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(-) Description

Title :  STRUCTURE OF HUMAN ORNITHINE DECARBOXYLASE IN COMPLEX WITH A C-TERMINAL FRAGMENT OF ANTIZYME
 
Authors :  H. Y. Wu, N. L. Chan
Date :  24 Apr 15  (Deposition) - 02 Sep 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.63
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Tim-Barrel Domain, Beta-Sheet Domain, Decarboxylation, Antizyme, Plasma, Lyase-Lyase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Y. Wu, S. F. Chen, J. Y. Hsieh, F. Chou, Y. H. Wang, W. T. Lin, P. Y. Lee, Y. J. Yu, L. Y. Lin, T. S. Lin, C. L. Lin, G. Y. Liu, S. R. Tzeng, H. C. Hung, N. L. Chan
Structural Basis Of Antizyme-Mediated Regulation Of Polyamine Homeostasis
Proc. Natl. Acad. Sci. Usa V. 112 11229 2015
PubMed-ID: 26305948  |  Reference-DOI: 10.1073/PNAS.1508187112

(-) Compounds

Molecule 1 - ORNITHINE DECARBOXYLASE
    Chains: A
    EC Number: 4.1.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: 28A-ODC
    Expression System Strain: BL-21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 2-421
    Gene: ODC1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ODC
 
Molecule 2 - ORNITHINE DECARBOXYLASE ANTIZYME 1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30-AZ95
    Expression System Strain: BL-21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 95-219
    Gene: OAZ1, OAZ
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ODC-AZ

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
2PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:69 , ASP A:88 , ALA A:111 , HIS A:197 , GLY A:237 , GLU A:274 , GLY A:276 , ARG A:277 , TYR A:389 , MG A:502 , PHE B:192binding site for residue PLP A 501
2AC2SOFTWAREPHE A:238 , GLY A:276 , ARG A:277 , TYR A:278 , PLP A:501binding site for residue MG A 502

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4ZGY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZGY)

(-) 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:383
                                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh...eeeeehhhhhhhhhhhhhhh..eeeeee.hhh.hhhhhhhhhhhh.eeee.hhhhhhhhhh...hhh.eee.....hhhhhhhhhhh...eeee.hhhhhhhhhhhh...eeeee...............hhhhhhhhhhhhhhh..eeeeee.........hhhhhhhhhhhhhhhhhhhhhh....eee.............hhhhhhhhhhhhhhhhhhhhhh.eeee..hhhhhh..eeeeeeeeeeeeeee......eeeeeeee.......hhhhhhhh.....ee.......eeeeee........eeeeeeee.......eeee...................eeee.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zgy A  19 TAKDILDQKINEKDAFYVADLGDILKKHLRWLKALPRVTPFYAVKCNDSKAIVKTLAATGTGFDCASKTEIQLVQSLGVPPERIIYANPCKQVSQIKYAANNGVQMMTFDSEVELMKVARAHPKAKLVLRIATDDSCRLSVKFGATLRTSRLLLERAKELNIDVVGVSFHVGSGCTDPETFVQAISDARCVFDMGAEVGFSMYLLDIGGGFPGSEDVKLKFEEITGVINPALDKYFPSDSGVRIIAEPGRYYVASAFTLAVNIIAKKIVLKEQTGSSEQTFMYYVNDGVYGSFNCILYDHAHVKPLLQKRPEKYYSSSIWGPTCDGLDRIVERCDLPEMHVGDWMLFENMGAYTVASTFNGFQRPTIYYVMSGPAWQLMQQFQ 421
                                    28 ||     44        54        64        74        84        94       104       114       124       134       144       154     ||167       177       187       197       207       217       227       237       247       257       267       277       287       297    || 313       323       333       343||     356       366       376       386     ||398       408       418   
                                      30|                                                                                                                        160|                                                                                                                                       302|                                344|                                         392|                          
                                       37                                                                                                                         164                                                                                                                                        309                                 348                                          395                          


Chain B from PDB  Type:PROTEIN  Length:125
                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...eeeeee....eeeeeee.......eeeeeeee..eeeee........hhhhhhhhhhhhhhhh....eeeeeee....hhhhhhhhhhhhh.ee.............eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zgy B  95 FYSDDRLNVTEELTSNDKTRILNVQSRLTDAKRINWRTVLSGGSLYIEIPGGALPEGSKDSFAVLLEFAEEQLRADHVFICFHKNREDRAALLRTFSFLGFEIVRPGHPLVPKRPDACFMAYTFE 219
                                   104       114       124       134       144       154       164       174       184       194       204       214
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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 4ZGY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (25, 30)

Asymmetric/Biological Unit(hide GO term definitions)

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  4zgy
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  DCOR_HUMAN | P11926
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  OAZ1_HUMAN | P54368
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  4.1.1.17
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 Related Entries

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

UniProtKB/Swiss-Prot
        DCOR_HUMAN | P11926: 1d7k 2on3 2oo0 5bwa
        OAZ1_HUMAN | P54368: 4zgz 5bwa

(-) Related Entries Specified in the PDB File

1zo0 RAT ORNITHINE DECARBOXYLASE ANTIZYME
1d7k HUMAN ORNITHINE DECARBOXYLASE