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(-) Description

Title :  PORPHOBILINOGEN SYNTHASE (HEMB) IN COMPLEX WITH 5-ACETAMIDO-4-OXOHEXANOIC ACID (ALAREMYCIN 2)
 
Authors :  I. U. Heinemann, C. Schulz, W. -D. Schubert, D. W. Heinz, Y. -G. Wang, Y. K Y. Awa, M. Wachi, D. Jahn, M. Jahn
Date :  27 Jul 09  (Deposition) - 27 Oct 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (8x)
Keywords :  Lyase-Antibiotic Complex, Lyase Antibiotic Complex, Metal-Binding, Heme Biosynthesis, Porphyrin Biosynthesis, Porpobilinogen Synthase, Hemb, Lyase, Inhibitor, (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. U. Heinemann, C. Schulz, W. D. Schubert, D. W. Heinz, Y. G. Wang, Y. Kobayashi, Y. Awa, M. Wachi, D. Jahn, M. Jahn
Structure Of The Heme Biosynthetic Pseudomonas Aeruginosa Porphobilinogen Synthase In Complex With The Antibiotic Alaremycin.
Antimicrob. Agents Chemother. V. 54 267 2010
PubMed-ID: 19822707  |  Reference-DOI: 10.1128/AAC.00553-09

(-) Compounds

Molecule 1 - DELTA-AMINOLEVULINIC ACID DEHYDRATASE
    Chains: A
    EC Number: 4.2.1.24
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 PLUS
    Expression System Taxid: 511693
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: PORPHOBILINOGEN SYNTHASE, ALADH, 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, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1AYC1Ligand/IonALAREMYCIN 2
2EPE2Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
3MG4Ligand/IonMAGNESIUM ION
4PE54Ligand/Ion3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL
Biological Unit 1 (3, 56)
No.NameCountTypeFull Name
1AYC8Ligand/IonALAREMYCIN 2
2EPE16Ligand/Ion4-(2-HYDROXYETHYL)-1-PIPERAZINEETHANESULFONIC ACID
3MG-1Ligand/IonMAGNESIUM ION
4PE532Ligand/Ion3,6,9,12,15,18,21,24-OCTAOXAHEXACOSAN-1-OL

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:131 , SER A:175 , TYR A:202 , LYS A:205 , TYR A:211 , PHE A:214 , LYS A:260 , TYR A:283 , VAL A:285 , SER A:286 , TYR A:324 , HOH A:2085 , HOH A:2173BINDING SITE FOR RESIDUE AYC A1333
02AC2SOFTWAREHOH A:2025 , HOH A:2059 , HOH A:2167 , HOH A:2169BINDING SITE FOR RESIDUE MG A1334
03AC3SOFTWAREGLU A:245 , HOH A:2107 , HOH A:2108 , HOH A:2137 , HOH A:2139 , HOH A:2140BINDING SITE FOR RESIDUE MG A1335
04AC4SOFTWAREASP A:131 , ASP A:139 , ASP A:176 , HOH A:2090 , HOH A:2105BINDING SITE FOR RESIDUE MG A1336
05AC5SOFTWARELEU A:27 , ASP A:37 , ASP A:319 , HOH A:2018 , HOH A:2022 , HOH A:2031BINDING SITE FOR RESIDUE MG A1337
06AC6SOFTWAREGLU A:30 , ASN A:31 , VAL A:32 , HOH A:2174BINDING SITE FOR RESIDUE EPE A1338
07AC7SOFTWAREARG A:20 , TYR A:147 , GLY A:193 , THR A:195 , ASN A:196 , HOH A:2092 , HOH A:2118BINDING SITE FOR RESIDUE EPE A1339
08AC8SOFTWARETYR A:10 , TYR A:12 , GLU A:190BINDING SITE FOR RESIDUE PE5 A1340
09AC9SOFTWAREILE A:141 , PE5 A:1342 , HOH A:2176BINDING SITE FOR RESIDUE PE5 A1341
10BC1SOFTWAREASP A:97 , VAL A:152 , ASP A:155 , PE5 A:1341 , HOH A:2175 , HOH A:2176BINDING SITE FOR RESIDUE PE5 A1342
11BC2SOFTWAREALA A:99 , TYR A:102 , ASN A:103 , PRO A:104 , ASP A:155 , VAL A:158 , ARG A:159 , HOH A:2065BINDING SITE FOR RESIDUE PE5 A1343

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WOQ)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:10 -Pro A:11
2Lys A:260 -Pro A:261

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WOQ)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1D_ALA_DEHYDRATASEPS00169 Delta-aminolevulinic acid dehydratase active site.HEM2_PSEAE253-265  1A:253-265
Biological Unit 1 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1D_ALA_DEHYDRATASEPS00169 Delta-aminolevulinic acid dehydratase active site.HEM2_PSEAE253-265  8A:253-265

(-) Exons   (0, 0)

(no "Exon" information available for 2WOQ)

(-) 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:329
 aligned with HEM2_PSEAE | Q59643 from UniProtKB/Swiss-Prot  Length:337

    Alignment length:329
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324         
           HEM2_PSEAE     5 PANRAYPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYNPEGIAQRATRALRERFPELGIITDVALDPFTTHGQDGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRIMAYSAKYASAYYGPFRDAVGSASNLGKGNKATYQMDPANSDEALHEVAADLAEGADMVMVKPGMPYLDIVRRVKDEFRAPTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQL 333
               SCOP domains d2woqa_ A: automated matches                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2woqA00 A:5-333 Aldolase class I                                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains -----ALAD-2woqA01 A:10-333                                                                                                                                                                                                                                                                                                                Pfam domains
         Sec.struct. author ..........hhhhhh.hhhhhhhh.....hhh.eeeeeee.....eee.......eeeehhhhhhhhhhhhhh...eeeeee...........hhhhh...hhhhhhhhhhhhh.....eeee.....................hhhhhhhhhhhhhhhhhh...eeee......hhhhhhhhhhhh.....eeeeeeee......hhhhhhh.........hhhhh......hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhh...eeeee..hhhhhhhhhhh......hhhhhhhhhhhhh.....ee.hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_ALA_DEHYDRA-------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2woq A   5 PANRAYPYTRLRRNRRDDFSRRLVRENVLTVDDLILPVFVLDGVNQRESIPSMPGVERLSIDQLLIEAEEWVALGIPALALFPVTPVEKKSLDAAEAYNPEGIAQRATRALRERFPELGIITDVALDPFTTHGQDGILDDDGYVLNDVSIDVLVRQALSHAEAGAQVVAPSDMMDGRIGAIREALESAGHTNVRIMAYSAKYASAYYGPFRDAVGSASNLGKGNKATYQMDPANSDEALHEVAADLAEGADMVMVKPGMPYLDIVRRVKDEFRAPTFVYQVSGEYAMHMGAIQNGWLAESVILESLTAFKRAGADGILTYFAKQAAEQL 333
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324
   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  (1, 1)

Asymmetric Unit
(-)
Clan: TIM_barrel (694)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A   (HEM2_PSEAE | Q59643)
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: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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  HEM2_PSEAE | Q59643
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 Related Entries

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

UniProtKB/Swiss-Prot
        HEM2_PSEAE | Q59643: 1b4k 1gzg 1w54 1w56 1w5m 1w5n 1w5o 1w5p 1w5q 2c13 2c14 2c15 2c16 2c18 2c19

(-) Related Entries Specified in the PDB File

1b4k HIGH RESOLUTION CRYSTAL STRUCTURE OF A MG2- DEPENDENT 5- AMINOLEVULINIC ACID DEHYDRATASE
1gzg COMPLEX OF A MG2-DEPENDENT PORPHOBILINOGEN SYNTHASE (MUTANT D139N) WITH 5-FLUOROLEVULINIC ACID
1w54 STEPWISE INTRODUCTION OF A ZINC BINDING SITE INTO PORPHOBILINOGEN SYNTHASE FROM PSEUDOMONAS AERUGINOSA (MUTATION D139C)
1w56 STEPWISE INTRODUCTION OF ZINC BINDING SITE INTO PORPHOBILINOGEN SYNTHASE OF PSEUDOMONAS AERUGINOSA (MUTANTIONS A129C AND D131C)
1w5m STEPWISE INTRODUCTION OF ZINC BINDING SITE INTO PORPHOBILINOGEN SYNTHASE OF PSEUDOMONAS AERUGINOSA (MUTANTIONS A129C AND D139C)
1w5n STEPWISE INTRODUCTION OF ZINC BINDING SITE INTO PORPHOBILINOGEN SYNTHASE OF PSEUDOMONAS AERUGINOSA (MUTANTIONS D131C AND D139C)
1w5o STEPWISE INTRODUCTION OF ZINC BINDING SITE INTO PORPHOBILINOGEN SYNTHASE OF PSEUDOMONAS AERUGINOSA (MUTANTIONS A129C, D131C AND D139C)
1w5p STEPWISE INTRODUCTION OF ZINC BINDING SITE INTO PORPHOBILINOGEN SYNTHASE OF PSEUDOMONAS AERUGINOSA (MUTANTIONS A129C, D131C, D139C, P132E)
1w5q STEPWISE INTRODUCTION OF ZINC BINDING SITE INTO PORPHOBILINOGEN SYNTHASE OF PSEUDOMONAS AERUGINOSA (MUTANTIONS A129C, D131C, D139C, P132E, K229R)
2c13 5-HYDROXY-LEVULINIC ACID BOUND TO PORPHOBILINOGEN SYNTHASE FROM PSEUDOMONAS AERUGINOSA
2c14 5-(4-CARBOXY-2-OXO-BUTYLAMINO)-4-OXO- PENTANOIC ACID ACID BOUND TO PORPHOBILINOGEN SYNTHASE FROM PSEUDOMONAS AERUGINOSA
2c15 5-(4-CARBOXY-2-OXO-BUTOXY)-4-OXO- PENTANOIC ACID ACID BOUND TO PORPHOBILINOGEN SYNTHASE FROM PSEUDOMONAS AERUGINOSA
2c16 5-(4-CARBOXY-2-OXO-BUTANE-1-SULFINYL)-4 -OXO-PENTANOIC ACID ACID BOUND TO PORPHOBILINOGEN SYNTHASE FROM PSEUDOMONAS AERUGINOSA
2c18 5-(4-CARBOXY-2-OXO-BUTANE-1-SULFONYL)-4 -OXO-PENTANOIC ACID BOUND TO PORPHOBILINOGEN SYNTHASE FROM PSEUDOMONAS AERUGINOSA
2c19 5-(4-CARBOXY-2-OXO-BUTYLSULFANYL)-4-OXO- PENTANOIC ACID ACID BOUND TO PORPHOBILINOGEN SYNTHASE FROM PSEUDOMONAS AERUGINOSA