1n06B01 B:19-148                                                                                                      -------------- Pfam domains (1)
           Pfam domains (2) -----------Flavokinase-1n06B02 B:19-148                                                                                                      -------------- Pfam domains (2)
         Sec.struct. author ................eeeeeeee..............eee.hhhh.........eeeeeeeee..eeeeeeeeeee........eeeeeee...........eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n06 B   8 KRPEIVGPEKVQSPYPIRFEGKVVHGFGRGSKELGIPTANISEDAIQELLRYRDSGVYFGYAMVQKRVFPMVMSVGWNPYYKNKLRSAEVHLIERQGEDFYEEIMRVIVLGYIRPELNYAGLDKLIEDIHTDIRVALNSMDRPSYSSYKKDPFFK 162
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157
   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, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (RIFK_SCHPO | O74866)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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: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.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    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: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).
    GO:0006771    riboflavin metabolic process    The chemical reactions and pathways involving riboflavin (vitamin B2), the precursor for the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD).
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RIFK_SCHPO | O74866: 1n05 1n07 1n08

(-) Related Entries Specified in the PDB File

1n05 RIBOFLAVIN KINASE, LIGAND FREE
1n07
1n08