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(-) Description

Title :  CRYSTAL STRUCTURE OF RIBOFLAVIN KINASE
 
Authors :  S. Karthikeyan, Q. Zhou, F. Mseeh, N. V. Grishin, A. L. Osterman, H. Zhan
Date :  23 Apr 03  (Deposition) - 13 May 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Barrel, Riboflavin Kinase, Flavin Mononucleotide, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Karthikeyan, Q. Zhou, F. Mseeh, N. V. Grishin, A. L. Osterman, H. Zhang
Crystal Structure Of Human Riboflavin Kinase Reveals A Beta Barrel Fold And A Novel Active Site Arch
Structure V. 11 265 2003
PubMed-ID: 12623014  |  Reference-DOI: 10.1016/S0969-2126(03)00024-8

(-) Compounds

Molecule 1 - RIBOFLAVIN KINASE
    Chains: A
    EC Number: 2.7.1.26
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PPROEX-HTA
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: FLJ11149
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HYPOTHETICAL PROTEIN FLJ11149

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2FMN1Ligand/IonFLAVIN MONONUCLEOTIDE
3MG1Ligand/IonMAGNESIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:34 , ADP A:301 , FMN A:401 , HOH A:502BINDING SITE FOR RESIDUE MG A 201
2AC2SOFTWAREVAL A:19 , GLY A:22 , GLY A:26 , SER A:27 , LYS A:28 , PRO A:33 , THR A:34 , ASN A:36 , THR A:87 , ILE A:89 , HIS A:91 , PHE A:93 , ASP A:96 , PHE A:97 , TYR A:98 , MG A:201 , FMN A:401 , HOH A:501 , HOH A:502 , HOH A:508 , HOH A:509 , HOH A:518 , HOH A:523BINDING SITE FOR RESIDUE ADP A 301
3AC3SOFTWAREPHE A:23 , ARG A:25 , GLY A:26 , SER A:27 , THR A:34 , ILE A:53 , VAL A:69 , GLU A:86 , ARG A:111 , LYS A:114 , PHE A:116 , ASP A:129 , MG A:201 , ADP A:301 , HOH A:502 , HOH A:508 , HOH A:545 , HOH A:547 , HOH A:597BINDING SITE FOR RESIDUE FMN A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1P4M)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:11 -Pro A:12

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1P4M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1P4M)

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003767361bENSE00001471519chr9:79009421-79009006416RIFK_HUMAN1-28281A:9-3527
1.4ENST000003767364ENSE00002160773chr9:79007485-79007334152RIFK_HUMAN28-78511A:35-8551
1.5aENST000003767365aENSE00002176811chr9:79003572-79003470103RIFK_HUMAN79-113351A:86-12035
1.6eENST000003767366eENSE00001471508chr9:79002445-790004332013RIFK_HUMAN113-155431A:120-15536

(-) 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:147
 aligned with RIFK_HUMAN | Q969G6 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:147
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       
           RIFK_HUMAN     2 RHLPYFCRGQVVRGFGRGSKQLGIPTANFPEQVVDNLPADISTGIYYGWASVGSGDVHKMVVSIGWNPYYKNTKKSMETHIMHTFKEDFYGEILNVAIVGYLRPEKNFDSLESLISAIQGDIEEAKKRLELPEHLKIKEDNFFQVSK 148
               SCOP domains d1p4ma_ A: Riboflavin kinase                                                                                                                        SCOP domains
               CATH domains 1p4mA00 A:9-155 Riboflavin kinase-like                                                                                                              CATH domains
               Pfam domains Flavokinase-1p4mA01 A:9-138                                                                                                       ----------------- Pfam domains
         Sec.struct. author ....eeeeee.......hhhhhh...ee.hhhhhhh.......eeeeeeeee.....eeeeeeeee........eeeeeee...........eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1b  PDB: A:9-35     --------------------------------------------------Exon 1.5a  PDB: A:86-120           ----------------------------------- Transcript 1 (1)
           Transcript 1 (2) --------------------------Exon 1.4  PDB: A:35-85 UniProt: 28-78              ----------------------------------Exon 1.6e  PDB: A:120-155            Transcript 1 (2)
                 1p4m A   9 RHLPYFCRGQVVRGFGRGSKQLGIPTANFPEQVVDNLPADISTGIYYGWASVGSGDVHKMVVSIGWNPYYKNTKKSMETHIMHTFKEDFYGEILNVAIVGYLRPEKNFDSLESLISAIQGDIEEAKKRLELPEYLKIKEDNFFQVSK 155
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148
   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, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (RIFK_HUMAN | Q969G6)
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.
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:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    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:0033864    positive regulation of NAD(P)H oxidase activity    Any process that activates or increases the activity of the enzyme NAD(P)H oxidase.
    GO:0072593    reactive oxygen species metabolic process    The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        RIFK_HUMAN | Q969G6: 1nb0 1nb9 1q9s

(-) Related Entries Specified in the PDB File

1nb0 1nb9