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(-) Description

Title :  STRUCTURE OF MAIZE CYTOKININ OXIDASE/DEHYDROGENASE 2 (ZMCKO2)
 
Authors :  S. Morera, D. Kopecny, P. Briozzo, R. Koncitikova
Date :  06 Sep 13  (Deposition) - 11 Mar 15  (Release) - 23 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Oxidoreductase, Fad Binding Protein, Flavoprotein, Cytokinin Oxidase/Dehydrogenase, Cytokinin Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Kopecny, R. Koncitikova, H. Popelka, P. Briozzo, A. Vigouroux, M. Kopecna, D. Zalabak, M. Sebela, J. Skopalova, I. Frebort, S. Morera
Kinetic And Structural Investigation Of The Cytokinin Oxidase/Dehydrogenase Active Site.
Febs J. V. 283 361 2016
PubMed-ID: 26519657  |  Reference-DOI: 10.1111/FEBS.13581

(-) Compounds

Molecule 1 - CYTOKININ OXIDASE 2
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PTYB12
    Gene: CKO2
    Organism Common: MAIZE
    Organism Scientific: ZEA MAYS
    Organism Taxid: 4577

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 5)
No.NameCountTypeFull Name
1FAD4Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:55 , ALA A:95 , GLY A:97 , HIS A:98 , GLY A:99 , HIS A:100 , SER A:101 , GLN A:105 , SER A:106 , THR A:157 , ASP A:158 , TYR A:159 , LEU A:162 , THR A:163 , GLY A:165 , GLY A:166 , THR A:167 , SER A:169 , ASN A:170 , GLY A:172 , VAL A:173 , GLY A:219 , GLY A:222 , ILE A:223 , ILE A:224 , TRP A:373 , TYR A:469 , GLN A:507BINDING SITE FOR RESIDUE FAD A 601
2AC2SOFTWAREARG A:53 , ARG A:96 , HIS A:98 , GLY A:99 , HIS A:100 , TYR A:159 , TRP A:367 , GLU A:368 , HOH A:727BINDING SITE FOR RESIDUE PEG A 602
3AC3SOFTWAREPHE B:55 , ALA B:95 , GLY B:97 , HIS B:98 , GLY B:99 , HIS B:100 , SER B:101 , GLN B:105 , SER B:106 , THR B:157 , ASP B:158 , TYR B:159 , THR B:163 , GLY B:166 , THR B:167 , SER B:169 , ASN B:170 , GLY B:172 , VAL B:173 , GLY B:219 , GLY B:222 , ILE B:223 , ILE B:224 , TRP B:373 , TYR B:469 , GLN B:507 , HOH B:721BINDING SITE FOR RESIDUE FAD B 601
4AC4SOFTWAREPHE C:55 , ALA C:95 , GLY C:97 , HIS C:98 , GLY C:99 , HIS C:100 , SER C:101 , GLN C:105 , SER C:106 , THR C:157 , ASP C:158 , TYR C:159 , LEU C:162 , THR C:163 , GLY C:165 , GLY C:166 , THR C:167 , SER C:169 , ASN C:170 , GLY C:172 , VAL C:173 , GLY C:219 , GLY C:222 , ILE C:223 , ILE C:224 , TRP C:373 , TYR C:469 , GLN C:507 , HOH C:719BINDING SITE FOR RESIDUE FAD C 601
5AC5SOFTWAREPHE D:55 , ALA D:95 , GLY D:97 , HIS D:98 , GLY D:99 , HIS D:100 , SER D:101 , GLN D:105 , SER D:106 , THR D:157 , ASP D:158 , TYR D:159 , LEU D:162 , THR D:163 , GLY D:166 , THR D:167 , SER D:169 , ASN D:170 , GLY D:172 , VAL D:173 , GLY D:219 , GLY D:222 , ILE D:223 , ILE D:224 , TRP D:373 , TYR D:469 , GLN D:507BINDING SITE FOR RESIDUE FAD D 601

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ML8)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Gly A:443 -Ser A:444
2Asp B:301 -Gly B:302
3Gly B:302 -Arg B:303
4Gly B:443 -Ser B:444
5Asp C:301 -Gly C:302
6Gly C:443 -Ser C:444
7Gly D:302 -Arg D:303
8Gly D:443 -Ser D:444

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ML8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ML8)

(-) Exons   (0, 0)

(no "Exon" information available for 4ML8)

(-) 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:488
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh....eee...hhhhhh...........eeee..hhhhhhhhhhhhhhh.......eeee...............eeee.hhh.....eee..eeeee...hhhhhhhhhhh..eee.........hhhhhhh......hhhhhhhhhh.eeeeeeee....eeee....hhhhhhhhh......eeeeeeeeeeee...eeeeeeeee.hhhhhhhhhhhhhhh.....eeeeeee..............ee.hhhhhh........eeeeeeeeeehhhhhhhhhhhhhhhhh....hhhh.eeeeeehhhhhhhhhhhhhhhhhh.........eeeeee..hhhhhhhhhhhh.........eeeeeee.hhh............eeeeeee...........hhhhhhhhhhhhhhhhhhh....ee......hhhhhhhhhh.hhhhhhhhhhhhh.....hhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ml8 A  29 DMLSPLGALRLDGHFSFHDVSAMARDFGNQCSFLPAAVLHPGSVSDIAATVRHVFSLGEGSPLTVAARGHGHSLMGQSQAAQGIVVRMESLRGARLQVHDGFVDAPGGELWINVLRETLKHGLAPKSWTDYLHLTVGGTLSNAGVSGQAFRHGPQVSNVNQLEIVTGRGDVVTCSPEDNSDLFYAALGGLGQFGIITRARIALEPAPEMVRWIRVLYSDFESFTEDQEMLIMAENSFDYIEGFVIINRTGILNNWRASFKPQDPVQASHFQSDGRVLYCLELTKNFNSGDTDTMEQEVAVLLSRLRFIQSTLFHTDVTYLEFLDRVHTSELKLRAQSLWEVPHPWLNLLIPRSSIRRFATEVFGRILKDSNNGPILLYPVNKSKWDNKTSVVIPDEEIFYLVGFLSSAPSLSGHGSIAHAMSLNSQIVEFCEEADIGMKQYLAHYTTQEQWKTHFGARWETFERRKHRYDPLAILAPGQRIFPKASLP 516
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508        


Chain B from PDB  Type:PROTEIN  Length:487
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eee...hhhhhh...........eeee..hhhhhhhhhhhhhhh.......eeee...............eeee.hhh.....eee..eeeee...hhhhhhhhhh...eee.........hhhhhhh......hhhhhhhhhh.eeeeeeee....eeee....hhhhhhhhh......eeeeeeeeeeee...eeeeeeeee.hhhhhhhhhhhhhhh.....eeeeeee....hhhhhhh...ee.hhhhhhh.......eeeeeeeeeehhhhhhhhhhhhhhhhhh...eeeeeeeeeeehhhhhhhhhhhhhhhhhh.........eeeeee..hhhhhhhhhh...........eeeeeee.hhh............eeeeeee...........hhhhhhhhhhhhhhhhhhh....ee......hhhhhhhhhh.hhhhhhhhhhhhh.....hhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ml8 B  29 DMLSPLGALRLDGHFSFHDVSAMARDFGNQCSFLPAAVLHPGSVSDIAATVRHVFSLGEGSPLTVAARGHGHSLMGQSQAAQGIVVRMESLRGARLQVHDGFVDAPGGELWINVLRETLKHGLAPKSWTDYLHLTVGGTLSNAGVSGQAFRHGPQVSNVNQLEIVTGRGDVVTCSPEDNSDLFYAALGGLGQFGIITRARIALEPAPEMVRWIRVLYSDFESFTEDQEMLIMAENSFDYIEGFVIINRTGILNNWRASFKPQDPVQASHFQSDGRVLYCLELTKNFNSGDTDTMEQEVAVLLSRLRFIQSTLFHTDVTYLEFLDRVHTSELKLRAQSLWEVPHPWLNLLIPRSSIRRFATEVFGRILKDSNNGPILLYPVNKSKWDNKTSVVIPDEEIFYLVGFLSSAPSLSGHGSIAHAMSLNSQIVEFCEEADIGMKQYLAHYTTQEQWKTHFGARWETFERRKHRYDPLAILAPGQRIFPKASL 515
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       


Chain C from PDB  Type:PROTEIN  Length:488
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh....eee...hhhhhh...........eeee..hhhhhhhhhhhhhhh.......eeee...............eeee.hhh.....eee..eeeee...hhhhhhhhhhh..eee.........hhhhhhh......hhhhhhhhhh.eeeeeeee....eeee....hhhhhhhhh......eeeeeeeeeeee...eeeeeeeee.hhhhhhhhhhhhh.......eeeeeee..............ee.hhhhhhh.......eeeeeeeeeehhhhhhhhhhhhhhhhh....hhhh.eeeeeehhhhhhhhhhhhhhhhhh.........eeeeee..hhhhhhhhhh...........eeeeeee.hhh............eeeeeee...........hhhhhhhhhhhhhhhhhhh....ee......hhhhhhhhhh.hhhhhhhhhhhhh.....hhhhh........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ml8 C  29 DMLSPLGALRLDGHFSFHDVSAMARDFGNQCSFLPAAVLHPGSVSDIAATVRHVFSLGEGSPLTVAARGHGHSLMGQSQAAQGIVVRMESLRGARLQVHDGFVDAPGGELWINVLRETLKHGLAPKSWTDYLHLTVGGTLSNAGVSGQAFRHGPQVSNVNQLEIVTGRGDVVTCSPEDNSDLFYAALGGLGQFGIITRARIALEPAPEMVRWIRVLYSDFESFTEDQEMLIMAENSFDYIEGFVIINRTGILNNWRASFKPQDPVQASHFQSDGRVLYCLELTKNFNSGDTDTMEQEVAVLLSRLRFIQSTLFHTDVTYLEFLDRVHTSELKLRAQSLWEVPHPWLNLLIPRSSIRRFATEVFGRILKDSNNGPILLYPVNKSKWDNKTSVVIPDEEIFYLVGFLSSAPSLSGHGSIAHAMSLNSQIVEFCEEADIGMKQYLAHYTTQEQWKTHFGARWETFERRKHRYDPLAILAPGQRIFPKASLP 516
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508        


Chain D from PDB  Type:PROTEIN  Length:479
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh....eee...hhhhh............eeee..hhhhhhhhhhhhhh........eeee...............eeee.hhh.....eee..eeeee...hhhhhhhhhhh..eee.........hhhhhhh......hhhhhhhhhh.eeeeeeee....eeee....hhhhhhhhh......eeeeeeeeeeee...eeeeeeeee.hhhhhhhhhhhhhhh.....eeeeeeee...hhhhhhh...ee.......eeeeeeeeeeehhhhhhhhhhhhhhhhhh...eeeeeeeeeeehhhhhhhhhhhhhhhhhh.........eeeeee..hhhhhhhhhhh....hhhhh.eeeeeee.hhh............eeeeeee...........hhhhhhhhhhhhhhhhhhh....ee......hhhhhhhhhh.hhhhhhhhhhhhh.....hhhhh...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ml8 D  29 DMLSPLGALRLDGHFSFHDVSAMARDFGNQCSFLPAAVLHPGSVSDIAATVRHVFSLGEGSPLTVAARGHGHSLMGQSQAAQGIVVRMESLRGARLQVHDGFVDAPGGELWINVLRETLKHGLAPKSWTDYLHLTVGGTLSNAGVSGQAFRHGPQVSNVNQLEIVTGRGDVVTCSPEDNSDLFYAALGGLGQFGIITRARIALEPAPEMVRWIRVLYSDFESFTEDQEMLIMAENSFDYIEGFVIINRTGILNNWRASFKPQDPVQGRVLYCLELTKNFNSGDTDTMEQEVAVLLSRLRFIQSTLFHTDVTYLEFLDRVHTSELKLRAQSLWEVPHPWLNLLIPRSSIRRFATEVFGRILKDSNNGPILLYPVNKSKWDNKTSVVIPDEEIFYLVGFLSSAPSLSGHGSIAHAMSLNSQIVEFCEEADIGMKQYLAHYTTQEQWKTHFGARWETFERRKHRYDPLAILAPGQRIFPKAS 514
                                    38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288     ||305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505         
                                                                                                                                                                                                                                                                                                   294|                                                                                                                                                                                                                    
                                                                                                                                                                                                                                                                                                    302
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  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 4ML8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ML8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ML8)

(-) Gene Ontology  (8, 8)

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 Related Entries

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        Q709Q5_MAIZE | Q709Q5: 4mla

(-) Related Entries Specified in the PDB File

1s1d 4mla