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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 :  2.04
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (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
    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

  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  (4, 40)

Asymmetric Unit (4, 40)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3GOL3Ligand/IonGLYCEROL
4IPA29Ligand/IonISOPROPYL ALCOHOL
Biological Unit 1 (4, 24)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3GOL1Ligand/IonGLYCEROL
4IPA17Ligand/IonISOPROPYL ALCOHOL
Biological Unit 2 (4, 16)
No.NameCountTypeFull Name
1EDO1Ligand/Ion1,2-ETHANEDIOL
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3GOL2Ligand/IonGLYCEROL
4IPA12Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (40, 40)

Asymmetric Unit (40, 40)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPHE 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 , 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:507 , EDO A:608 , IPA A:610 , HOH A:702 , HOH A:712 , HOH A:727BINDING SITE FOR RESIDUE FAD A 601
02AC2SOFTWAREASP A:414 , ASN A:415 , THR A:417 , VAL A:419 , HOH A:812BINDING SITE FOR RESIDUE IPA A 602
03AC3SOFTWAREASP A:132 , GLN A:189 , LEU A:190 , GLU A:191 , ARG A:226BINDING SITE FOR RESIDUE IPA A 603
04AC4SOFTWAREPHE A:55 , ARG A:96 , HIS A:98 , GLY A:99 , GLU A:368BINDING SITE FOR RESIDUE IPA A 604
05AC5SOFTWARETRP A:413 , ASP A:414 , ASN A:415BINDING SITE FOR RESIDUE EDO A 605
06AC6SOFTWARELEU A:31 , SER A:32 , GLY A:35 , PHE A:45 , ALA B:363BINDING SITE FOR RESIDUE IPA A 606
07AC7SOFTWAREVAL A:187 , PRO A:204 , ASP A:414 , HOH A:755BINDING SITE FOR RESIDUE EDO A 607
08AC8SOFTWAREASP A:158 , FAD A:601BINDING SITE FOR RESIDUE EDO A 608
09AC9SOFTWAREPRO A:372 , LEU A:374 , LEU A:395 , PHE A:432 , SER A:434 , ALA A:448 , ASN A:452BINDING SITE FOR RESIDUE GOL A 609
10BC1SOFTWARETRP A:373 , ASN A:375 , LEU A:404 , FAD A:601BINDING SITE FOR RESIDUE IPA A 610
11BC2SOFTWAREPHE A:61 , GLY A:104 , GLN A:107 , ALA A:109 , PRO A:505 , GLY A:506 , ARG A:508BINDING SITE FOR RESIDUE IPA A 611
12BC3SOFTWAREPHE A:178 , ILE A:259 , ALA A:261 , LYS A:412BINDING SITE FOR RESIDUE IPA A 612
13BC4SOFTWAREGLN A:58 , SER A:60 , PHE A:61BINDING SITE FOR RESIDUE IPA A 613
14BC5SOFTWARECYS A:459 , GLU A:460 , ASP A:463 , GLY A:465 , MET A:466BINDING SITE FOR RESIDUE IPA A 614
15BC6SOFTWAREGLY A:129 , LYS A:154 , ALA A:230 , LEU A:231BINDING SITE FOR RESIDUE IPA A 615
16BC7SOFTWAREARG A:179 , HIS A:180 , SER A:185BINDING SITE FOR RESIDUE IPA A 616
17BC8SOFTWAREALA A:363 , LEU B:31 , SER B:32 , PHE B:45BINDING SITE FOR RESIDUE IPA A 617
18BC9SOFTWARETYR A:473 , GLN A:478BINDING SITE FOR RESIDUE IPA A 618
19CC1SOFTWAREGLU A:87 , SER A:89 , PRO A:90 , LYS A:512BINDING SITE FOR RESIDUE IPA A 619
20CC2SOFTWAREPRO A:370 , ALA A:436 , PRO A:437 , SER A:438 , LEU A:439 , LEU B:439BINDING SITE FOR RESIDUE IPA A 620
21CC3SOFTWARELEU A:439 , PRO B:437BINDING SITE FOR RESIDUE IPA A 621
22CC4SOFTWAREHIS A:127 , ASP A:128 , GLY A:129 , LEU A:151BINDING SITE FOR RESIDUE IPA A 622
23CC5SOFTWARELYS A:467 , THR A:481 , GLY A:484 , ALA A:485BINDING SITE FOR RESIDUE EDO A 623
24CC6SOFTWAREHIS A:46 , HOH A:797 , ARG B:362 , SER B:365 , HOH B:847BINDING SITE FOR RESIDUE EDO A 624
25CC7SOFTWAREPHE B:61 , GLY B:104 , GLN B:107 , PRO B:505 , GLY B:506 , ARG B:508BINDING SITE FOR RESIDUE IPA B 601
26CC8SOFTWAREPHE 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:165 , 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 , EDO B:605 , IPA B:609 , HOH B:723 , HOH B:730 , HOH B:736BINDING SITE FOR RESIDUE FAD B 602
27CC9SOFTWAREARG B:96 , HIS B:98 , GLY B:99 , HIS B:100 , TRP B:367 , GLU B:368 , HOH B:726BINDING SITE FOR RESIDUE GOL B 603
28DC1SOFTWAREILE B:259 , ALA B:261BINDING SITE FOR RESIDUE IPA B 604
29DC2SOFTWAREFAD B:602BINDING SITE FOR RESIDUE EDO B 605
30DC3SOFTWARETYR B:473 , GLN B:478BINDING SITE FOR RESIDUE IPA B 606
31DC4SOFTWARECYS B:459 , GLU B:460 , GLY B:465 , MET B:466BINDING SITE FOR RESIDUE IPA B 607
32DC5SOFTWARETRP B:240 , THR B:343BINDING SITE FOR RESIDUE IPA B 608
33DC6SOFTWAREASP B:158 , TRP B:373 , ASN B:375 , LEU B:404 , FAD B:602BINDING SITE FOR RESIDUE IPA B 609
34DC7SOFTWARECYS B:59 , SER B:60 , PHE B:61BINDING SITE FOR RESIDUE IPA B 610
35DC8SOFTWAREASP B:132 , GLN B:189 , ARG B:226 , ARG B:228 , HOH B:813BINDING SITE FOR RESIDUE IPA B 611
36DC9SOFTWAREASP B:414 , ASN B:415 , THR B:417 , VAL B:419BINDING SITE FOR RESIDUE IPA B 612
37EC1SOFTWAREPRO B:372 , PHE B:432 , SER B:434 , ALA B:448 , ASN B:452BINDING SITE FOR RESIDUE IPA B 613
38EC2SOFTWAREHIS B:127 , ASP B:128BINDING SITE FOR RESIDUE IPA B 614
39EC3SOFTWAREASP B:128 , GLY B:129 , PHE B:130 , LYS B:154 , LEU B:231BINDING SITE FOR RESIDUE GOL B 615
40EC4SOFTWAREHIS B:180 , SER B:185BINDING SITE FOR RESIDUE IPA B 616

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (7, 7)

Asymmetric Unit
No.Residues
1Gly A:121 -Ala A:122
2Gln A:290 -Asp A:291
3Gly A:443 -Ser A:444
4Glu B:87 -Gly B:88
5Gly B:121 -Ala B:122
6Gly B:443 -Ser B:444
7Lys B:512 -Ala B:513

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MLA)

(-) 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:477
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.....eee...hhhhhh...........eeee..hhhhhhhhhhhhhhhhhhh...eeee...............eeee.hhhh....eee..eeeee...hhhhhhhhhhh..eee.........hhhhhhh......hhhhhhhhhh.eeeeeeee....eeee....hhhhhhhhh......eeeeeeeeeeee...eeeeeeeee.hhhhhhhhhhhhhhh.....eeeeeeee...hhhhhhh...ee....eeeeeeeeeeehhhhhhhhhhhhhhhhhh...eeeeeeeeeeehhhhhhhhhhhhhhhhhh.........eeeeee..hhhhhhhhhhhh.........eeeeeee.hhh............eeeeeee...........hhhhhhhhhhhhhhhhhhh....ee......hhhhhhhhhh.hhhhhhhhhhhhh.....hhhhh....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mla A  29 DMLSPLGALRLDGHFSFHDVSAMARDFGNQCSFLPAAVLHPGSVSDIAATVRHVFSLGEGSPLTVAARGHGHSLMGQSQAAQGIVVRMESLRGARLQVHDGFVDAPGGELWINVLRETLKHGLAPKSWTDYLHLTVGGTLSNAGVSGQAFRHGPQVSNVNQLEIVTGRGDVVTCSPEDNSDLFYAALGGLGQFGIITRARIALEPAPEMVRWIRVLYSDFESFTEDQEMLIMAENSFDYIEGFVIINRTGILNNWRASFKPQDPRVLYCLELTKNFNSGDTDTMEQEVAVLLSRLRFIQSTLFHTDVTYLEFLDRVHTSELKLRAQSLWEVPHPWLNLLIPRSSIRRFATEVFGRILKDSNNGPILLYPVNKSKWDNKTSVVIPDEEIFYLVGFLSSAPSLSGHGSIAHAMSLNSQIVEFCEEADIGMKQYLAHYTTQEQWKTHFGARWETFERRKHRYDPLAILAPGQRIFPKASL 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   ||  308       318       328       338       348       358       368       378       388       398       408       418       428       438       448       458       468       478       488       498       508       
                                                                                                                                                                                                                                                                                                 292|                                                                                                                                                                                                                    
                                                                                                                                                                                                                                                                                                  303                                                                                                                                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:460
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.....eee...hhhhh............eeee..hhhhhhhhhhhhhhh.......eeee...............eeee.hhhh....eee..eeeee...hhhhhhhhhhh..eee.........hhhhhhh......hhhhhhhhhh.eeeeeeee....eeee....hhhhhhhhh......eeeeeeeeeeee...eeeeeeeee.hhhhhhhhhhhhh.......eeeeeee....eeeeeeeeeehhhhhhhhhhhhhhhhhh...hhhhheeeeeehhhhhhhhhhhhhhhhhh.........eeeeee..hhhhhhhhhhhh.........eeeeeee.hhh............eeeeeee...........hhhhhhhhhhhhhhhhhhh....ee......hhhhhhhhhh.hhhhhhhhhhhhh.....hhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mla B  29 DMLSPLGALRLDGHFSFHDVSAMARDFGNQCSFLPAAVLHPGSVSDIAATVRHVFSLGEGSPLTVAARGHGHSLMGQSQAAQGIVVRMESLRGARLQVHDGFVDAPGGELWINVLRETLKHGLAPKSWTDYLHLTVGGTLSNAGVSGQAFRHGPQVSNVNQLEIVTGRGDVVTCSPEDNSDLFYAALGGLGQFGIITRARIALEPAPEMVRWIRVLYSDFESFTEDQEMLIMAENSFDYIEGFVIINRVLYCLELTKNFNSGDTDTMEQEVAVLLSRLRFIQSTLFHTDVTYLEFLDRVHTSELKLRAQSLWEVPHPWLNLLIPRSSIRRFATEVFGRILKDSNNGPILLYPVNKSKWDNKTSVVIPDEEIFYLVGFLSSAPSLSGHGSIAHAMSLNSQIVEFCEEADIGMKQYLAHYTTQEQWKTHFGARWETFERRKHRYDPLAILAPGQRIFPKASL 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      |305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515
                                                                                                                                                                                                                                                                                275|                                                                                                                                                                                                                    
                                                                                                                                                                                                                                                                                 303
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  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  (0, 0)

(no "SCOP Domain" information available for 4MLA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gln A:290 - Asp A:291   [ RasMol ]  
    Glu B:87 - Gly B:88   [ RasMol ]  
    Gly A:121 - Ala A:122   [ RasMol ]  
    Gly A:443 - Ser A:444   [ RasMol ]  
    Gly B:121 - Ala B:122   [ RasMol ]  
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    Lys B:512 - Ala B:513   [ RasMol ]  
 
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        Q709Q5_MAIZE | Q709Q5: 4ml8

(-) Related Entries Specified in the PDB File

3s1d 4ml8