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(-) Description

Title :  CRYSTAL STRUCTURES OF THE WILD-TYPE, MUTANT-P1A AND INACTIVATED MALONATE SEMIALDEHYDE DECARBOXYLASE: A STRUCTURAL BASIS FOR THE DECARBOXYLASE AND HYDRATASE ACTIVITIES
 
Authors :  J. J. Almrud, G. J. Poelarends, W. H. Johnson Jr. , H. Serrano, M. L. Hack C. P. Whitman
Date :  13 Jul 05  (Deposition) - 22 Nov 05  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B,C  (1x)
Biol. Unit 2:  D,E,F  (1x)
Keywords :  Tautomerase Superfamily; Beta-Alpha-Beta; Homotrimeric, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. J. Almrud, G. J. Poelarends, W. H. Johnson Jr. , H. Serrano, M. L. Hackert, C. P. Whitman
Crystal Structures Of The Wild-Type, P1A Mutant, And Inactivated Malonate Semialdehyde Decarboxylase: A Structural Basis For The Decarboxylase And Hydratase Activities
Biochemistry V. 44 14818 2005
PubMed-ID: 16274229  |  Reference-DOI: 10.1021/BI051383M

(-) Compounds

Molecule 1 - MALONATE SEMIALDEHYDE DECARBOXYLASE
    Chains: A, B, C, D, E, F
    EC Number: 4.1.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET3A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ORF130
    Organism Scientific: PSEUDOMONAS PAVONACEAE
    Organism Taxid: 47881
    Strain: 170

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): ABC   
Biological Unit 2 (1x):    DEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2AAG)

(-) Sites  (0, 0)

(no "Site" information available for 2AAG)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Val B:129 -Gly B:130

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2AAG)

(-) 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:129
 aligned with Q9EV83_PSEPV | Q9EV83 from UniProtKB/TrEMBL  Length:130

    Alignment length:129
                                    11        21        31        41        51        61        71        81        91       101       111       121         
         Q9EV83_PSEPV     2 PLLKFDIFYGRTDAQIKSLLDAAHGAMVDAFGVPANDRYQTVSQHRPGEMVLEDTGLGYGRSSAVVLLTVISRPRSEEQKVCFYKLLTGALERDCGISPDDVIVALVENSDADWSFGRGRAEFLTGDLV 130
               SCOP domains d2aaga_ A: Malonate semialdehyde decarboxylase, MSAD                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh......eeeeeeehhh.eee.............eeeeeee...hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhh.ee.....hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aag A   1 PLLKFDLFYGRTDAQIKSLLDAAHGAMVDAFGVPANDRYQTVSQHRPGEMVLEDTGLGYGRSSAVVLLTVISRPRSEEQKVCFYKLLTGALERDCGISPDDVIVALVENSDADWSFGRGRAEFLTGDLV 129
                                    10        20        30        40        50        60        70        80        90       100       110       120         


Chain B from PDB  Type:PROTEIN  Length:130
 aligned with Q9EV83_PSEPV | Q9EV83 from UniProtKB/TrEMBL  Length:130

    Alignment length:130
                                                                                                                                                          130 
                                    11        21        31        41        51        61        71        81        91       101       111       121        |-
         Q9EV83_PSEPV     2 PLLKFDIFYGRTDAQIKSLLDAAHGAMVDAFGVPANDRYQTVSQHRPGEMVLEDTGLGYGRSSAVVLLTVISRPRSEEQKVCFYKLLTGALERDCGISPDDVIVALVENSDADWSFGRGRAEFLTGDLV-   -
               SCOP domains d2aagb_ B: Malonate semialdehyde decarboxylase, MSAD                                                                               SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh......eeeeeeehhh.eee.............eeeeeee...hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhh.ee.....hhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aag B   1 PLLKFDLFYGRTDAQIKSLLDAAHGAMVDAFGVPANDRYQTVSQHRPGEMVLEDTGLGYGRSSAVVLLTVISRPRSEEQKVCFYKLLTGALERDCGISPDDVIVALVENSDADWSFGRGRAEFLTGDLVG 130
                                    10        20        30        40        50        60        70        80        90       100       110       120       130


Chain C from PDB  Type:PROTEIN  Length:129
 aligned with Q9EV83_PSEPV | Q9EV83 from UniProtKB/TrEMBL  Length:130

    Alignment length:129
                                    11        21        31        41        51        61        71        81        91       101       111       121         
         Q9EV83_PSEPV     2 PLLKFDIFYGRTDAQIKSLLDAAHGAMVDAFGVPANDRYQTVSQHRPGEMVLEDTGLGYGRSSAVVLLTVISRPRSEEQKVCFYKLLTGALERDCGISPDDVIVALVENSDADWSFGRGRAEFLTGDLV 130
               SCOP domains d2aagc_ C: Malonate semialdehyde decarboxylase, MSAD                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh......eeeeeeehhh.eee.............eeeeeee...hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhh.ee.....hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aag C   1 PLLKFDLFYGRTDAQIKSLLDAAHGAMVDAFGVPANDRYQTVSQHRPGEMVLEDTGLGYGRSSAVVLLTVISRPRSEEQKVCFYKLLTGALERDCGISPDDVIVALVENSDADWSFGRGRAEFLTGDLV 129
                                    10        20        30        40        50        60        70        80        90       100       110       120         


Chain D from PDB  Type:PROTEIN  Length:129
 aligned with Q9EV83_PSEPV | Q9EV83 from UniProtKB/TrEMBL  Length:130

    Alignment length:129
                                    11        21        31        41        51        61        71        81        91       101       111       121         
         Q9EV83_PSEPV     2 PLLKFDIFYGRTDAQIKSLLDAAHGAMVDAFGVPANDRYQTVSQHRPGEMVLEDTGLGYGRSSAVVLLTVISRPRSEEQKVCFYKLLTGALERDCGISPDDVIVALVENSDADWSFGRGRAEFLTGDLV 130
               SCOP domains d2aagd_ D: Malonate semialdehyde decarboxylase, MSAD                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh......eeeeeeehhh.eee.............eeeeeee...hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhh.ee.....hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aag D   1 PLLKFDLFYGRTDAQIKSLLDAAHGAMVDAFGVPANDRYQTVSQHRPGEMVLEDTGLGYGRSSAVVLLTVISRPRSEEQKVCFYKLLTGALERDCGISPDDVIVALVENSDADWSFGRGRAEFLTGDLV 129
                                    10        20        30        40        50        60        70        80        90       100       110       120         


Chain E from PDB  Type:PROTEIN  Length:129
 aligned with Q9EV83_PSEPV | Q9EV83 from UniProtKB/TrEMBL  Length:130

    Alignment length:129
                                    11        21        31        41        51        61        71        81        91       101       111       121         
         Q9EV83_PSEPV     2 PLLKFDIFYGRTDAQIKSLLDAAHGAMVDAFGVPANDRYQTVSQHRPGEMVLEDTGLGYGRSSAVVLLTVISRPRSEEQKVCFYKLLTGALERDCGISPDDVIVALVENSDADWSFGRGRAEFLTGDLV 130
               SCOP domains d2aage_ E: Malonate semialdehyde decarboxylase, MSAD                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh......eeeeeeehhh.eee.............eeeeeee...hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhh.ee.....hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aag E   1 PLLKFDLFYGRTDAQIKSLLDAAHGAMVDAFGVPANDRYQTVSQHRPGEMVLEDTGLGYGRSSAVVLLTVISRPRSEEQKVCFYKLLTGALERDCGISPDDVIVALVENSDADWSFGRGRAEFLTGDLV 129
                                    10        20        30        40        50        60        70        80        90       100       110       120         


Chain F from PDB  Type:PROTEIN  Length:129
 aligned with Q9EV83_PSEPV | Q9EV83 from UniProtKB/TrEMBL  Length:130

    Alignment length:129
                                    11        21        31        41        51        61        71        81        91       101       111       121         
         Q9EV83_PSEPV     2 PLLKFDIFYGRTDAQIKSLLDAAHGAMVDAFGVPANDRYQTVSQHRPGEMVLEDTGLGYGRSSAVVLLTVISRPRSEEQKVCFYKLLTGALERDCGISPDDVIVALVENSDADWSFGRGRAEFLTGDLV 130
               SCOP domains d2aagf_ F: Malonate semialdehyde decarboxylase, MSAD                                                                              SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...hhhhhhhhhhhhhhhhhhhhh......eeeeeeehhh.eee.............eeeeeee...hhhhhhhhhhhhhhhhhhhhh.hhh.eeeeeee.hhh.ee.....hhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2aag F   1 PLLKFDLFYGRTDAQIKSLLDAAHGAMVDAFGVPANDRYQTVSQHRPGEMVLEDTGLGYGRSSAVVLLTVISRPRSEEQKVCFYKLLTGALERDCGISPDDVIVALVENSDADWSFGRGRAEFLTGDLV 129
                                    10        20        30        40        50        60        70        80        90       100       110       120
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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, 6)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (Q9EV83_PSEPV | Q9EV83)
molecular function
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
biological process
    GO:0006725    cellular aromatic compound metabolic process    The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.

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    Val B:129 - Gly B:130   [ RasMol ]  
 
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 Related Entries

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        Q9EV83_PSEPV | Q9EV83: 2aaj 2aal

(-) Related Entries Specified in the PDB File

2aaj 2aal