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(-) Description

Title :  X-RAY STRUCTURE OF 5-AMINOLEVULINIC ACID DEHYDRATASE COMPLEXED WITH THE INHIBITOR LEVULINIC ACID
 
Authors :  P. T. Erskine, J. B. Cooper, G. Lewis, P. Spencer, S. P. Wood, P. M. Shooli Jordan
Date :  19 Dec 98  (Deposition) - 17 Dec 99  (Release) - 18 Jan 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (8x)
Keywords :  Dehydratase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. T. Erskine, E. Norton, J. B. Cooper, R. Lambert, A. Coker, G. Lewis, P. Spencer, M. Sarwar, S. P. Wood, M. J. Warren, P. M. Shoolingin-Jorda
X-Ray Structure Of 5-Aminolevulinic Acid Dehydratase From Escherichia Coli Complexed With The Inhibitor Levulinic Aci At 2. 0 A Resolution.
Biochemistry V. 38 4266 1999
PubMed-ID: 10194344  |  Reference-DOI: 10.1021/BI982137W

(-) Compounds

Molecule 1 - PROTEIN (5-AMINOLEVULINIC ACID DEHYDRATASE)
    Chains: A
    EC Number: 4.2.1.24
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: HEM2
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: ALAD

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
2SHF1Ligand/IonLAEVULINIC ACID
3SO43Ligand/IonSULFATE ION
4ZN3Ligand/IonZINC ION
Biological Unit 1 (3, 56)
No.NameCountTypeFull Name
1GOL24Ligand/IonGLYCEROL
2SHF8Ligand/IonLAEVULINIC ACID
3SO424Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:15 , ARG A:18 , LYS A:217 , HOH A:536 , HOH A:538 , HOH A:776BINDING SITE FOR RESIDUE SO4 A 401
02AC2SOFTWAREARG A:226 , ARG A:227 , ARG A:257 , HOH A:564 , HOH A:728 , HOH A:791BINDING SITE FOR RESIDUE SO4 A 402
03AC3SOFTWARESER A:14 , LYS A:107 , PRO A:111 , HOH A:524 , HOH A:861BINDING SITE FOR RESIDUE SO4 A 403
04AC4SOFTWAREGLU A:40 , HIS A:84BINDING SITE FOR RESIDUE ZN A 404
05AC5SOFTWARECYS A:120 , CYS A:122 , CYS A:130 , HOH A:869BINDING SITE FOR RESIDUE ZN A 405
06AC6SOFTWAREGLU A:232 , HOH A:697 , HOH A:698 , HOH A:699 , HOH A:870 , HOH A:871BINDING SITE FOR RESIDUE ZN A 406
07AC7SOFTWAREPHE A:79 , LYS A:195 , TYR A:201 , PHE A:204 , LYS A:247 , TYR A:270 , VAL A:272 , SER A:273 , TYR A:312BINDING SITE FOR RESIDUE SHF A 407
08AC8SOFTWAREGLU A:275 , SER A:297 , HOH A:746 , HOH A:864BINDING SITE FOR RESIDUE GOL A 408
09AC9SOFTWAREGLU A:22 , LEU A:295 , GLU A:296 , HOH A:558 , HOH A:717BINDING SITE FOR RESIDUE GOL A 409
10BC1SOFTWAREALA A:156 , ALA A:182 , PHE A:184 , HOH A:656BINDING SITE FOR RESIDUE GOL A 410

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1B4E)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Lys A:247 -Pro A:248

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1B4E)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1D_ALA_DEHYDRATASEPS00169 Delta-aminolevulinic acid dehydratase active site.HEM2_ECOLI240-252  1A:240-252
Biological Unit 1 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1D_ALA_DEHYDRATASEPS00169 Delta-aminolevulinic acid dehydratase active site.HEM2_ECOLI240-252  8A:240-252

(-) Exons   (0, 0)

(no "Exon" information available for 1B4E)

(-) 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:323
 aligned with HEM2_ECOLI | P0ACB2 from UniProtKB/Swiss-Prot  Length:324

    Alignment length:323
                                    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       261       271       281       291       301       311       321   
           HEM2_ECOLI     2 TDLIQRPRRLRKSPALRAMFEETTLSLNDLVLPIFVEEEIDDYKAVEAMPGVMRIPEKHLAREIERIANAGIRSVMTFGISHHTDETGSDAWREDGLVARMSRICKQTVPEMIVMSDTCFCEYTSHGHCGVLCEHGVDNDATLENLGKQAVVAAAAGADFIAPSAAMDGQVQAIRQALDAAGFKDTAIMSYSTKFASSFYGPFREAAGSALKGDRKSYQMNPMNRREAIRESLLDEAQGADCLMVKPAGAYLDIVRELRERTELPIGAYQVSGEYAMIKFAALAGAIDEEKVVLESLGSIKRAGADLIFSYFALDLAEKKILR 324
               SCOP domains d1b4ea_ A: 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)                                                                                                                                                                                                                                                          SCOP domains
               CATH domains 1b4eA00 A:2-324 Aldolase class I                                                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhh...hhhhhhh......hhh..eeeeee...................hhhhhhhhhhhhh....eeeeeee........hhhh....hhhhhhhhhhhh....eeeeee....................hhhhhhhhhhhhhhhhhh...eeee......hhhhhhhhhhh.................hhhhhhhhhh.................hhhhhhhhhhhhh....eeee...hhhhhhhhhhh.....eeeee..hhhhhhhhhhhh.....hhhhhhhhhhhhhh....eee...hhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_ALA_DEHYDRA------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1b4e A   2 TDLSQRPRRLRKSPALRAMFEETTLSLNDLVLPIFVEEEIDDYKAVEAMPGVMRIPEKHLAREIERIANAGIRSVMTFGISHHTDETGSDAWREDGLVARMSRICKQTVPEMIVMSDTCFCEYTSHGHCGVLKEHGVDNDATLENLGKQAVVAAAAGADFIAPSAAMDGQVQAIRQALDAAGFKDTAIMSYSTKFASSFYGPFREAAGSALKGDRKSYQMNPMNRREAIRESLLDEAQGADCLMVKPAGAYLDIVRELRERTELPIGAYQVSGEYAMIKFAALAGAIDEEKVVLESLGSIKRAGADLIFSYFALDLAEKKILR 324
                                    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       261       271       281       291       301       311       321
   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 1B4E)

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A   (HEM2_ECOLI | P0ACB2)
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: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:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    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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