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(-) Description

Title :  THE CRYSTAL STRUCTURE OF METHYLGLYOXAL SYNTHASE FROM THERMUS SP. GH5 BOUND TO MALONATE.
 
Authors :  A. Shahsavar, M. Erfani Moghaddam, S. V. Antonyuk, K. Khajeh, H. Nader
Date :  13 Mar 10  (Deposition) - 23 Mar 11  (Release) - 23 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (6x)
Keywords :  Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Shahsavar, M. Erfani Moghaddam, S. V. Antonyuk, K. Khajeh, H. Naderi-Manesh
Crystal Structures Of Methylglyoxal Synthase From Thermus Sp. Gh5 In The Open And Closed Conformational States Provide Insight Into The Mechanism Of Allosteric Regulation
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - METHYLGLYOXAL SYNTHASE
    Chains: A
    EC Number: 4.2.99.11
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 28A
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMUS SP. GH5
    Organism Taxid: 405418

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (6x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1MLI1Ligand/IonMALONATE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1MLI6Ligand/IonMALONATE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:8 , HIS A:9 , THR A:35 , THR A:37 , THR A:38 , SER A:55 , GLY A:56 , PRO A:57 , HIS A:88 , HOH A:2038 , HOH A:2058 , HOH A:2099BINDING SITE FOR RESIDUE MLI A1126

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X8W)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2X8W)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2X8W)

(-) Exons   (0, 0)

(no "Exon" information available for 2X8W)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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SAPs(SNPs) PROSITE motifs Exons
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Chain A from PDB  Type:PROTEIN  Length:125
 aligned with B3VH91_9DEIN | B3VH91 from UniProtKB/TrEMBL  Length:132

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
         B3VH91_9DEIN     1 MRALALIAHDAKKEEMVAFCQRHREVLARFPLVATGTTGRRIEEATGLTVEKLLSGPLGGDQQMGARVAEGRILAVIFFRDPLTAQPHEPDVQALLRVCDVHGVPLATNPMAAEALIPWLQSLVG 125
               SCOP domains d2x8wa_ A: automated matches                                                                                                  SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------MGS-2x8wA01 A:15-108                                                                          ----------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh...ee......hhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhhhh..ee.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x8w A   1 MRALALIAHDAKKEEMVAFCQRHREVLARFPLVATGTTGRRIEEATGLTVEKLLSGPLGGDQQMGARVAEGRILAVIFFRDPLTAQPHEPDVQALLRVCDVHGVPLATNPMAAEALIPWLQSLVG 125
                                    10        20        30        40        50        60        70        80        90       100       110       120
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  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  (0, 0)

(no "CATH Domain" information available for 2X8W)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: no clan defined [family: MGS] (13)
(-)
Family: MGS (13)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A   (B3VH91_9DEIN | B3VH91)
molecular function
    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:0008929    methylglyoxal synthase activity    Catalysis of the reaction: glycerone phosphate = methylglyoxal + phosphate.
biological process
    GO:0019242    methylglyoxal biosynthetic process    The chemical reactions and pathways resulting in the formation of methylglyoxal, CH3-CO-CHO, the aldehyde of pyruvic acid.

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2x8v THE CRYSTAL STRUCTURE OF METHYLGLYOXAL SYNTHASE FROM THERMUS SP. GH5 BOUND TO PHOSPHATE ION.