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
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF UROPORPHYRINOGEN III SYNTHASE FROM PSEUDOMONAS SYRINGAE PV. TOMATO DC3000
 
Authors :  W. R. Chang, M. Li, S. X. Peng
Date :  02 Apr 11  (Deposition) - 22 Jun 11  (Release) - 22 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hemd-Like Family, Uroporphyrinogen Iii Synthase, Hmb, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. X. Peng, H. Zhang, Y. Gao, X. Pan, P. Cao, M. Li, W. R. Chang
Crystal Structure Of Uroporphyrinogen Iii Synthase From Pseudomonas Syringae Pv. Tomato Dc3000
Biochem. Biophys. Res. Commun. V. 408 576 2011
PubMed-ID: 21527255  |  Reference-DOI: 10.1016/J.BBRC.2011.04.064

(-) Compounds

Molecule 1 - UROPORPHYRINOGEN-III SYNTHETASE
    Chains: A, B
    EC Number: 4.2.1.75
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHAT2
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: HEMD
    Organism Scientific: PSEUDOMONAS SYRINGAE PV. TOMATO
    Organism Taxid: 223283
    Strain: DC3000

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3RE1)

(-) Sites  (0, 0)

(no "Site" information available for 3RE1)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3RE1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RE1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RE1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RE1)

(-) Exons   (0, 0)

(no "Exon" information available for 3RE1)

(-) 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:250
 aligned with Q88B90_PSESM | Q88B90 from UniProtKB/TrEMBL  Length:258

    Alignment length:257
                                    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       
         Q88B90_PSESM     2 SAWRLLLTRPAEESAALARVLADAGIFSSSLPLLETEPLPLTPAQRSIIFELLNYSAVIVVSKPAARLAIELIDEVWPQPPMQPWFSVGSATGQILLDYGLDASWPEQGDDSEALLDHPRLKQAIAVPGSRVLIMRGNEGRELLAEQLRERGVGVDYLPLYRRYLPQHAPGTLLQRVEVERLNGLVVSSGQGFEHLLQLAGDSWPDLAGLPLFVPSPRVASLAQAAGARNVIDCRGASAAALLAALRDQPQPAVKAY 258
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhhh...eeee....eeee..hhhhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhh.......eee.hhhhhhhhhhh...ee..-------hhhhhhhhhhhhh....eeeeee.....hhhhhhhhhh..eeeeee.eeee........hhhhhhhh...eee..hhhhhh.hhhhhh.hhhhhh...eee.hhhhhhhhhhhh...eee....hhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3re1 A   2 SAWRLLLTRPAEESAALARVLADAGIFSSSLPLLETEPLPLTPAQRSIIFELLNYSAVIVVSKPAARLAIELIDEVWPQPPMQPWFSVGSATGQILLDYGLDASWP-------ALLDHPRLKQAIAVPGSRVLIMRGNEGRELLAEQLRERGVGVDYLPLYRRYLPQHAPGTLLQRVEVERLNGLVVSSGQGFEHLLQLAGDSWPDLAGLPLFVPSPRVASLAQAAGARNVIDCRGASAAALLAALRDQPQPAVKAY 258
                                    11        21        31        41        51        61        71        81        91       101     |   -   |   121       131       141       151       161       171       181       191       201       211       221       231       241       251       
                                                                                                                                   107     115                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:257
 aligned with Q88B90_PSESM | Q88B90 from UniProtKB/TrEMBL  Length:258

    Alignment length:257
                                    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       
         Q88B90_PSESM     2 SAWRLLLTRPAEESAALARVLADAGIFSSSLPLLETEPLPLTPAQRSIIFELLNYSAVIVVSKPAARLAIELIDEVWPQPPMQPWFSVGSATGQILLDYGLDASWPEQGDDSEALLDHPRLKQAIAVPGSRVLIMRGNEGRELLAEQLRERGVGVDYLPLYRRYLPQHAPGTLLQRVEVERLNGLVVSSGQGFEHLLQLAGDSWPDLAGLPLFVPSPRVASLAQAAGARNVIDCRGASAAALLAALRDQPQPAVKAY 258
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------------HEM4-3re1B01 B:16-245                                                                                                                                                                                                                 ------------- Pfam domains (1)
           Pfam domains (2) --------------HEM4-3re1B02 B:16-245                                                                                                                                                                                                                 ------------- Pfam domains (2)
         Sec.struct. author ...eeee..hhhhhhhhhhhhhhh..eeee....eeee......hhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhh......eeee.hhhhhhhhhh...eee......hhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhh..eeeeee.eeee......hhhhhhhhhh...eee..hhhhhhhhhhhh..hhhhhh...eee.hhhhhhhhhhhh...eee....hhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3re1 B   2 SAWRLLLTRPAEESAALARVLADAGIFSSSLPLLETEPLPLTPAQRSIIFELLNYSAVIVVSKPAARLAIELIDEVWPQPPMQPWFSVGSATGQILLDYGLDASWPEQGDDSEALLDHPRLKQAIAVPGSRVLIMRGNEGRELLAEQLRERGVGVDYLPLYRRYLPQHAPGTLLQRVEVERLNGLVVSSGQGFEHLLQLAGDSWPDLAGLPLFVPSPRVASLAQAAGARNVIDCRGASAAALLAALRDQPQPAVKAY 258
                                    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
   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 3RE1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3RE1)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: HEM4] (6)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q88B90_PSESM | Q88B90)
molecular function
    GO:0004852    uroporphyrinogen-III synthase activity    Catalysis of the reaction: hydroxymethylbilane = H(2)O + uroporphyrinogen III.
biological process
    GO:0033014    tetrapyrrole biosynthetic process    The chemical reactions and pathways leading to the formation of tetrapyrroles, natural pigments containing four pyrrole rings joined by one-carbon units linking position 2 of one pyrrole ring to position 5 of the next.

 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 3re1)
 
  Sites
(no "Sites" information available for 3re1)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3re1)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 2 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
  3re1
    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
  Q88B90_PSESM | Q88B90
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  4.2.1.75
    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
  Q88B90_PSESM | Q88B90
    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 3RE1)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3RE1)