Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF UROPORPHYRINOGEN DECARBOXYLASE FROM SHIGELLA FLEXINERI: NEW INSIGHTS INTO ITS CATALYTIC MECHANISM
 
Authors :  H. Liu, H. Zhou, R. Bi
Date :  26 Apr 08  (Deposition) - 28 Apr 09  (Release) - 28 Apr 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Alpha/Beta Barrel, Cytoplasm, Decarboxylase, Lyase, Porphyrin Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Liu, H. Zhou, R. Bi
Crystal Structure Of Uroporphyrinogen Iii Decarboxylase From Shigella Flexineri: New Insights Into Its Catalytic Mechanism
To Be Published
PubMed: search
(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 Plasmid: PET22B(+)
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: UROD
    Organism Scientific: SHIGELLA FLEXNERI
    Organism Taxid: 623
    Strain: 2A STR. 301
    Synonym: URO-D, UPD

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3CYV)

(-) Sites  (0, 0)

(no "Site" information available for 3CYV)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3CYV)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3CYV)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CYV)

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UROD_1PS00906 Uroporphyrinogen decarboxylase signature 1.DCUP_SHIFL22-31  1A:22-31
2UROD_2PS00907 Uroporphyrinogen decarboxylase signature 2.DCUP_SHIFL142-158  1A:142-158
Biological Unit 1 (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UROD_1PS00906 Uroporphyrinogen decarboxylase signature 1.DCUP_SHIFL22-31  2A:22-31
2UROD_2PS00907 Uroporphyrinogen decarboxylase signature 2.DCUP_SHIFL142-158  2A:142-158

(-) Exons   (0, 0)

(no "Exon" information available for 3CYV)

(-) 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:352
 aligned with DCUP_SHIFL | Q83PB7 from UniProtKB/Swiss-Prot  Length:354

    Alignment length:352
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352  
           DCUP_SHIFL     3 ELKNDRYLRALLRQPVDVTPVWMMRQAGRYLPEYKATRAQAGDFMSLCKNAELACEVTLQPLRRYPLDAAILFSDILTVPDAMGLGLYFEAGEGPRFTSPVTCKADVDKLPIPDPEDELGYVMNAVRTIRHELKGEVPLIGFSGSPWTLATYMVEGGSSKAFTVIKKMMYADPQALHALLDKLAKSVTLYLNAQIKAGAQAVMIFDTWGGVLTGRDYQQFSLYYMHKIVDGLLRENDGRRVPVTLFTKGGGQWLEAMAETGCDALGLDWTTDIADARRRVGNKVALQGNMDPSMLYAPPARIEEEVATILAGFGHGEGHVFNLGHGIHQDVPPEHAGVFVEAVHRLSEQYHR 354
               SCOP domains d3cyva_ A: Uroporphyrinogen decarboxylase, UROD                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 3cyvA00 A:3-354  [code=3.20.20.210, no name defined]                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhh..................hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.....ee.....hhhhhh....eee.....eee.....hhhhhhh.........hhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhh.....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh...eeeee..hhhhhhhhhhhhhhhhhhhhhhhhh..ee..ee..eeee......hhhhhhh....eee.....hhhhhhhhhh...eee...hhhhhhhhhhhhhhhhhhhhh.......ee...........hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------UROD_1    --------------------------------------------------------------------------------------------------------------UROD_2           ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3cyv A   3 ELKNDRYLRALLRQPVDVTPVWMMRQAGRYLPEYKATRAQAGDFMSLCKNAELACEVTLQPLRRYPLDAAILFSDILTVPDAMGLGLYFEAGEGPRFTSPVTCKADVDKLPIPDPEDELGYVMNAVRTIRHELKGEVPLIGFSGSPWTLATYMVEGGSSKAFTVIKKMMYADPQALHALLDKLAKSVTLYLNAQIKAGAQAVMIFDTWGGVLTGRDYQQFSLYYMHKIVDGLLRENDGRRVPVTLFTKGGGQWLEAMAETGCDALGLDWTTDIADARRRVGNKVALQGNMDPSMLYAPPARIEEEVATILAGFGHGEGHVFNLGHGIHQDVPPEHAGVFVEAVHRLSEQYHR 354
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352
   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, 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 3CYV)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A   (DCUP_SHIFL | Q83PB7)
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: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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 3cyv)
 
  Sites
(no "Sites" information available for 3cyv)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3cyv)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Biol. Unit 1 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3cyv
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DCUP_SHIFL | Q83PB7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.1.1.37
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  DCUP_SHIFL | Q83PB7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3CYV)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3CYV)