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(-) Description

Title :  CRYSTAL STRUCTURE OF A BIFUNCTIONAL DEAMINASE AND REDUCTASE INVOLVED IN RIBOFLAVIN BIOSYNTHESIS
 
Authors :  S. H. Liaw, S. J. Chen, Y. C. Chang
Date :  02 Nov 05  (Deposition) - 29 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.97
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Alpha/Beta/Alpha; Two Separate Functional Domains, Hydrolase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. J. Chen, Y. C. Chang, S. H. Liaw
Crystal Structure Of A Bifunctional Deaminase And Reductase Involved In Riboflavin Biosynthesis
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBD
    Chains: A, B, C, D
    EC Number: 3.5.4.26, 1.1.1.193
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: BL21 PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RIBG
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
2ZN4Ligand/IonZINC ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:49 , GLU A:51 , CYS A:74 , CYS A:83BINDING SITE FOR RESIDUE ZN A 1360
2AC2SOFTWAREHIS B:49 , GLU B:51 , CYS B:74 , CYS B:83BINDING SITE FOR RESIDUE ZN B 1360
3AC3SOFTWAREHIS C:49 , GLU C:51 , CYS C:74 , CYS C:83BINDING SITE FOR RESIDUE ZN C 1360
4AC4SOFTWAREHIS D:49 , GLU D:51 , CYS D:74 , CYS D:83BINDING SITE FOR RESIDUE ZN D 1360
5AC5SOFTWAREALA B:152 , ALA B:153 , ILE B:160 , GLY B:165 , GLY B:192 , VAL B:193 , GLY B:194 , THR B:195 , ASP B:199 , THR B:221 , ILE B:270 , GLU B:290 , GLY B:292 , SER B:293 , ALA B:294 , VAL B:295 , SER B:298 , HOH B:1407 , HOH B:1424BINDING SITE FOR RESIDUE NDP B 381

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1A:74 -A:83
2B:74 -B:83
3C:74 -C:83
4D:74 -D:83

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2D5N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2D5N)

(-) PROSITE Motifs  (2, 8)

Asymmetric/Biological Unit (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYT_DCMP_DEAMINASES_2PS51747 Cytidine and deoxycytidylate deaminases domain profile.RIBD_BACSU1-122
 
 
 		  4A:1-122
B:1-122
C:1-122
D:1-122
2CYT_DCMP_DEAMINASES_1PS00903 Cytidine and deoxycytidylate deaminases zinc-binding region signature.RIBD_BACSU49-87
 
 
 		  4A:49-87
B:49-87
C:49-87
D:49-87

(-) Exons   (0, 0)

(no "Exon" information available for 2D5N)

(-) 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:359
 aligned with RIBD_BACSU | P17618 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:359
                                    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       340       350         
           RIBD_BACSU     1 MEEYYMKLALDLAKQGEGQTESNPLVGAVVVKDGQIVGMGAHLKYGEAHAEVHAIHMAGAHAEGADIYVTLEPCSHYGKTPPCAELIINSGIKRVFVAMRDPNPLVAGRGISMMKEAGIEVREGILADQAERLNEKFLHFMRTGLPYVTLKAAASLDGKIATSTGDSKWITSEAARQDAQQYRKTHQSILVGVGTVKADNPSLTCRLPNVTKQPVRVILDTVLSIPEDAKVICDQIAPTWIFTTARADEEKKKRLSAFGVNIFTLETERIQIPDVLKILAEEGIMSVYVEGGSAVHGSFVKEGCFQEIIFYFAPKLIGGTHAPSLISGEGFQSMKDVPLLQFTDITQIGRDIKLTAKPT 359
               SCOP domains d2d5na2 A:1-145 Riboflavin biosynthesis protein RibD                                                                                             d2d5na1 A:146-359 Riboflavin biosynthesis protein RibD                                                                                                                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh.........eeeee....eeeeee.......hhhhhhhhhhhhhhh..eeee............hhhhhhhhhh..eeee..........hhhhhhhhh...eee...hhhhhhhhhhhhhhhhhhh..eeeeeeeee................hhhhhhhhhhhhhhh.eeeeehhhhhhhh..............eeeee.........hhhhhh....eeeee....hhhhhhhhhh...eeee......hhhhhhhhhhhh...eeee..hhhhhhhhhhh....eeeeeee..........................eeeeeee.....eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CYT_DCMP_DEAMINASES_2  PDB: A:1-122 UniProt: 1-122                                                                        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: A:49-87    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d5n A   1 MEEYYMKLALDLAKQGEGQTESNPLVGAVVVKDGQIVGMGAHLKYGEAHAEVHAIHMAGAHAEGADIYVTLEPCSHYGKTPPCAELIINSGIKRVFVAMRDPNPLVAGRGISMMKEAGIEVREGILADQAERLNEKFLHFMRTGLPYVTLKAAASLDGKIATSTGDSKWITSEAARQDAQQYRKTHQSILVGVGTVKADNPSLTCRLPNVTKQPVRVILDTVLSIPEDAKVICDQIAPTWIFTTARADEEKKKRLSAFGVNIFTLETERIQIPDVLKILAEEGIMSVYVEGGSAVHGSFVKEGCFQEIIFYFAPKLIGGTHAPSLISGEGFQSMKDVPLLQFTDITQIGRDIKLTAKPT 359
                                    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       340       350         


Chain B from PDB  Type:PROTEIN  Length:359
 aligned with RIBD_BACSU | P17618 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:359
                                    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       340       350         
           RIBD_BACSU     1 MEEYYMKLALDLAKQGEGQTESNPLVGAVVVKDGQIVGMGAHLKYGEAHAEVHAIHMAGAHAEGADIYVTLEPCSHYGKTPPCAELIINSGIKRVFVAMRDPNPLVAGRGISMMKEAGIEVREGILADQAERLNEKFLHFMRTGLPYVTLKAAASLDGKIATSTGDSKWITSEAARQDAQQYRKTHQSILVGVGTVKADNPSLTCRLPNVTKQPVRVILDTVLSIPEDAKVICDQIAPTWIFTTARADEEKKKRLSAFGVNIFTLETERIQIPDVLKILAEEGIMSVYVEGGSAVHGSFVKEGCFQEIIFYFAPKLIGGTHAPSLISGEGFQSMKDVPLLQFTDITQIGRDIKLTAKPT 359
               SCOP domains d2d5nb2 B:1-145 Riboflavin biosynthesis protein RibD                                                                                             d2d5nb1 B:146-359 Riboflavin biosynthesis protein RibD                                                                                                                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh...........eeeee....eeeeee.......hhhhhhhhhhhhhhh..eeeeee..........hhhhhhhhh...eeeeee........hhhhhhhhh...eee.....hhhhhhhhhhhhhhhhh..eeeeeeee.................hhhhhhhhhhhhhhh.eeeeehhhhh.................eeeee...................eeeeee...hhhhhhhhh....eeeee.....hhhhhhhhhhhh...eeee..hhhhhhhhhhhh...eeeeee....................hhhhh...eeeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CYT_DCMP_DEAMINASES_2  PDB: B:1-122 UniProt: 1-122                                                                        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: B:49-87    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d5n B   1 MEEYYMKLALDLAKQGEGQTESNPLVGAVVVKDGQIVGMGAHLKYGEAHAEVHAIHMAGAHAEGADIYVTLEPCSHYGKTPPCAELIINSGIKRVFVAMRDPNPLVAGRGISMMKEAGIEVREGILADQAERLNEKFLHFMRTGLPYVTLKAAASLDGKIATSTGDSKWITSEAARQDAQQYRKTHQSILVGVGTVKADNPSLTCRLPNVTKQPVRVILDTVLSIPEDAKVICDQIAPTWIFTTARADEEKKKRLSAFGVNIFTLETERIQIPDVLKILAEEGIMSVYVEGGSAVHGSFVKEGCFQEIIFYFAPKLIGGTHAPSLISGEGFQSMKDVPLLQFTDITQIGRDIKLTAKPT 359
                                    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       340       350         


Chain C from PDB  Type:PROTEIN  Length:359
 aligned with RIBD_BACSU | P17618 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:359
                                    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       340       350         
           RIBD_BACSU     1 MEEYYMKLALDLAKQGEGQTESNPLVGAVVVKDGQIVGMGAHLKYGEAHAEVHAIHMAGAHAEGADIYVTLEPCSHYGKTPPCAELIINSGIKRVFVAMRDPNPLVAGRGISMMKEAGIEVREGILADQAERLNEKFLHFMRTGLPYVTLKAAASLDGKIATSTGDSKWITSEAARQDAQQYRKTHQSILVGVGTVKADNPSLTCRLPNVTKQPVRVILDTVLSIPEDAKVICDQIAPTWIFTTARADEEKKKRLSAFGVNIFTLETERIQIPDVLKILAEEGIMSVYVEGGSAVHGSFVKEGCFQEIIFYFAPKLIGGTHAPSLISGEGFQSMKDVPLLQFTDITQIGRDIKLTAKPT 359
               SCOP domains d2d5nc2 C:1-145 Riboflavin biosynthesis protein RibD                                                                                             d2d5nc1 C:146-359 Riboflavin biosynthesis protein RibD                                                                                                                                                                 SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhh...............ee..ee............hhhhhhhhhhhhhhh..................hhhhhhhhh...eeee..........hhhhhhhhh...eeee....hhhhhhhhhhhhhhhhh..eeeeeeeee................hhhhhhhhhhhhhh..eeeeehhhhhhhh..............eeeee.........hhhhhh....eeeee....hhhhhhhhhh...eeee......hhhhhhhhhhh....eeee..hhhhhhhhhhhh...eeeeeee...................hhhhh...eeeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) CYT_DCMP_DEAMINASES_2  PDB: C:1-122 UniProt: 1-122                                                                        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: C:49-87    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2d5n C   1 MEEYYMKLALDLAKQGEGQTESNPLVGAVVVKDGQIVGMGAHLKYGEAHAEVHAIHMAGAHAEGADIYVTLEPCSHYGKTPPCAELIINSGIKRVFVAMRDPNPLVAGRGISMMKEAGIEVREGILADQAERLNEKFLHFMRTGLPYVTLKAAASLDGKIATSTGDSKWITSEAARQDAQQYRKTHQSILVGVGTVKADNPSLTCRLPNVTKQPVRVILDTVLSIPEDAKVICDQIAPTWIFTTARADEEKKKRLSAFGVNIFTLETERIQIPDVLKILAEEGIMSVYVEGGSAVHGSFVKEGCFQEIIFYFAPKLIGGTHAPSLISGEGFQSMKDVPLLQFTDITQIGRDIKLTAKPT 359
                                    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       340       350         


Chain D from PDB  Type:PROTEIN  Length:360
 aligned with RIBD_BACSU | P17618 from UniProtKB/Swiss-Prot  Length:361

    Alignment length:360
                             1                                                                                                                                                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359
           RIBD_BACSU     - -MEEYYMKLALDLAKQGEGQTESNPLVGAVVVKDGQIVGMGAHLKYGEAHAEVHAIHMAGAHAEGADIYVTLEPCSHYGKTPPCAELIINSGIKRVFVAMRDPNPLVAGRGISMMKEAGIEVREGILADQAERLNEKFLHFMRTGLPYVTLKAAASLDGKIATSTGDSKWITSEAARQDAQQYRKTHQSILVGVGTVKADNPSLTCRLPNVTKQPVRVILDTVLSIPEDAKVICDQIAPTWIFTTARADEEKKKRLSAFGVNIFTLETERIQIPDVLKILAEEGIMSVYVEGGSAVHGSFVKEGCFQEIIFYFAPKLIGGTHAPSLISGEGFQSMKDVPLLQFTDITQIGRDIKLTAKPT 359
               SCOP domains d2d5nd2 D:0-145 Riboflavin biosynthesis protein RibD                                                                                              d2d5nd1 D:146-359 Riboflavin biosynthesis protein RibD                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhh...........eeeeee..eeeeeee.......hhhhhhhhhhhhhhh..eeee............hhhhhhhhhh..eeee..........hhhhhhhhhh..eeee..hhhhhhhhhhhhhhhhhhh..eeeeeeeee................hhhhhhhhhhhhhhh.eeeeehhhhhhhh..............eeeee...................eeeee....hhhhhhhhh....eeee......hhhhhhhhhhhh...eeee..hhhhhhhhhhh....eeeeeee...................hhhhh..eeeeeeeee..eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -CYT_DCMP_DEAMINASES_2  PDB: D:1-122 UniProt: 1-122                                                                        --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------------------------CYT_DCMP_DEAMINASES_1  PDB: D:49-87    -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2d5n D   0 SMEEYYMKLALDLAKQGEGQTESNPLVGAVVVKDGQIVGMGAHLKYGEAHAEVHAIHMAGAHAEGADIYVTLEPCSHYGKTPPCAELIINSGIKRVFVAMRDPNPLVAGRGISMMKEAGIEVREGILADQAERLNEKFLHFMRTGLPYVTLKAAASLDGKIATSTGDSKWITSEAARQDAQQYRKTHQSILVGVGTVKADNPSLTCRLPNVTKQPVRVILDTVLSIPEDAKVICDQIAPTWIFTTARADEEKKKRLSAFGVNIFTLETERIQIPDVLKILAEEGIMSVYVEGGSAVHGSFVKEGCFQEIIFYFAPKLIGGTHAPSLISGEGFQSMKDVPLLQFTDITQIGRDIKLTAKPT 359
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359
   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  (2, 8)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2D5N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2D5N)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (RIBD_BACSU | P17618)
molecular function
    GO:0008703    5-amino-6-(5-phosphoribosylamino)uracil reductase activity    Catalysis of the reaction: 5-amino-6-(5-phosphoribitylamino)uracil + NADP(+) = 5-amino-6-(5-phosphoribosylamino)uracil + H(+) + NADPH.
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    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:0008835    diaminohydroxyphosphoribosylaminopyrimidine deaminase activity    Catalysis of the reaction: 2,5-diamino-6-hydroxy-4-(5-phosphoribosylamino)-pyrimidine + H(2)O + H(+) = 5-amino-6-(5-phosphoribosylamino)uracil + NH(4)(+).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0009451    RNA modification    The covalent alteration of one or more nucleotides within an RNA molecule to produce an RNA molecule with a sequence that differs from that coded genetically.
    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:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    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).
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.

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  2d5n
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 Related Entries

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

UniProtKB/Swiss-Prot
        RIBD_BACSU | P17618: 2b3z 3ex8 4g3m

(-) Related Entries Specified in the PDB File

2b3z THE CRYSTAL STRUCTURE OF THE ENZYME ALONE