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(-) Description

Title :  CRYSTAL STRUCTURE OF UROPORPHYRINOGEN DECARBOXYLASE FROM AQUIFEX AEOLICUS
 
Authors :  B. Bagautdinov, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  16 Mar 07  (Deposition) - 18 Mar 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Uroporphyrinogen Decarboxylase, Dimer, X-Ray Diffraction, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Bagautdinov, N. Kunishima
Crystal Structure Of Uroporphyrinogen Decarboxylase From Aquifex Aeolicus
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - UROPORPHYRINOGEN DECARBOXYLASE
    Chains: A, B
    EC Number: 4.1.1.37
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A
    Expression System Strain: (DE3)RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363
    Synonym: URO-D, UPD

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:175 , TYR A:218BINDING SITE FOR RESIDUE ACT A 1209

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2EJA)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:277 -Asn A:278
2Gly B:277 -Asn B:278

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2EJA)

(-) PROSITE Motifs  (2, 4)

Asymmetric/Biological Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UROD_1PS00906 Uroporphyrinogen decarboxylase signature 1.DCUP_AQUAE20-29
 		  2A:20-29
B:20-29
2UROD_2PS00907 Uroporphyrinogen decarboxylase signature 2.DCUP_AQUAE134-150
 		  2A:134-150
B:134-150

(-) Exons   (0, 0)

(no "Exon" information available for 2EJA)

(-) 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:337
 aligned with DCUP_AQUAE | O66667 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:337
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       
           DCUP_AQUAE     2 PKNDLLLRSLRGEPIGRFPVWLMRQAGRYMPEYRKIRNRVKNFLELCKNVDLATEISLLPLKILGVDAIIIFSDILVPLEPLGVKVEFVEGEGPKLSWSGKVSDLKKYDPSQNAYVYEIIKRVKEAQDEVPVIGFAGAPFTLLSYLIEGGASKDFKSTKLFMWENPKEYKRLMDILTETVLAYLKEQIKAGADVVQIFDSWVNNLSLEDYGEYVYPYVNYLISELKDFSDTPVIYFFRGSSSFIDLAVDYRADALSVDWSVDIPELFKIYDKGFQGNLEPAVLYASEEVIEEKTLGLLRRIPVKTRYVFNLGHGLAPDMELEKVKYLVDLVKSFPLT 338
               SCOP domains d2ejaa_ A: automated matches                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2ejaA00 A:2-338  [code=3.20.20.210, no name defined]                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh..................hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...ee.....hhhhhhhh.eeeee...eeeee...hhhhh...hhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhh.....eee.....hhhhhhhhh..eee...hhhhhhhhhhhhhhhhhhhhh.......ee...........hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------UROD_1    --------------------------------------------------------------------------------------------------------UROD_2           -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2eja A   2 PKNDLLLRSLRGEPIGRFPVWLMRQAGRYMPEYRKIRNRVKNFLELCKNVDLATEISLLPLKILGVDAIIIFSDILVPLEPLGVKVEFVEGEGPKLSWSGKVSDLKKYDPSQNAYVYEIIKRVKEAQDEVPVIGFAGAPFTLLSYLIEGGASKDFKSTKLFMWENPKEYKRLMDILTETVLAYLKEQIKAGADVVQIFDSWVNNLSLEDYGEYVYPYVNYLISELKDFSDTPVIYFFRGSSSFIDLAVDYRADALSVDWSVDIPELFKIYDKGFQGNLEPAVLYASEEVIEEKTLGLLRRIPVKTRYVFNLGHGLAPDMELEKVKYLVDLVKSFPLT 338
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       


Chain B from PDB  Type:PROTEIN  Length:336
 aligned with DCUP_AQUAE | O66667 from UniProtKB/Swiss-Prot  Length:338

    Alignment length:336
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331      
           DCUP_AQUAE     2 PKNDLLLRSLRGEPIGRFPVWLMRQAGRYMPEYRKIRNRVKNFLELCKNVDLATEISLLPLKILGVDAIIIFSDILVPLEPLGVKVEFVEGEGPKLSWSGKVSDLKKYDPSQNAYVYEIIKRVKEAQDEVPVIGFAGAPFTLLSYLIEGGASKDFKSTKLFMWENPKEYKRLMDILTETVLAYLKEQIKAGADVVQIFDSWVNNLSLEDYGEYVYPYVNYLISELKDFSDTPVIYFFRGSSSFIDLAVDYRADALSVDWSVDIPELFKIYDKGFQGNLEPAVLYASEEVIEEKTLGLLRRIPVKTRYVFNLGHGLAPDMELEKVKYLVDLVKSFPL 337
               SCOP domains d2ejab_ B: automated matches                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2ejaB00 B:2-337  [code=3.20.20.210, no name defined]                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhh..................hhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhh...ee.....hhhhhhhh.eeeee...eeeee...hhhhh...hhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee.hhhhhhhhhh.....eee.....hhhhhhhhh...ee...hhhhhhhhhhhhhhhhhhhhh.......ee...........hhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------UROD_1    --------------------------------------------------------------------------------------------------------UROD_2           ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2eja B   2 PKNDLLLRSLRGEPIGRFPVWLMRQAGRYMPEYRKIRNRVKNFLELCKNVDLATEISLLPLKILGVDAIIIFSDILVPLEPLGVKVEFVEGEGPKLSWSGKVSDLKKYDPSQNAYVYEIIKRVKEAQDEVPVIGFAGAPFTLLSYLIEGGASKDFKSTKLFMWENPKEYKRLMDILTETVLAYLKEQIKAGADVVQIFDSWVNNLSLEDYGEYVYPYVNYLISELKDFSDTPVIYFFRGSSSFIDLAVDYRADALSVDWSVDIPELFKIYDKGFQGNLEPAVLYASEEVIEEKTLGLLRRIPVKTRYVFNLGHGLAPDMELEKVKYLVDLVKSFPL 337
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331
   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  (1, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2EJA)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DCUP_AQUAE | O66667)
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:0006783    heme biosynthetic process    The chemical reactions and pathways resulting in the formation of heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring, 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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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