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(-) Description

Title :  REDUCED FORM HYDROXYMETHYLBILANE SYNTHASE (K59Q MUTANT) CRYSTAL STRUCTURE AFTER 2 HOURS IN A FLOW CELL DETERMINED BY TIME-RESOLVED LAUE DIFFRACTION
 
Authors :  J. R. Helliwell, Y. P. Nieh, J. Raftery, A. Cassetta, J. Habash, P. D. Car T. Ursby, M. Wulff, A. W. Thompson, A. C. Niemann, A. Haedener
Date :  26 Jun 98  (Deposition) - 02 Mar 99  (Release) - 18 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Biosynthesis Of Linear Tetrapyrrole, All Alpha/Beta, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Helliwell, Y. P. Nieh, A. Cassetta, J. Habash, P. D. Carr, T. Ursby M. Wulff, A. W. Thompson, A. C. Niemann, A. Haedener
Time-Resolved Structures Of Hydroxymethylbilane Synthase (Lys59Gln Mutant) As It Isloaded With Substrate In The Crystal Determined By Laue Diffraction
J. Chem. Soc. , Faraday Trans. V. 94 2615 1998
PubMed: search  |  Reference-DOI: 10.1039/A802217H
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYDROXYMETHYLBILANE SYNTHASE
    Chains: A
    EC Number: 2.5.1.61
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: THREE DOMAINS
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Other Details: CONTAINS A DIPYRROMETHANE COFACTOR LINKED TO CYSTEINE 242
    Synonym: PORPHOBILINOGEN DEAMINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1DPM1Ligand/Ion3-[5-{[3-(2-CARBOXYETHYL)-4-(CARBOXYMETHYL)-5-METHYL-1H-PYRROL-2-YL]METHYL}-4-(CARBOXYMETHYL)-1H-PYRROL-3-YL]PROPANOIC ACID

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:81 , LYS A:83 , ASP A:84 , THR A:127 , SER A:128 , SER A:129 , ARG A:131 , ARG A:132 , LEU A:148 , ARG A:155 , LEU A:169 , ALA A:170 , CYS A:242 , HOH A:336 , HOH A:349 , HOH A:376 , HOH A:392BINDING SITE FOR RESIDUE DPM A 314

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PORPHOBILINOGEN_DEAMPS00533 Porphobilinogen deaminase cofactor-binding site.HEM3_ECOLI231-247  1A:231-247

(-) Exons   (0, 0)

(no "Exon" information available for 1YPN)

(-) 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:294
 aligned with HEM3_ECOLI | P06983 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:304
                                    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    
           HEM3_ECOLI     3 DNVLRIATRQSPLALWQAHYVKDKLMASHPGLVVELVPMVTRGDVILDTPLAKVGGKGLFVKELEVALLENRADIAVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALPAGSIVGTSSLRRQCQLAERRPDLIIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGLESRIRAALPPEISLPAVGQGAVGIECRLDDSRTRELLAALNHHETALRVTAERAMNTRLEGGCQVPIGSYAELIDGEIWLRALVGAPDGSQIIRGERRGAPQDAEQMGISLAEELLNNGAREILAEV 306
               SCOP domains d1ypna1 A:3-219 Porphobilinogen deaminase (hy          droxymethylbilane synthase), N-terminal domain                                                                                                                    d1ypna2 A:220-306                                                                       SCOP domains
               CATH domains 1ypnA01 A:3-99,A:200-220 Periplasmic binding           protein-like II                           1ypnA02 A:100-199 Periplasmic binding protein-like II                                               1ypnA01              1ypnA03 A:221-305  [code=3.30.160.40, no name defined]                               - CATH domains
               Pfam domains --Porphobil_deam-1ypnA02 A:5-217                                                                                                                                                                                       -------Porphobil_deamC-1ypnA01 A:225-296                                       ---------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhhhh....eeeeee.......----------......hhhhhhhh.....eeeeehhh........eeeeee.......eeee..............eee...hhhhhhhhhh....eee.....hhhhhhhhh......eeeehhhhhh...hhh..eee.............eeeeee...hhhhhhhhhh..hhhhhhhhhhhhhhhhh.......eeeeeeee..eeeeeeeee......eeeeeeeeehhhhhhhhhhhhhhhhh..hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PORPHOBILINOGEN_D----------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ypn A   3 DNVLRIATRQSPLALWQAHYVKDKLMASHPGLVVELVPMVTRGDV----------GQGLFVKELEVALLENRADIAVHSMKDVPVEFPQGLGLVTICEREDPRDAFVSNNYDSLDALPAGSIVGTSSLRRQCQLAERRPDLIIRSLRGNVGTRLSKLDNGEYDAIILAVAGLKRLGLESRIRAALPPEISLPAVGQGAVGIECRLDDSRTRELLAALNHHETALRVTAERAMNTRLEGGCQVPIGSYAELIDGEIWLRALVGAPDGSQIIRGERRGAPQDAEQMGISLAEELLNNGAREILAEV 306
                                    12        22        32        42    |    -     |  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    
                                                                       47         58
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 3)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Porphobil_deamC] (3)
(-)
Clan: no clan defined [family: Porphobil_deam] (3)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HEM3_ECOLI | P06983)
molecular function
    GO:0004418    hydroxymethylbilane synthase activity    Catalysis of the reaction: H(2)O + 4 porphobilinogen = hydroxymethylbilane + 4 NH(4)(+).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
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:0018160    peptidyl-pyrromethane cofactor linkage    The covalent binding of a pyrromethane (dipyrrin) cofactor to protein via the sulfur atom of cysteine forming dipyrrolylmethanemethyl-L-cysteine.
    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.
    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.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        HEM3_ECOLI | P06983: 1ah5 1gtk 1pda 2ypn

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