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(-) Description

Title :  CRYSTAL STRUCTURE OF ALPHA-AMINO-BETA-CARBOXYMUCONATE-EPSILON-SEMIALDEHYDE-DECARBOXYLASE (ACMSD)
 
Authors :  D. Martynowski, Y. Eyobo, T. Li, K. Yang, A. Liu, H. Zhang
Date :  14 Jun 06  (Deposition) - 19 Sep 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Acmsd, Tim-Barrel, Decarboxylase, Metaloenzyme, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. Martynowski, Y. Eyobo, T. Li, K. Yang, A. Liu, H. Zhang
Crystal Structure Of Alpha-Amino-Beta-Carboxymuconate-Epsilon-Semialdehyde Decarboxylase: Insight Into The Active Site And Catalytic Mechanism Of A Novel Decarboxylation Reaction.
Biochemistry V. 45 10412 2006
PubMed-ID: 16939194  |  Reference-DOI: 10.1021/BI060903Q

(-) Compounds

Molecule 1 - 2-AMINO-3-CARBOXYMUCONATE 6-SEMIALDEHYDE DECARBOXYLASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PSD 80
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: NBAD
    Organism Scientific: PSEUDOMONAS FLUORESCENS
    Organism Taxid: 294
    Strain: KU-7
    Synonym: ALPHA-AMINO-BETA-CARBOXYMUCONATE-EPSILON-SEMIALDEHYDE- DECARBOXYLASE, ACMSD

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CO2Ligand/IonCOBALT (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS B:9 , HIS B:11 , HIS B:177 , HIS B:228 , ASP B:294 , HOH B:402BINDING SITE FOR RESIDUE CO B 401
2AC2SOFTWAREHIS A:9 , HIS A:11 , HIS A:177 , HIS A:228 , ASP A:294 , HOH A:578BINDING SITE FOR RESIDUE CO A 501

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Tyr A:295 -Pro A:296
2Tyr B:295 -Pro B:296

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2HBX)

(-) Exons   (0, 0)

(no "Exon" information available for 2HBX)

(-) 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:332
 aligned with Q83V25_PSEFL | Q83V25 from UniProtKB/TrEMBL  Length:334

    Alignment length:332
                                    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       312       322       332  
         Q83V25_PSEFL     3 KPRIDMHSHFFPRISEQEAAKFDANHAPWLQVSAKGDTGSIMMGKNNFRPVYQALWDPAFRIEEMDAQGVDVQVTCATPVMFGYTWEANKAAQWAERMNDFALEFAAHNPQRIKVLAQVPLQDLDLACKEASRAVAAGHLGIQIGNHLGDKDLDDATLEAFLTHCANEDIPILVHPWDMMGGQRMKKWMLPWLVAMPAETQLAILSLILSGAFERIPKSLKICFGHGGGSFAFLLGRVDNAWRHRDIVREDCPRPPSEYVDRFFVDSAVFNPGALELLVSVMGEDRVMLGSDYPFPLGEQKIGGLVLSSNLGESAKDKIISGNASKFFNINV 334
               SCOP domains d2hbxa_ A: 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase NbaD                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee...ee....hhhhhhhhhh...eeeee.....eeeeee..eeeeeee.hhhhhhhhhhhhhhhh..eeeeee.hhhh....hhhhhhhhhhhhhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhh...eeeee.........hhhhhhhhhhhhhh...eeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhheee....hhhhhhhhhhhhh...ee..............hhhhhh...hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hbx A   3 KPRIDMHSHFFPRISEQEAAKFDANHAPWLQVSAKGDTGSIMMGKNNFRPVYQALWDPAFRIEEMDAQGVDVQVTCATPVMFGYTWEANKAAQWAERMNDFALEFAAHNPQRIKVLAQVPLQDLDLACKEASRAVAAGHLGIQIGNHLGDKDLDDATLEAFLTHCANEDIPILVHPWDMMGGQRMKKWMLPWLVAMPAETQLAILSLILSGAFERIPKSLKICFGHGGGSFAFLLGRVDNAWRHRDIVREDCPRPPSEYVDRFFVDSAVFNPGALELLVSVMGEDRVMLGSDYPFPLGEQKIGGLVLSSNLGESAKDKIISGNASKFFNINV 334
                                    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       312       322       332  


Chain B from PDB  Type:PROTEIN  Length:332
 aligned with Q83V25_PSEFL | Q83V25 from UniProtKB/TrEMBL  Length:334

    Alignment length:332
                                    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       312       322       332  
         Q83V25_PSEFL     3 KPRIDMHSHFFPRISEQEAAKFDANHAPWLQVSAKGDTGSIMMGKNNFRPVYQALWDPAFRIEEMDAQGVDVQVTCATPVMFGYTWEANKAAQWAERMNDFALEFAAHNPQRIKVLAQVPLQDLDLACKEASRAVAAGHLGIQIGNHLGDKDLDDATLEAFLTHCANEDIPILVHPWDMMGGQRMKKWMLPWLVAMPAETQLAILSLILSGAFERIPKSLKICFGHGGGSFAFLLGRVDNAWRHRDIVREDCPRPPSEYVDRFFVDSAVFNPGALELLVSVMGEDRVMLGSDYPFPLGEQKIGGLVLSSNLGESAKDKIISGNASKFFNINV 334
               SCOP domains d2hbxb_ B: 2-amino-3-carboxymuconate 6-semialdehyde decarboxylase NbaD                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee....hhhhhhh.......eeee.....eeeeee..eeeeeee.hhhhhhhhhhhhhhhh..eeeeee.hhhh....hhhhhhhhhhhhhhhhhhhhhh....eee.......hhhhhhhhhhhhhhh....eeee.........hhhhhhhhhhhhhhh..eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhheee....hhhhhhhhhhhhh...ee..............hhhhhh...hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2hbx B   3 KPRIDMHSHFFPRISEQEAAKFDANHAPWLQVSAKGDTGSIMMGKNNFRPVYQALWDPAFRIEEMDAQGVDVQVTCATPVMFGYTWEANKAAQWAERMNDFALEFAAHNPQRIKVLAQVPLQDLDLACKEASRAVAAGHLGIQIGNHLGDKDLDDATLEAFLTHCANEDIPILVHPWDMMGGQRMKKWMLPWLVAMPAETQLAILSLILSGAFERIPKSLKICFGHGGGSFAFLLGRVDNAWRHRDIVREDCPRPPSEYVDRFFVDSAVFNPGALELLVSVMGEDRVMLGSDYPFPLGEQKIGGLVLSSNLGESAKDKIISGNASKFFNINV 334
                                    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       312       322       332
   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, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2HBX)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q83V25_PSEFL | Q83V25)
molecular function
    GO:0001760    aminocarboxymuconate-semialdehyde decarboxylase activity    Catalysis of the reaction: 2-amino-3-carboxymuconate 6-semialdehyde + H(+) = 2-aminomuconate 6-semialdehyde + CO(2).
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:1904984    regulation of quinolinate biosynthetic process    Any process that modulates the frequency, rate or extent of quinolinate biosynthetic process.
    GO:0006568    tryptophan metabolic process    The chemical reactions and pathways involving tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.

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 Related Entries

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UniProtKB/TrEMBL
        Q83V25_PSEFL | Q83V25: 2hbv 4epk 4era 4erg 4eri 4ifk 4ifo 4ifr 4ig2

(-) Related Entries Specified in the PDB File

2hbv