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(-) Description

Title :  CRYSTAL STRUCTURE OF METHYLGLYOXAL SYNTHASE (TM1185) FROM THERMOTOGA MARITIMA AT 2.06 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  20 Sep 04  (Deposition) - 28 Sep 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.06
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Tm1185, Methylglyoxal Synthase, Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Joint Center For Structural Genomics, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Methylglyoxal Synthase (Tm1185) From Thermotoga Maritima At 2. 06 A Resolution
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - METHYLGLYOXAL SYNTHASE
    Chains: A, B
    EC Number: 4.2.3.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MGSA,TM1185
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: MGS

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2SO46Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:27 , THR A:49 , THR A:51 , THR A:52 , SER A:69 , GLY A:70 , HOH A:174 , HOH A:189 , HOH A:204 , ILE B:155BINDING SITE FOR RESIDUE SO4 A 167
2AC2SOFTWARELYS B:27 , THR B:49 , THR B:51 , THR B:52 , SER B:69 , GLY B:70 , HOH B:187BINDING SITE FOR RESIDUE SO4 B 167
3AC3SOFTWAREASN A:117 , ARG B:26 , ARG B:124BINDING SITE FOR RESIDUE CL B 168
4AC4SOFTWAREARG A:26 , ARG A:124 , HOH B:181BINDING SITE FOR RESIDUE CL A 168

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1VMD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1VMD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1VMD)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1METHYLGLYOXAL_SYNTHPS01335 Methylglyoxal synthase active site.MGSA_THEMA58-66
 		  2A:69-77
B:69-77
Biological Unit 1 (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1METHYLGLYOXAL_SYNTHPS01335 Methylglyoxal synthase active site.MGSA_THEMA58-66
 		  6A:69-77
B:69-77

(-) Exons   (0, 0)

(no "Exon" information available for 1VMD)

(-) 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:156
 aligned with MGSA_THEMA | Q9X0R7 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:156
                                   1                                                                                                                                                    
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143      
           MGSA_THEMA     - -------MDKKKRIALIAHDRRKRDLLEWVSFNLGTLSKHELYATGTTGALLQEKLGLKVHRLKSGPLGGDQQIGAMIAEGKIDVLIFFWDPLEPQAHDVDVKALIRIATVYNIPVAITRSTADFLISSPLMNDVYEKIQIDYEEELERRIRKVVE 149
               SCOP domains d1vmda_ A: Methylglyoxal synthase, MgsA                                                                                                                      SCOP domains
               CATH domains 1vmdA00 A:5-160  [code=3.40.50.1380, no name defined]                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee....eeeeee...hhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------METHYLGLY----------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vmd A   5 PRRYKIFMDKKKRIALIAHDRRKRDLLEWVSFNLGTLSKHELYATGTTGALLQEKLGLKVHRLKSGPLGGDQQIGAMIAEGKIDVLIFFWDPLEPQAHDVDVKALIRIATVYNIPVAITRSTADFLISSPLMNDVYEKIQIDYEEELERRIRKVVE 160
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154      


Chain B from PDB  Type:PROTEIN  Length:156
 aligned with MGSA_THEMA | Q9X0R7 from UniProtKB/Swiss-Prot  Length:155

    Alignment length:156
                                   1                                                                                                                                                    
                                   | 3        13        23        33        43        53        63        73        83        93       103       113       123       133       143      
           MGSA_THEMA     - -------MDKKKRIALIAHDRRKRDLLEWVSFNLGTLSKHELYATGTTGALLQEKLGLKVHRLKSGPLGGDQQIGAMIAEGKIDVLIFFWDPLEPQAHDVDVKALIRIATVYNIPVAITRSTADFLISSPLMNDVYEKIQIDYEEELERRIRKVVE 149
               SCOP domains d1vmdb_ B: Methylglyoxal synthase, MgsA                                                                                                                      SCOP domains
               CATH domains 1vmdB00 B:5-160  [code=3.40.50.1380, no name defined]                                                                                                        CATH domains
           Pfam domains (1) -------------------------MGS-1vmdB01 B:30-122                                                                         -------------------------------------- Pfam domains (1)
           Pfam domains (2) -------------------------MGS-1vmdB02 B:30-122                                                                         -------------------------------------- Pfam domains (2)
         Sec.struct. author ..eeeeee....eeeeee...hhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhh....eeeee...........hhhhhhhhhhhh...ee.hhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------METHYLGLY----------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1vmd B   5 PRRYKIFMDKKKRIALIAHDRRKRDLLEWVSFNLGTLSKHELYATGTTGALLQEKLGLKVHRLKSGPLGGDQQIGAMIAEGKIDVLIFFWDPLEPQAHDVDVKALIRIATVYNIPVAITRSTADFLISSPLMNDVYEKIQIDYEEELERRIRKVVE 160
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: MGS] (13)
(-)
Family: MGS (13)
(-)
Thermotoga maritima (2)
1aMGS-1vmdB01B:30-122
1bMGS-1vmdB02B:30-122

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (MGSA_THEMA | Q9X0R7)
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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