Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  NATIVE CYTOKININ DEHYDROGENASE
 
Authors :  E. Malito, A. Mattevi
Date :  23 Jun 04  (Deposition) - 26 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Flavin, Cytokinin, Oxidoreductase, Flavoprotein, Fad (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Malito, A. Coda, K. Bilyeu, M. W. Fraaije, A. Mattevi
Structures Of Michaelis And Product Complexes Of Plant Cytokinin Dehydrogenase: Implications For Flavoenzyme Catalysis
J. Mol. Biol. V. 341 1237 2004
PubMed-ID: 15321719  |  Reference-DOI: 10.1016/J.JMB.2004.06.083

(-) Compounds

Molecule 1 - CYTOKININ DEHYDROGENASE 1
    Chains: A
    EC Number: 1.5.99.12
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Taxid: 4922
    Organism Common: MAIZE
    Organism Scientific: ZEA MAYS
    Organism Taxid: 4577
    Synonym: CYTOKININ OXIDASE 1, CKO 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2NAG5Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:59 , ASN A:63 , ILE A:64 , HOH A:2049 , HOH A:2611 , HOH A:2612 , HOH A:2613 , HOH A:2614 , HOH A:2615BINDING SITE FOR RESIDUE NAG A1536
2AC2SOFTWARESER A:86 , ASN A:89 , HIS A:207 , HOH A:2616 , HOH A:2617BINDING SITE FOR RESIDUE NAG A1537
3AC3SOFTWAREPRO A:130 , PRO A:131 , ARG A:132 , ASN A:134 , ARG A:237 , NAG A:1539 , HOH A:2619BINDING SITE FOR RESIDUE NAG A1538
4AC4SOFTWAREPRO A:130 , NAG A:1538 , HOH A:2622 , HOH A:2623 , HOH A:2624 , HOH A:2626BINDING SITE FOR RESIDUE NAG A1539
5AC5SOFTWAREASN A:294 , ASN A:323 , HOH A:2627BINDING SITE FOR RESIDUE NAG A1540
6AC6SOFTWAREPHE A:61 , PHE A:100 , ARG A:101 , GLY A:102 , ARG A:103 , GLY A:104 , HIS A:105 , SER A:106 , GLN A:110 , ALA A:111 , MET A:121 , THR A:168 , ASP A:169 , TYR A:170 , LEU A:173 , THR A:174 , GLY A:176 , GLY A:177 , SER A:180 , ASN A:181 , GLY A:183 , ILE A:184 , GLY A:230 , GLY A:233 , VAL A:234 , ILE A:235 , TRP A:397 , TYR A:491 , LEU A:492 , SER A:527 , GLN A:530 , HOH A:2110 , HOH A:2112 , HOH A:2608BINDING SITE FOR RESIDUE FAD A1535

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W1O)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:129 -Pro A:130

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W1O)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FAD_PCMHPS51387 PCMH-type FAD-binding domain profile.CKX1_MAIZE65-245  1A:65-245
2OX2_COVAL_FADPS00862 Oxygen oxidoreductases covalent FAD-binding site.CKX1_MAIZE69-105  1A:69-105

(-) Exons   (0, 0)

(no "Exon" information available for 1W1O)

(-) 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:479
 aligned with CKX1_MAIZE | Q9T0N8 from UniProtKB/Swiss-Prot  Length:534

    Alignment length:495
                                    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       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529     
           CKX1_MAIZE    40 ALALDGKLRTDSNATAAASTDFGNITSALPAAVLYPSSTGDLVALLSAANSTPGWPYTIAFRGRGHSLMGQAFAPGGVVVNMASLGDAAAPPRINVSADGRYVDAGGEQVWIDVLRASLARGVAPRSWNDYLYLTVGGTLSNAGISGQAFRHGPQISNVLEMDVITGHGEMVTCSKQLNADLFDAVLGGLGQFGVITRARIAVEPAPARARWVRFVYTDFAAFSADQERLTAPRPGGGGASFGPMSYVEGSVFVNQSLATDLANTGFFTDADVARIVALAGERNATTVYSIEATLNYDNATAAAAAVDQELASVLGTLSYVEGFAFQRDVAYAAFLDRVHGEEVALNKLGLWRVPHPWLNMFVPRSRIADFDRGVFKGILQGTDIVGPLIVYPLNKSMWDDGMSAATPSEDVFYAVSLLFSSVAPNDLARLQEQNRRILRFCDLAGIQYKTYLARHTDRSDWVRHFGAAKWNRFVEMKNKYDPKRLLSPGQDIFN 534
               SCOP domains d1w1oa2 A:40-245 Cytokinin dehydrogenase 1                                                                                                                                                                    d1w1oa1 A:246-534 Cytokinin       dehydrogenase 1                                                                                                                                                                                                                                                 SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------FAD_binding_4-1w1oA02 A:69-214                                                                                                                    -------------------------------Cytokin-bind-1w1oA01 A:246-5      33                                                                                                                                                                                                                                                            - Pfam domains
         Sec.struct. author .......ee.hhhhhhhh.............eee...hhhhhhhhhhhhhhh......eeee...............eeee.hhhhh......eee.....eeeee...hhhhhhhhhhh..eee.........hhhhhhh......hhhhhhhhhh.eeeeeeee....eeeee...hhhhhhhhh......eeeeeeeeeeee...eeeeeeeee.hhhhhhhhhhhhhh..------......eeeeeeee..hhhhhhhh....hhhhhhhhhhhhhhh...eeeeeeeeeee-------hhhhhhhhhhhh........eeeeeeehhhhhhhhhhhhhhhhhh.........eeeeee..hhhhhhhhhh............eeeeeee.hhh............eeeeeee....---hhhhhhhhhhhhhhhhhhhh....ee......hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------FAD_PCMH  PDB: A:65-245 UniProt: 65-245                                                                                                                                              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -----------------------------OX2_COVAL_FAD  PDB: A:69-105         --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1w1o A  40 ALALDGKLRTDSNATAAASTDFGNITSALPAAVLYPSSTGDLVALLSAANSTPGWPYTIAFRGRGHSLMGQAFAPGGVVVNMASLGDAAAPPRINVSADGRYVDAGGEQVWIDVLRASLARGVAPRSWTDYLYLTVGGTLSNAGISGQAFRHGPQISNVLEMDVITGHGEMVTCSKQLNADLFDAVLGGLGQFGVITRARIAVEPAPARARWVRFVYTDFAAFSADQERLTAPR------SFGPMSYVEGSVFVNQSLATDLANTGFFTDADVARIVALAGERNATTVYSIEATLNY-------AAVDQELASVLGTLSYVEGFAFQRDVAYAAFLDRVHGEEVALNKLGLWRVPHPWLNMFVPRSRIADFDRGVFKGILQGTDIVGPLIVYPLNKSMWDDGMSAATPSEDVFYAVSLLFSS---NDLARLQEQNRRILRFCDLAGIQYKTYLARHTDRSDWVRHFGAAKWNRFVEMKNKYDPKRLLSPGQDIFN 534
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269   |     -|      289       299       309       319       329      |  -    |  349       359       369       379       389       399       409       419       429       439       449       459 |   | 469       479       489       499       509       519       529     
                                                                                                                                                                                                                                                                   273    280                                                     336     344                                                                                                                  461 465
   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, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1W1O)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: FAD-oxidase_C (26)
(-)
Clan: FAD_PCMH (53)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CKX1_MAIZE | Q9T0N8)
molecular function
    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:0019139    cytokinin dehydrogenase activity    Catalysis of the reaction: N6-dimethylallyladenine + acceptor + H2O = adenine + 3-methylbut-2-enal + reduced electron acceptor.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    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:0016614    oxidoreductase activity, acting on CH-OH group of donors    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
biological process
    GO:0009690    cytokinin metabolic process    The chemical reactions and pathways involving cytokinins, a class of adenine-derived compounds that can function in plants as growth regulators.
    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.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    FAD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala A:129 - Pro A:130   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1w1o
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  CKX1_MAIZE | Q9T0N8
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  1.5.99.12
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  CKX1_MAIZE | Q9T0N8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CKX1_MAIZE | Q9T0N8: 1w1q 1w1r 1w1s 2qkn 2qpm 3bw7 3c0p 3dq0 3kjm 3s1c 3s1d 3s1e 3s1f

(-) Related Entries Specified in the PDB File

1w1q NATIVE CYTOKININ DEHYDROGENASE IN COMPLEX WITH ISOPENTENYLADENINE
1w1r PLANT CYTOKININ DEHYDROGENASE IN COMPLEX WITH TRANS-ZEATIN
1w1s PLANT CYTOKININ DEHYDROGENASE IN COMPLEX WITH BENZYLAMINOPURINE