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(-) Description

Title :  THE X-RAY STRUCTURE OF CHLOROBIUM VIBRIOFORME 5-AMINOLAEVULINIC ACID DEHYDRATASE COMPLEXED WITH A DIACID INHIBITOR
 
Authors :  L. Coates, G. Beaven, P. T. Erskine, S. Beale, S. P. Wood, P. M. Shoolingin-Jordan, J. B. Cooper
Date :  14 Sep 05  (Deposition) - 02 Dec 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Keywords :  Lyase, Alad, 5-Aminolaevulinic Acid Dehydratase, Heme Biosynthesis, Magnesium, Porphyrin Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Coates, G. Beaven, P. T. Erskine, S. Beale, S. P. Wood, P. M. Shoolingin-Jordan, J. B. Cooper
Structure Of Chlorobium Vibrioforme 5- Aminolaevulinic Acid Dehydratase Complexed With A Diacid Inhibitor.
Acta Crystallogr. , Sect. D V. 61 1594 2005
PubMed-ID: 16304458  |  Reference-DOI: 10.1107/S0907444905030350

(-) Compounds

Molecule 1 - DELTA-AMINOLEVULINIC ACID DEHYDRATASE
    ChainsA, B
    EC Number4.2.1.24
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificCHLOROBIUM VIBRIOFORME
    Organism Taxid1098
    Other DetailsSCHIFF BASE LINK BETWEEN LYS 200 AND DSB, SCHIFF BASE LINK BETWEEN LYS 253 AND DSB
    Synonym5-AMINOLAEVULINIC ACID DEHYDRATASE, PORPHOBILINOGEN SYNTHASE, ALAD, ALADH

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (4x)AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1DSB2Ligand/Ion4,7-DIOXOSEBACIC ACID
2MG2Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1DSB8Ligand/Ion4,7-DIOXOSEBACIC ACID
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:176 , GLU A:238 , HOH A:2070 , HOH A:2071 , HOH A:2072 , HOH A:2096BINDING SITE FOR RESIDUE MG A1329
2AC2SOFTWAREARG B:176 , GLU B:238 , ASP B:242 , HOH B:2070 , HOH B:2071 , HOH B:2091 , HOH B:2095BINDING SITE FOR RESIDUE MG B1329
3AC3SOFTWARESER A:170 , LYS A:200 , TYR A:206 , PHE A:209 , ARG A:210 , LYS A:222 , LYS A:253 , TYR A:276 , VAL A:278 , SER A:279 , TYR A:318BINDING SITE FOR RESIDUE DSB A1330
4AC4SOFTWARESER B:170 , LYS B:200 , TYR B:206 , PHE B:209 , ARG B:210 , LYS B:222 , LYS B:253 , TYR B:276 , VAL B:278 , SER B:279 , TYR B:318 , HOH B:2125 , HOH B:2126BINDING SITE FOR RESIDUE DSB B1330

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2C1H)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:253 -Pro A:254
2Lys B:253 -Pro B:254

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2C1H)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1D_ALA_DEHYDRATASEPS00169 Delta-aminolevulinic acid dehydratase active site.HEM2_CHLP8246-258
 
  2A:246-258
B:246-258
Biological Unit 1 (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1D_ALA_DEHYDRATASEPS00169 Delta-aminolevulinic acid dehydratase active site.HEM2_CHLP8246-258
 
  8A:246-258
B:246-258

(-) Exons   (0, 0)

(no "Exon" information available for 2C1H)

(-) 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:319
 aligned with HEM2_CHLP8 | Q59334 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:319
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319         
           HEM2_CHLP8    10 VHRPRRLRRTAALRNLVQENTLTVNDLVFPLFVMPGTNAVEEVSSMPGSFRFTIDRAVEECKELYDLGIQGIDLFGIPEQKTEDGSEAYNDNGILQQAIRAIKKAVPELCIMTDVALDPFTPFGHDGLVKDGIILNDETVEVLQKMAVSHAEAGADFVSPSDMMDGRIGAIREALDETDHSDVGILSYAAKYASSFYGPFRDALHSAPQFGDKSTYQMNPANTEEAMKEVELDIVEGADIVMVKPGLAYLDIVWRTKERFDVPVAIYHVSGEYAMVKAAAAKGWIDEDRVMMESLLCMKRAGADIIFTYYAKEAAKKLR 328
               SCOP domains d2c1ha_ A: 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2c1hA00 A:10-328 Aldolase class I                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.hhhhhhhhh....hhh.eeeeeee...................hhhhhhhhhhhhhhh...eeeeee........hhhhhh..hhhhhhhhhhhhhh...eeeee..hhhhh..............hhhhhhhhhhhhhhhhhhh..eee......hhhhhhhhhhhhh.....eeeeeeee.....hhhhhhhh..................hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..eeee.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_ALA_DEHYDRA---------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c1h A  10 VHRPRRLRRTAALRNLVQENTLTVNDLVFPLFVMPGTNAVEEVSSMPGSFRFTIDRAVEECKELYDLGIQGIDLFGIPEQKTEDGSEAYNDNGILQQAIRAIKKAVPELCIMTDVALDPFTPFGHDGLVKDGIILNDETVEVLQKMAVSHAEAGADFVSPSDMMDGRIGAIREALDETDHSDVGILSYAAKYASSFYGPFRDALHSAPQFGDKSTYQMNPANTEEAMKEVELDIVEGADIVMVKPGLAYLDIVWRTKERFDVPVAIYHVSGEYAMVKAAAAKGWIDEDRVMMESLLCMKRAGADIIFTYYAKEAAKKLR 328
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319         

Chain B from PDB  Type:PROTEIN  Length:319
 aligned with HEM2_CHLP8 | Q59334 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:319
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319         
           HEM2_CHLP8    10 VHRPRRLRRTAALRNLVQENTLTVNDLVFPLFVMPGTNAVEEVSSMPGSFRFTIDRAVEECKELYDLGIQGIDLFGIPEQKTEDGSEAYNDNGILQQAIRAIKKAVPELCIMTDVALDPFTPFGHDGLVKDGIILNDETVEVLQKMAVSHAEAGADFVSPSDMMDGRIGAIREALDETDHSDVGILSYAAKYASSFYGPFRDALHSAPQFGDKSTYQMNPANTEEAMKEVELDIVEGADIVMVKPGLAYLDIVWRTKERFDVPVAIYHVSGEYAMVKAAAAKGWIDEDRVMMESLLCMKRAGADIIFTYYAKEAAKKLR 328
               SCOP domains d2c1hb_ B: 5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2c1hB00 B:10-328 Aldolase class I                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh....hhh.eeeeeee...................hhhhhhhhhhhhhhh...eeeeee........hhhhhh..hhhhhhhhhhhhhh...eeeeee....................hhhhhhhhhhhhhhhhhhh..eeee.....hhhhhhhhhhhhh.....eeeeeeee.....hhhhhhhh..................hhhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh...eeee.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------D_ALA_DEHYDRA---------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c1h B  10 VHRPRRLRRTAALRNLVQENTLTVNDLVFPLFVMPGTNAVEEVSSMPGSFRFTIDRAVEECKELYDLGIQGIDLFGIPEQKTEDGSEAYNDNGILQQAIRAIKKAVPELCIMTDVALDPFTPFGHDGLVKDGIILNDETVEVLQKMAVSHAEAGADFVSPSDMMDGRIGAIREALDETDHSDVGILSYAAKYASSFYGPFRDALHSAPQFGDKSTYQMNPANTEEAMKEVELDIVEGADIVMVKPGLAYLDIVWRTKERFDVPVAIYHVSGEYAMVKAAAAKGWIDEDRVMMESLLCMKRAGADIIFTYYAKEAAKKLR 328
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319         

   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, 2)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2C1H)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HEM2_CHLP8 | Q59334)
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.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HEM2_CHLP8 | Q593341w1z

(-) Related Entries Specified in the PDB File

1w1z STRUCTURE OF THE PLANT LIKE 5- AMINOLAEVULINIC ACID DEHYDRATASE FROM CHLOROBIUM VIBRIOFORME