1WO8 - JenaLib

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Title :   CRYSTAL STRUCTURE OF METHYLGLYOXAL SYNTHASE FROM THERMUS THERMOPHILUS HB8

Authors :   M. Sugahara, N. Kunishima, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   12 Aug 04 (Deposition) - 23 Aug 05 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F  (1x)
Biol. Unit 2: A,B,C,D,E,F  (2x)

Keywords :   Methylglyoxal Synthase, Thermus Thermophilus Hb8, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Sugahara, N. Kunishima
Crystal Structure Of Methylglyoxal Synthase From Thermus Thermophilus Hb8
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - METHYLGLYOXAL SYNTHASE
	Chains	:	A, B, C, D, E, F
	EC Number	:	4.2.3.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET11A
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS THERMOPHILUS HB8
	Organism Taxid	:	300852
	Strain	:	HB8 / ATCC 27634 / DSM 579

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B	C	D	E	F
Biological Unit 2 (2x)	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 7)

No.	Name	Count	Type	Full Name
1	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 1 (1, 7)

No.	Name	Count	Type	Full Name
1	SO4	7	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 14)

No.	Name	Count	Type	Full Name
1	SO4	14	Ligand/Ion	SULFATE ION

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:13 , THR A:35 , THR A:37 , THR A:38 , SER A:55 , GLY A:56 , HOH A:1061 , HOH A:1073 , HOH A:1143	BINDING SITE FOR RESIDUE SO4 A 1001
2	AC2	SOFTWARE	LYS B:13 , THR B:35 , GLY B:36 , THR B:37 , THR B:38 , SER B:55 , GLY B:56 , HOH B:1066 , HOH B:1083 , HOH B:1118	BINDING SITE FOR RESIDUE SO4 B 1002
3	AC3	SOFTWARE	LYS C:13 , THR C:35 , THR C:37 , THR C:38 , SER C:55 , GLY C:56 , HOH C:1021 , HOH C:1062 , HOH C:1099	BINDING SITE FOR RESIDUE SO4 C 1003
4	AC4	SOFTWARE	LYS D:13 , THR D:35 , THR D:37 , THR D:38 , SER D:55 , GLY D:56 , HOH D:1111 , HOH D:1144	BINDING SITE FOR RESIDUE SO4 D 1004
5	AC5	SOFTWARE	LYS E:13 , THR E:35 , THR E:37 , THR E:38 , SER E:55 , GLY E:56 , HOH E:1037 , HOH E:1102	BINDING SITE FOR RESIDUE SO4 E 1005
6	AC6	SOFTWARE	LYS F:13 , THR F:35 , GLY F:36 , THR F:37 , THR F:38 , SER F:55 , GLY F:56 , HOH F:1077 , HOH F:1083	BINDING SITE FOR RESIDUE SO4 F 1006
7	AC7	SOFTWARE	GLN D:43 , ARG D:52 , HOH D:1028 , HOH D:1131	BINDING SITE FOR RESIDUE SO4 D 1007

(no "SS Bond" information available for 1WO8)

(no "Cis Peptide Bond" information available for 1WO8)

(no "SAP(SNP)/Variant" information available for 1WO8)

Asymmetric Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	METHYLGLYOXAL_SYNTH	PS01335	Methylglyoxal synthase active site.	MGSA_THET8	55-63	6	A:55-63 B:55-63 C:55-63 D:55-63 E:55-63 F:55-63

Biological Unit 1 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	METHYLGLYOXAL_SYNTH	PS01335	Methylglyoxal synthase active site.	MGSA_THET8	55-63	6	A:55-63 B:55-63 C:55-63 D:55-63 E:55-63 F:55-63

Biological Unit 2 (1, 12)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	METHYLGLYOXAL_SYNTH	PS01335	Methylglyoxal synthase active site.	MGSA_THET8	55-63	12	A:55-63 B:55-63 C:55-63 D:55-63 E:55-63 F:55-63

(no "Exon" information available for 1WO8)

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:126
 aligned with MGSA_THET8 | Q5SHD6 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:126
                                    10        20        30        40        50        60        70        80        90       100       110       120      
           MGSA_THET8     1 MKALALIAHDAKKDEMVAFCLRHKDVLARYPLLATGTTGARIQEATGLAVERVLSGPLGGDLQIGARVAEGKVLAVVFLQDPLTAKPHEPDVQALMRVCNVHGVPLATNLVAAEALIAWIRKGTPQ 126
               SCOP domains d1wo8a1 A:1-126 Methylglyoxal synthase, MgsA                                                                                   SCOP domains
               CATH domains 1wo8A00 A:1-126  [code=3.40.50.1380, no name defined]                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh...ee......hhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------METHYLGLY--------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1wo8 A   1 MKALALIAHDAKKDEMVAFCLRHKDVLARYPLLATGTTGARIQEATGLAVERVLSGPLGGDLQIGARVAEGKVLAVVFLQDPLTAKPHEPDVQALMRVCNVHGVPLATNLVAAEALIAWIRKGTPQ 126
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain B from PDB  Type:PROTEIN  Length:123
 aligned with MGSA_THET8 | Q5SHD6 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:123
                                    10        20        30        40        50        60        70        80        90       100       110       120   
           MGSA_THET8     1 MKALALIAHDAKKDEMVAFCLRHKDVLARYPLLATGTTGARIQEATGLAVERVLSGPLGGDLQIGARVAEGKVLAVVFLQDPLTAKPHEPDVQALMRVCNVHGVPLATNLVAAEALIAWIRKG 123
               SCOP domains d1wo8b_ B: Methylglyoxal synthase, MgsA                                                                                     SCOP domains
               CATH domains 1wo8B00 B:1-123  [code=3.40.50.1380, no name defined]                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh..eee......hhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------METHYLGLY------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wo8 B   1 MKALALIAHDAKKDEMVAFCLRHKDVLARYPLLATGTTGARIQEATGLAVERVLSGPLGGDLQIGARVAEGKVLAVVFLQDPLTAKPHEPDVQALMRVCNVHGVPLATNLVAAEALIAWIRKG 123
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain C from PDB  Type:PROTEIN  Length:123
 aligned with MGSA_THET8 | Q5SHD6 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:123
                                    10        20        30        40        50        60        70        80        90       100       110       120   
           MGSA_THET8     1 MKALALIAHDAKKDEMVAFCLRHKDVLARYPLLATGTTGARIQEATGLAVERVLSGPLGGDLQIGARVAEGKVLAVVFLQDPLTAKPHEPDVQALMRVCNVHGVPLATNLVAAEALIAWIRKG 123
               SCOP domains d1wo8c_ C: Methylglyoxal synthase, MgsA                                                                                     SCOP domains
               CATH domains 1wo8C00 C:1-123  [code=3.40.50.1380, no name defined]                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------METHYLGLY------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wo8 C   1 MKALALIAHDAKKDEMVAFCLRHKDVLARYPLLATGTTGARIQEATGLAVERVLSGPLGGDLQIGARVAEGKVLAVVFLQDPLTAKPHEPDVQALMRVCNVHGVPLATNLVAAEALIAWIRKG 123
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain D from PDB  Type:PROTEIN  Length:123
 aligned with MGSA_THET8 | Q5SHD6 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:123
                                    10        20        30        40        50        60        70        80        90       100       110       120   
           MGSA_THET8     1 MKALALIAHDAKKDEMVAFCLRHKDVLARYPLLATGTTGARIQEATGLAVERVLSGPLGGDLQIGARVAEGKVLAVVFLQDPLTAKPHEPDVQALMRVCNVHGVPLATNLVAAEALIAWIRKG 123
               SCOP domains d1wo8d_ D: Methylglyoxal synthase, MgsA                                                                                     SCOP domains
               CATH domains 1wo8D00 D:1-123  [code=3.40.50.1380, no name defined]                                                                       CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh...ee......hhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------METHYLGLY------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wo8 D   1 MKALALIAHDAKKDEMVAFCLRHKDVLARYPLLATGTTGARIQEATGLAVERVLSGPLGGDLQIGARVAEGKVLAVVFLQDPLTAKPHEPDVQALMRVCNVHGVPLATNLVAAEALIAWIRKG 123
                                    10        20        30        40        50        60        70        80        90       100       110       120

Chain E from PDB  Type:PROTEIN  Length:122
 aligned with MGSA_THET8 | Q5SHD6 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:122
                                    11        21        31        41        51        61        71        81        91       101       111       121  
           MGSA_THET8     2 KALALIAHDAKKDEMVAFCLRHKDVLARYPLLATGTTGARIQEATGLAVERVLSGPLGGDLQIGARVAEGKVLAVVFLQDPLTAKPHEPDVQALMRVCNVHGVPLATNLVAAEALIAWIRKG 123
               SCOP domains d1wo8e_ E: Methylglyoxal synthase, MgsA                                                                                    SCOP domains
               CATH domains 1wo8E00 E:2-123  [code=3.40.50.1380, no name defined]                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhhhhhhh...eeehhhhhhhhhhhhh...ee......hhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------METHYLGLY------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wo8 E   2 KALALIAHDAKKDEMVAFCLRHKDVLARYPLLATGTTGARIQEATGLAVERVLSGPLGGDLQIGARVAEGKVLAVVFLQDPLTAKPHEPDVQALMRVCNVHGVPLATNLVAAEALIAWIRKG 123
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain F from PDB  Type:PROTEIN  Length:123
 aligned with MGSA_THET8 | Q5SHD6 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:123
                                    10        20        30        40        50        60        70        80        90       100       110       120   
           MGSA_THET8     1 MKALALIAHDAKKDEMVAFCLRHKDVLARYPLLATGTTGARIQEATGLAVERVLSGPLGGDLQIGARVAEGKVLAVVFLQDPLTAKPHEPDVQALMRVCNVHGVPLATNLVAAEALIAWIRKG 123
               SCOP domains d1wo8f_ F: Methylglyoxal synthase, MgsA                                                                                     SCOP domains
               CATH domains 1wo8F00 F:1-123  [code=3.40.50.1380, no name defined]                                                                       CATH domains
           Pfam domains (1) --------------MGS-1wo8F01 F:15-108                                                                          --------------- Pfam domains (1)
           Pfam domains (2) --------------MGS-1wo8F02 F:15-108                                                                          --------------- Pfam domains (2)
           Pfam domains (3) --------------MGS-1wo8F03 F:15-108                                                                          --------------- Pfam domains (3)
           Pfam domains (4) --------------MGS-1wo8F04 F:15-108                                                                          --------------- Pfam domains (4)
           Pfam domains (5) --------------MGS-1wo8F05 F:15-108                                                                          --------------- Pfam domains (5)
           Pfam domains (6) --------------MGS-1wo8F06 F:15-108                                                                          --------------- Pfam domains (6)
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhhh...eee.....hhhhhhhhhhhhh.eeeeeee........hhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------METHYLGLY------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 1wo8 F   1 MKALALIAHDAKKDEMVAFCLRHKDVLARYPLLATGTTGARIQEATGLAVERVLSGPLGGDLQIGARVAEGKVLAVVFLQDPLTAKPHEPDVQALMRVCNVHGVPLATNLVAAEALIAWIRKG 123
                                    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)
		→ 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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Methylglyoxal synthase-like (31)

Superfamily: Methylglyoxal synthase-like (31)

Family: Methylglyoxal synthase, MgsA (9)

Protein domain: Methylglyoxal synthase, MgsA (7)

Thermus thermophilus [TaxId: 274] (1)

1a	d1wo8a1	A:1-126
1b	d1wo8b_	B:
1c	d1wo8c_	C:
1d	d1wo8d_	D:
1e	d1wo8e_	E:
1f	d1wo8f_	F:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1380, no name defined] (29)

Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8 / atcc 27634 / dsm 579. (1)

1a	1wo8A00	A:1-126
1b	1wo8B00	B:1-123
1c	1wo8C00	C:1-123
1d	1wo8D00	D:1-123
1e	1wo8F00	F:1-123
1f	1wo8E00	E:2-123

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: MGS] (13)

Family: MGS (13)

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (1)

1a	MGS-1wo8F01	F:15-108
1b	MGS-1wo8F02	F:15-108
1c	MGS-1wo8F03	F:15-108
1d	MGS-1wo8F04	F:15-108
1e	MGS-1wo8F05	F:15-108
1f	MGS-1wo8F06	F:15-108

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (MGSA_THET8 | Q5SHD6)

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.

Asymmetric Unit
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Description

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Ligands, Modified Residues, Ions (1, 7)

Sites (7, 7)

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