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(-) Description

Title :  CRYSTAL STRUCTURE OF UROPORPHYRINOGEN-III SYNTHETASE FROM HELICOBACTER PYLORI 26695
 
Authors :  B. Nocek, A. Stein, G. Chhor, R. J. Fenske, K. Buck, A. Joachimiak, Midwe For Structural Genomics (Mcsg)
Date :  18 Oct 10  (Deposition) - 03 Nov 10  (Release) - 03 Nov 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Mcsg, Psi2, Structural Genomics, Protein Structure Initiative, Midwest Center For Structural Genomics, Uroporphyrinogen-Iii Synthetase, Tetrapyrrole Biosynthesis, Heme, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nocek, A. Stein, G. Chhor, R. J. Fenske, K. Buck, A. Joachimiak
Crystal Structure Of Uroporphyrinogen-Iii Synthetase From Helicobacter Pylori 26695
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UROPORPHYRINOGEN III COSYNTHASE (HEMD)
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21DE3
    Expression System Taxid: 562
    Expression System Vector: PMCSG19B
    Gene: HP_1224
    Organism Scientific: HELICOBACTER PYLORI
    Organism Taxid: 210

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1MLI1Ligand/IonMALONATE ION
2MSE3Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:41 , TYR A:112 , ARG A:114 , GLU A:117 , ILE A:118 , VAL A:119 , SER A:120 , SER A:121 , LEU A:122 , HOH A:259BINDING SITE FOR RESIDUE MLI A 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P9Z)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:13 -Pro A:14

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P9Z)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P9Z)

(-) Exons   (0, 0)

(no "Exon" information available for 3P9Z)

(-) 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:213
 aligned with O25822_HELPY | O25822 from UniProtKB/TrEMBL  Length:226

    Alignment length:222
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  
         O25822_HELPY     1 MREIVWVHSQRIAPYKTLILNEFCYYPLELDPTPFNALIFTSKNAVFSLLETLKNSPKLKMLQNIPAYALSEPTAKTLQDHHFKVAFMGEKAHGKEFVQEIFPLLEKKSVLYLRAKEIVSSLDTILLEHGIDFKQAVVYENKLKHLTLSEQNALKPKEKSILIFTAISHAKAFLHYFEFLENYTAISIGNTTALYLQEQGIPSYIAKKPSLEACLELALSLR 222
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ---------HEM4-3p9zA01 A:10-216                                                                                                                                                                                          ------ Pfam domains
         Sec.struct. author ...eeee........eee..eeeee...........eeee.hhhhhhhhhhhh..hhhhhhhhh..eee.hhhhhhhhhhh.........---------.hhhhhh..eeeeeee.....hhhhhhhhh..eeeeeeeeeeee...hhhhhhhhh.....eeee.hhhhhhhhhhhh......eeee.hhhhhhhhhhh...eee....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3p9z A   1 mREIVWVHSQRIAPYKTLILNEFCYYPLELDPTPFNALIFTSKNAVFSLLETLKNSPKLKmLQNIPAYALSEPTAKTLQDHHFKVAFmGE---------EIFPLLEKKSVLYLRAKEIVSSLDTILLEHGIDFKQAVVYENKLKHLTLSEQNALKPKEKSILIFTAISHAKAFLHYFEFLENYTAISIGNTTALYLQEQGIPSYIAKKPSLEACLELALSLR 222
                            |       10        20        30        40        50        60|       70        80       |90       100       110       120       130       140       150       160       170       180       190       200       210       220  
                            |                                                          61-MSE                     88-MSE     100                                                                                                                          
                            1-MSE                                                                                   90
   Legend:   → Mismatch (orange background)
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  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 3P9Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P9Z)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O25822_HELPY | O25822)
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.

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