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(-) Description

Title :  CRYSTAL STRUCTURE AND SUBSTRATE BINDING MODELING OF THE UROPORPHYRINOGEN-III DECARBOXYLASE FROM NICOTIANA TABACUM: IMPLICATIONS FOR THE CATALYTIC MECHANISM
 
Authors :  B. M. Martins, B. Grimm, H. -P. Mock, R. Huber, A. Messerschmidt
Date :  23 May 01  (Deposition) - 17 Oct 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Beta Barrel, Plastidial Enzyme, Crystallographic Dimer, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. M. Martins, B. Grimm, H. -P. Mock, R. Huber, A. Messerschmidt
Crystal Structure And Substrate Binding Modeling Of The Uroporphyrinogen-Iii Decarboxylase From Nicotiana Tabacum. Implications For The Catalytic Mechanism
J. Biol. Chem. V. 276 44108 2001
PubMed-ID: 11524417  |  Reference-DOI: 10.1074/JBC.M104759200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UROPORPHYRINOGEN DECARBOXYLASE
    Chains: A
    EC Number: 4.1.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: COMMON TOBACCO
    Organism Scientific: NICOTIANA TABACUM
    Organism Taxid: 4097
    Synonym: UROD

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 5)

Asymmetric Unit (1, 5)
No.NameCountTypeFull Name
1SO45Ligand/IonSULFATE ION
Biological Unit 1 (1, 10)
No.NameCountTypeFull Name
1SO410Ligand/IonSULFATE ION

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:212 , SER A:214 , TRP A:215 , TYR A:251 , SER A:253 , HIS A:329BINDING SITE FOR RESIDUE SO4 A 584
2AC2SOFTWARELYS A:233 , HOH A:581BINDING SITE FOR RESIDUE SO4 A 585
3AC3SOFTWARESER A:166 , LYS A:167 , ASN A:168 , PHE A:169 , HOH A:538BINDING SITE FOR RESIDUE SO4 A 586
4AC4SOFTWAREARG A:118 , GLU A:119 , LYS A:189BINDING SITE FOR RESIDUE SO4 A 587
5AC5SOFTWAREARG A:137 , HOH A:418 , HOH A:488BINDING SITE FOR RESIDUE SO4 A 588

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1J93)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1J93)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1J93)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UROD_1PS00906 Uroporphyrinogen decarboxylase signature 1.DCUP_TOBAC66-75  1A:27-36
2UROD_2PS00907 Uroporphyrinogen decarboxylase signature 2.DCUP_TOBAC186-202  1A:147-163
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UROD_1PS00906 Uroporphyrinogen decarboxylase signature 1.DCUP_TOBAC66-75  2A:27-36
2UROD_2PS00907 Uroporphyrinogen decarboxylase signature 2.DCUP_TOBAC186-202  2A:147-163

(-) Exons   (0, 0)

(no "Exon" information available for 1J93)

(-) 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:343
 aligned with DCUP_TOBAC | Q42967 from UniProtKB/Swiss-Prot  Length:391

    Alignment length:343
                                    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   
           DCUP_TOBAC    49 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGSGGLLERLPLTGVDVVSLDWTVDMADGRRRLGPNVAIQGNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEIAKGLRY 391
               SCOP domains d1j93a_ A: Uroporphyrinogen decarboxylase, UROD                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1j93A00 A:10-352  [code=3.20.20.210, no name defined]                                                                                                                                                                                                                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhh..................hhhhhhhhh.........hhhhhhhhhhhhhhhhh..eee.....hhhhhhhh..eeee...eeee.....hhhhhhhh...hhhhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeee......hhhhhhhhh..eee.....hhhhhhhhh....eee...hhhhhhhhhhhhhhhhhhhhhhhh...ee...........hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------UROD_1    --------------------------------------------------------------------------------------------------------------UROD_2           --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1j93 A  10 TQPLLLDAVRGKEVERPPVWLMRQAGRYMKSYQLLCEKYPLFRDRSENVDLVVEISLQPWKVFRPDGVILFSDILTPLSGMNIPFDIIKGKGPVIFDPLRTAADVEKVREFIPEKSVPYVGEALTILRKEVNNQAAVLGFVGAPFTLASYVVEGGSSKNFTKIKRLAFAEPKVLHALLQKFATSMAKYIRYQADSGAQAVQIFDSWATELSPVDFEEFSLPYLKQIVDSVKLTHPNLPLILYASGSGGLLERLPLTGVDVVSLDWTVDMADGRRRLGPNVAIQGNVDPGVLFGSKEFITNRINDTVKKAGKGKHILNLGHGIKVGTPEENFAHFFEIAKGLRY 352
                                    19        29        39        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
   Legend:   → Mismatch (orange background)
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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  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1J93)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A   (DCUP_TOBAC | Q42967)
molecular function
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    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:0004853    uroporphyrinogen decarboxylase activity    Catalysis of the reaction: uroporphyrinogen-III = coproporphyrinogen + 4 CO2.
biological process
    GO:0015995    chlorophyll biosynthetic process    The chemical reactions and pathways resulting in the formation of chlorophyll, any compound of magnesium complexed in a porphyrin (tetrapyrrole) ring and which functions as a photosynthetic pigment, from less complex precursors.
    GO:0006779    porphyrin-containing compound biosynthetic process    The chemical reactions and pathways resulting in the formation of any member of a large group of derivatives or analogs of porphyrin. Porphyrin consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.
    GO:0006782    protoporphyrinogen IX biosynthetic process    The chemical reactions and pathways resulting in the formation of protoporphyrinogen IX.
cellular component
    GO:0009507    chloroplast    A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
    GO:0009536    plastid    Any member of a family of organelles found in the cytoplasm of plants and some protists, which are membrane-bounded and contain DNA. Plant plastids develop from a common type, the proplastid.

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