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(-) Description

Title :  CRYSTAL STRUCTURE OF ORNITHINE DECARBOXYLASE FROM ENTAMOEBA HISTOLYTICA.
 
Authors :  P. Preeti, P. Kumar, S. Tomar
Date :  09 Feb 12  (Deposition) - 30 Jan 13  (Release) - 30 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.87
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Preeti, S. Tapas, P. Kumar, S. Tomar
Structural Insight Into Dfmo Resistant Ornithine Decarboxylase From Entamoeba Histolytica: An Inkling To Adaptive Evolution.
Plos One V. 8 53397 2013
PubMed-ID: 23326423  |  Reference-DOI: 10.1371/JOURNAL.PONE.0053397

(-) Compounds

Molecule 1 - ORNITHINE DECARBOXYLASE
    Chains: A, B, C, D
    EC Number: 4.1.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28C
    Expression System Vector Type: PLASMID
    Organism Scientific: ENTAMOEBA HISTOLYTICA
    Organism Taxid: 294381
    Strain: HM-1:IMSS

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4AIB)

(-) Sites  (0, 0)

(no "Site" information available for 4AIB)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro B:385 -Leu B:386

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4AIB)

(-) 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:339
 aligned with Q58P26_ENTHI | Q58P26 from UniProtKB/TrEMBL  Length:413

    Alignment length:382
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384  
         Q58P26_ENTHI     5 SLEVKEFALNLISQFEPENQPLGFWIFDTEGVEKAVERWKKNMPTVRPCFAVKCNPEPHLVKLLGELGCGFDCASLNEIKEVLDLGFNPEDITYSQTFKPYNQLIEASHLGINHTIVDSIDEVQKIAKYAPKMGIMIRIMENDTSAGHVFGEKFGLHDDEVEIVLKEIKDKGLNLDGVHFHVGSDSHNSEVFTKALTKARNTVTLAEQFGMKPYLIDIGGGFSQVAPFEEFAATIEKTIKELEFPERTRFIAEPGRYMASNAFHLVSSLHGKRVRIQNGKKQIEYTSGDGLHGSFGCCIWFEKQKSCECITQKVNENTKMYESIIYGPSCNGSDKVATQELPEMEPGKDWLLFPNMGAYTISMATNFNGFEERNHVIYTLPL 386
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.........eeeeehhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhh..eeee.hhhhhhhhhhh..hhh.eee.....hhhhhhhhhhhh..eeee.hhhhhhhhhhhh...eeeeee.------------......hhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhhhhhhh.....eee.........hhhhhhhhhhhhhhhh......eeee..hhhhhhh.eeeeeeeeeeeeeee..eeeeeeee.....------------...ee..........eeeeeee.------...eeeeee.......eeeeeee.....-------------.eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aib A   5 SLEVKEFALNLISQFEPENQPLGFWIFDTEGVEKAVERWKKNMPTVRPCFAVKCNPEPHLVKLLGELGCGFDCASLNEIKEVLDLGFNPEDITYSQTFKPYNQLIEASHLGINHTIVDSIDEVQKIAKYAPKMGIMIRIM------------KFGLHDDEVEIVLKEIKDKGLNLDGVHFHVGSDSHNSEVFTKALTKARNTVTLAEQFGMKPYLIDIGGGFSQVAPFEEFAATIEKTIKELEFPERTRFIAEPGRYMASNAFHLVSSLHGKRVRIQNGKKQIEYTSGDGLH------------KSCECITQKVNENTKMYESIIYG------DKVATQELPEMEPGKDWLLFPNMGAYTI-------------HVIYTLPL 386
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144         -  |    164       174       184       194       204       214       224       234       244       254       264       274       284       294 |       -    |  314       324      |  -   |   344       354       364|        -    |  384  
                                                                                                                                                                     144          157                                                                                                                                        296          309                   331    338                        365           379       


Chain B from PDB  Type:PROTEIN  Length:328
 aligned with Q58P26_ENTHI | Q58P26 from UniProtKB/TrEMBL  Length:413

    Alignment length:382
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384  
         Q58P26_ENTHI     5 SLEVKEFALNLISQFEPENQPLGFWIFDTEGVEKAVERWKKNMPTVRPCFAVKCNPEPHLVKLLGELGCGFDCASLNEIKEVLDLGFNPEDITYSQTFKPYNQLIEASHLGINHTIVDSIDEVQKIAKYAPKMGIMIRIMENDTSAGHVFGEKFGLHDDEVEIVLKEIKDKGLNLDGVHFHVGSDSHNSEVFTKALTKARNTVTLAEQFGMKPYLIDIGGGFSQVAPFEEFAATIEKTIKELEFPERTRFIAEPGRYMASNAFHLVSSLHGKRVRIQNGKKQIEYTSGDGLHGSFGCCIWFEKQKSCECITQKVNENTKMYESIIYGPSCNGSDKVATQELPEMEPGKDWLLFPNMGAYTISMATNFNGFEERNHVIYTLPL 386
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.........eeeeehhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhh..eeee.hhhhhhhhhhh......eee.....hhhhhhhhhhhh..eeee.hhhhhhhhhhhh...eeeeee.---------------...hhhhhhhhhhhhh...eeeeee..------hhhhhhhhhhhhhhhhhhhhhh....eee......--..hhhhhhhhhhhhhhhh.....eeee..hhhhhhh.eeeeeeeeeeeeeee..eeeeeeee.----------------...............eeeeeee.....--.eeeeeeee.......eeee........-------------.eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aib B   5 SLEVKEFALNLISQFEPENQPLGFWIFDTEGVEKAVERWKKNMPTVRPCFAVKCNPEPHLVKLLGELGCGFDCASLNEIKEVLDLGFNPEDITYSQTFKPYNQLIEASHLGINHTIVDSIDEVQKIAKYAPKMGIMIRIM---------------LHDDEVEIVLKEIKDKGLNLDGVHFHV------SEVFTKALTKARNTVTLAEQFGMKPYLIDIGGGFS--APFEEFAATIEKTIKELEFPERTRFIAEPGRYMASNAFHLVSSLHGKRVRIQNGKKQIEYTSG----------------KSCECITQKVNENTKMYESIIYGPSCN--DKVATQELPEMEPGKDWLLFPNMGAYTI-------------HVIYTLPL 386
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144         -     | 164       174       184 |     194       204       214       224  |  | 234       244       254       264       274       284       | -         -    |  314       324       334|  |   344       354       364|        -    |  384  
                                                                                                                                                                     144             160                       186    193                               227  |                                                           292              309                       335  |                        365           379       
                                                                                                                                                                                                                                                           230                                                                                                         338                                                


Chain C from PDB  Type:PROTEIN  Length:323
 aligned with Q58P26_ENTHI | Q58P26 from UniProtKB/TrEMBL  Length:413

    Alignment length:384
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384    
         Q58P26_ENTHI     5 SLEVKEFALNLISQFEPENQPLGFWIFDTEGVEKAVERWKKNMPTVRPCFAVKCNPEPHLVKLLGELGCGFDCASLNEIKEVLDLGFNPEDITYSQTFKPYNQLIEASHLGINHTIVDSIDEVQKIAKYAPKMGIMIRIMENDTSAGHVFGEKFGLHDDEVEIVLKEIKDKGLNLDGVHFHVGSDSHNSEVFTKALTKARNTVTLAEQFGMKPYLIDIGGGFSQVAPFEEFAATIEKTIKELEFPERTRFIAEPGRYMASNAFHLVSSLHGKRVRIQNGKKQIEYTSGDGLHGSFGCCIWFEKQKSCECITQKVNENTKMYESIIYGPSCNGSDKVATQELPEMEPGKDWLLFPNMGAYTISMATNFNGFEERNHVIYTLPLKS 388
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.........eeeeehhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhh..eeee.hhhhhhhhhhh......eee.....hhhhhhhhhhhh..eeee.hhhhhhhhhhhh...eeeeee.------------------hhhhhhhhhhhhh...eeeeee..------.hhhhhhhhhhhhhhhhhhhh.....eee......--..hhhhhhhhhhhhhhhh.....eeee..hhhhhh..eeeeee..eeeeeee..eeeeeee..----------------................eeeeee.------...eeeee........eeee........-------------.eeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4aib C   5 SLEVKEFALNLISQFEPENQPLGFWIFDTEGVEKAVERWKKNMPTVRPCFAVKCNPEPHLVKLLGELGCGFDCASLNEIKEVLDLGFNPEDITYSQTFKPYNQLIEASHLGINHTIVDSIDEVQKIAKYAPKMGIMIRIM------------------DEVEIVLKEIKDKGLNLDGVHFHV------SEVFTKALTKARNTVTLAEQFGMKPYLIDIGGGFS--APFEEFAATIEKTIKELEFPERTRFIAEPGRYMASNAFHLVSSLHGKRVRIQNGKKQIEYTSG----------------KSCECITQKVNENTKMYESIIYG------DKVATQELPEMEPGKDWLLFPNMGAYTI-------------HVIYTLPLKS 388
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144         -       164       174       184 |     194       204       214       224  |  | 234       244       254       264       274       284       | -         -    |  314       324      |  -   |   344       354       364|        -    |  384    
                                                                                                                                                                     144                163                    186    193                               227  |                                                           292              309                   331    338                        365           379         
                                                                                                                                                                                                                                                           230                                                                                                                                                              


Chain D from PDB  Type:PROTEIN  Length:325
 aligned with Q58P26_ENTHI | Q58P26 from UniProtKB/TrEMBL  Length:413

    Alignment length:382
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384  
         Q58P26_ENTHI     5 SLEVKEFALNLISQFEPENQPLGFWIFDTEGVEKAVERWKKNMPTVRPCFAVKCNPEPHLVKLLGELGCGFDCASLNEIKEVLDLGFNPEDITYSQTFKPYNQLIEASHLGINHTIVDSIDEVQKIAKYAPKMGIMIRIMENDTSAGHVFGEKFGLHDDEVEIVLKEIKDKGLNLDGVHFHVGSDSHNSEVFTKALTKARNTVTLAEQFGMKPYLIDIGGGFSQVAPFEEFAATIEKTIKELEFPERTRFIAEPGRYMASNAFHLVSSLHGKRVRIQNGKKQIEYTSGDGLHGSFGCCIWFEKQKSCECITQKVNENTKMYESIIYGPSCNGSDKVATQELPEMEPGKDWLLFPNMGAYTISMATNFNGFEERNHVIYTLPL 386
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.........eeeeehhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhh.eeee.hhhhhhhhhhh..hhh.eee.....hhhhhhhhhhhh..eeee.hhhhhhhhhhhh...eeeeee.------------------hhhhhhhhhhhhh...eeeeee..------.hhhhhhhhhhhhhhhhhhhhh....eee......--..hhhhhhhhhhhhhhhh.....eeee..hhhhhh..eeeeeeeeeeeeeee..eeeeeeee.------------...................eeeeeee.------.eeeeeeee.......eeee........-------------.eeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4aib D   5 SLEVKEFALNLISQFEPENQPLGFWIFDTEGVEKAVERWKKNMPTVRPCFAVKCNPEPHLVKLLGELGCGFDCASLNEIKEVLDLGFNPEDITYSQTFKPYNQLIEASHLGINHTIVDSIDEVQKIAKYAPKMGIMIRIM------------------DEVEIVLKEIKDKGLNLDGVHFHV------SEVFTKALTKARNTVTLAEQFGMKPYLIDIGGGFS--APFEEFAATIEKTIKELEFPERTRFIAEPGRYMASNAFHLVSSLHGKRVRIQNGKKQIEYTSG------------FEKQKSCECITQKVNENTKMYESIIYG------DKVATQELPEMEPGKDWLLFPNMGAYTI-------------HVIYTLPL 386
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144         -       164       174       184 |     194       204       214       224  |  | 234       244       254       264       274       284       | -         -|      314       324      |  -   |   344       354       364|        -    |  384  
                                                                                                                                                                     144                163                    186    193                               227  |                                                           292          305                       331    338                        365           379       
                                                                                                                                                                                                                                                           230
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q58P26_ENTHI | Q58P26)
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:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0004586    ornithine decarboxylase activity    Catalysis of the reaction: L-ornithine + H(+) = CO(2) + putrescine.
biological process
    GO:0006596    polyamine biosynthetic process    The chemical reactions and pathways resulting in the formation of polyamines, any organic compound containing two or more amino groups.
    GO:0033387    putrescine biosynthetic process from ornithine    The chemical reactions and pathways resulting in the formation of putrescine, 1,4-diaminobutane by decarboxylation of ornithine.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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