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(-) Description

Title :  YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE 5-HYDROXYLAEVULINIC ACID COMPLEX
 
Authors :  P. T. Erskine, L. Coates, R. Newbold, A. A. Brindley, F. Stauffer, G. D. E. Beaven, R. Gill, S. P. Wood, M. J. Warren, J. B. Cooper, P. M. Shoolingin-Jordan, R. Neier
Date :  11 Jul 04  (Deposition) - 23 Aug 05  (Release) - 13 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (8x)
Keywords :  Dehydratase, Aldolase, Tim Barrel, Tetrapyrrole Synthesis, Heme Biosynthesis, Lyase, Zinc (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. T. Erskine, L. Coates, R. Newbold, A. A. Brindley, F. Stauffer, G. D. E. Beaven, R. Gill, A. Coker, S. P. Wood, M. J. Warren, P. M. Shoolingin-Jordan, R. Neier, J. B. Cooper
Structure Of Yeast 5-Aminolaevulinic Acid Dehydratase Complexed With The Inhibitor 5-Hydroxylaevulinic Acid
Acta Crystallogr. , Sect. D V. 61 1222 2005
PubMed-ID: 16131755  |  Reference-DOI: 10.1107/S0907444905018834

(-) Compounds

Molecule 1 - DELTA-AMINOLEVULINIC ACID DEHYDRATASE
    Chains: A
    EC Number: 4.2.1.24
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Other Details: COMPLEX WITH 5-HYDROXYLAEVULINIC ACID
    Strain: NS1(JM109/PNS1)
    Synonym: 5-AMINOLAEVULINIC ACID DEHYDRATASE, ALADH

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (8x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 2)
No.NameCountTypeFull Name
1SHO1Ligand/Ion5-HYDROXYLAEVULINIC ACID
2ZN1Ligand/IonZINC ION
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1SHO8Ligand/Ion5-HYDROXYLAEVULINIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:133 , CYS A:135 , CYS A:143 , HOH A:2269BINDING SITE FOR RESIDUE ZN A 400
2AC2SOFTWAREPHE A:89 , ASP A:131 , SER A:179 , TYR A:207 , PHE A:219 , LYS A:263 , TYR A:287 , SER A:290 , TYR A:329BINDING SITE FOR RESIDUE SHO A 363

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1W31)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:263 -Pro A:264

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W31)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1D_ALA_DEHYDRATASEPS00169 Delta-aminolevulinic acid dehydratase active site.HEM2_YEAST256-268  1A:256-268
Biological Unit 1 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1D_ALA_DEHYDRATASEPS00169 Delta-aminolevulinic acid dehydratase active site.HEM2_YEAST256-268  8A:256-268

(-) Exons   (1, 1)

Asymmetric Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YGL040C1YGL040C.1VII:420561-4195331029HEM2_YEAST1-3423421A:1-340340

(-) 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:340
 aligned with HEM2_YEAST | P05373 from UniProtKB/Swiss-Prot  Length:342

    Alignment length:340
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340
           HEM2_YEAST     1 MHTAEFLETEPTEISSVLAGGYNHPLLRQWQSERQLTKNMLIFPLFISDNPDDFTEIDSLPNINRIGVNRLKDYLKPLVAKGLRSVILFGVPLIPGTKDPVGTAADDPAGPVIQGIKFIREYFPELYIICDVCLCEYTSHGHCGVLYDDGTINRERSVSRLAAVAVNYAKAGAHCVAPSDMIDGRIRDIKRGLINANLAHKTFVLSYAAKFSGNLYGPFRDAACSAPSNGDRKCYQLPPAGRGLARRALERDMSEGADGIIVKPSTFYLDIMRDASEICKDLPICAYHVSGEYAMLHAAAEKGVVDLKTIAFESHQGFLRAGARLIITYLAPEFLDWLDE 340
               SCOP domains d1w31a_ A: automated matches                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1w31A00 A:1-340 Aldolase class I                                                                                                                                                                                                                                                                                                                     CATH domains
               Pfam domains -------------ALAD-1w31A01 A:14-338                                                                                                                                                                                                                                                                                                                -- Pfam domains
         Sec.struct. author ............hhhhhhhhhh.hhhhhhhh.....hhh.eeeeeeee..................hhhhhhhhhhhhhhh...eeeeeee..........hhhhhh..hhhhhhhhhhhhhh...eeeeee.hhhh...............hhhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh......eeeeeeee.....hhhhhhhh.................hhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhh....eeee.hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...eee..hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_ALA_DEHYDRA------------------------------------------------------------------------ PROSITE
               Transcript 1 Exon 1.1  PDB: A:1-340 UniProt: 1-342 [INCOMPLETE]                                                                                                                                                                                                                                                                                                   Transcript 1
                 1w31 A   1 MHTAEFLETEPTEISSVLAGGYNHPLLRQWQSERQLTKNMLIFPLFISDNPDDFTEIDSLPNINRIGVNRLKDYLKPLVAKGLRSVILFGVPLIPGTKDPVGTAADDPAGPVIQGIKFIREYFPELYIICDVCLCEYTSHGHCGVLYDDGTINRERSVSRLAAVAVNYAKAGAHCVAPSDMIDGRIRDIKRGLINANLAHKTFVLSYAAKFSGNLYGPFRDAACSAPSNGDRKCYQLPPAGRGLARRALERDMSEGADGIIVKPSTFYLDIMRDASEICKDLPICAYHVSGEYAMLHAAAEKGVVDLKTIAFESHQGFLRAGARLIITYLAPEFLDWLDE 340
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340
   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  (1, 1)

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

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (HEM2_YEAST | P05373)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0032791    lead ion binding    Interacting selectively and non-covalently with lead (Pb) ions.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004655    porphobilinogen synthase activity    Catalysis of the reaction: 2 5-aminolevulinate = 2 H(2)O + H(+) + porphobilinogen.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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.
    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: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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  1w31
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  HEM2_YEAST | P05373
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  4.2.1.24
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 Related Entries

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

UniProtKB/Swiss-Prot
        HEM2_YEAST | P05373: 1aw5 1eb3 1gjp 1h7n 1h7o 1h7p 1h7r 1ohl 1qml 1qnv 1ylv

(-) Related Entries Specified in the PDB File

1aw5 5-AMINOLEVULINATE DEHYDRATASE FROM SACCHAROMYCES CEREVISIAE
1eb3 YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE 4,7 -DIOXOSEBACIC ACID COMPLEX
1gjp SCHIFF-BASE COMPLEX OF YEAST 5- AMINOLAEVULINIC ACID DEHYDRATASE WITH 4- OXOSEBACIC ACID
1h7n SCHIFF-BASE COMPLEX OF YEAST 5- AMINOLAEVULINIC ACID DEHYDRATASE WITH LAEVULINIC ACID AT 1.6 A RESOLUTION
1h7o SCHIFF-BASE COMPLEX OF YEAST 5- AMINOLAEVULINIC ACID DEHYDRATASE WITH 5- AMINOLAEVULINIC ACID AT 1.7 A RESOLUTION
1h7p SCHIFF-BASE COMPLEX OF YEAST 5- AMINOLAEVULINIC ACID DEHYDRATASE WITH 4-KETO- 5-AMINO-HEXANOIC (KAH) AT 1.64 A RESOLUTION
1h7r SCHIFF-BASE COMPLEX OF YEAST 5- AMINOLAEVULINIC ACID DEHYDRATASE WITH SUCCINYLACETONE AT 2.0 A RESOLUTION.
1ohl YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE PUTATIVE CYCLIC REACTION INTERMEDIATE COMPLEX
1qml HG COMPLEX OF YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE
1qnv YEAST 5-AMINOLAEVULINIC ACID DEHYDRATASE LEAD (PB) COMPLEX
1ylv SCHIFF-BASE COMPLEX OF YEAST 5- AMINOLAEVULINIC ACID DEHYDRATASE WITH LAEVULINIC ACID