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Title :   STRUCTURE OF METHYLGLYOXAL SYNTHASE COMPLEXED WITH THE COMPETITIVE INHIBITOR 2-PHOSPHOGLYCOLATE

Authors :   D. Saadat, D. H. T. Harrison

Date :   15 Feb 00 (Deposition) - 01 Mar 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B,C,D,E,F

Keywords :   Beta/Alpha Protein, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Saadat, D. H. Harrison
Mirroring Perfection: The Structure Of Methylglyoxal Synthase Complexed With The Competitive Inhibitor 2-Phosphoglycolate.
Biochemistry V. 39 2950 2000
PubMed-ID: 10715115 | Reference-DOI: 10.1021/BI992666F
(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	:	PET16B
	Expression System Taxid	:	562
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 6)

No.	Name	Count	Type	Full Name
1	PGA	6	Ligand/Ion	2-PHOSPHOGLYCOLIC ACID

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	VAL A:17 , ALA A:18 , HIS A:19 , LYS A:23 , THR A:45 , THR A:47 , THR A:48 , SER A:65 , GLY A:66 , ASP A:71 , HIS A:98 , HOH A:381 , HOH A:482 , ARG F:150	BINDING SITE FOR RESIDUE PGA A 201
2	AC2	SOFTWARE	VAL B:17 , ALA B:18 , LYS B:23 , THR B:45 , THR B:47 , THR B:48 , SER B:65 , GLY B:66 , PRO B:67 , ASP B:71 , HIS B:98 , HOH B:367 , HOH B:527 , ARG E:150	BINDING SITE FOR RESIDUE PGA B 211
3	AC3	SOFTWARE	VAL C:17 , ALA C:18 , HIS C:19 , LYS C:23 , THR C:45 , THR C:47 , THR C:48 , SER C:65 , GLY C:66 , ASP C:71 , HIS C:98 , HOH C:353 , ARG D:150	BINDING SITE FOR RESIDUE PGA C 221
4	AC4	SOFTWARE	ARG C:150 , VAL D:17 , ALA D:18 , HIS D:19 , LYS D:23 , THR D:45 , THR D:47 , THR D:48 , SER D:65 , GLY D:66 , ASP D:71 , HIS D:98 , HOH D:339 , HOH D:533	BINDING SITE FOR RESIDUE PGA D 231
5	AC5	SOFTWARE	ARG B:150 , VAL E:17 , ALA E:18 , HIS E:19 , LYS E:23 , THR E:45 , THR E:47 , THR E:48 , SER E:65 , GLY E:66 , ASP E:71 , HIS E:98 , HOH E:326 , HOH E:529	BINDING SITE FOR RESIDUE PGA E 241
6	AC6	SOFTWARE	ARG A:150 , VAL F:17 , ALA F:18 , LYS F:23 , THR F:45 , THR F:47 , THR F:48 , SER F:65 , GLY F:66 , ASP F:71 , HIS F:98 , HOH F:312	BINDING SITE FOR RESIDUE PGA F 251

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

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

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

Asymmetric/Biological Unit (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	METHYLGLYOXAL_SYNTH	PS01335	Methylglyoxal synthase active site.	MGSA_ECOLI	65-73	6	A:65-73 B:65-73 C:65-73 D:65-73 E:65-73 F:65-73

(no "Exon" information available for 1EGH)

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:152
 aligned with MGSA_ECOLI | P0A731 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  
           MGSA_ECOLI     1 MELTTRTLPARKHIALVAHDHCKQMLMSWVERHQPLLEQHVLYATGTTGNLISRATGMNVNAMLSGPMGGDQQVGALISEGKIDVLIFFWDPLNAVPHDPDVKALLRLATVWNIPVATNVATADFIIQSPHFNDAVDILIPDYQRYLADRLK 152
               SCOP domains d1egha_ A: Methylglyoxal synthase, MgsA                                                                                                                  SCOP domains
               CATH domains 1eghA00 A:1-152  [code=3.40.50.1380, no name defined]                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeee...hhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------METHYLGLY------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1egh A   1 MELTTRTLPARKHIALVAHDHCKQMLMSWVERHQPLLEQHVLYATGTTGNLISRATGMNVNAMLSGPMGGDQQVGALISEGKIDVLIFFWDPLNAVPHDPDVKALLRLATVWNIPVATNVATADFIIQSPHFNDAVDILIPDYQRYLADRLK 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B from PDB  Type:PROTEIN  Length:151
 aligned with MGSA_ECOLI | P0A731 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 
           MGSA_ECOLI     1 MELTTRTLPARKHIALVAHDHCKQMLMSWVERHQPLLEQHVLYATGTTGNLISRATGMNVNAMLSGPMGGDQQVGALISEGKIDVLIFFWDPLNAVPHDPDVKALLRLATVWNIPVATNVATADFIIQSPHFNDAVDILIPDYQRYLADRL 151
               SCOP domains d1eghb_ B: Methylglyoxal synthase, MgsA                                                                                                                 SCOP domains
               CATH domains 1eghB00 B:1-151  [code=3.40.50.1380, no name defined]                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeee...hhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------METHYLGLY------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1egh B   1 MELTTRTLPARKHIALVAHDHCKQMLMSWVERHQPLLEQHVLYATGTTGNLISRATGMNVNAMLSGPMGGDQQVGALISEGKIDVLIFFWDPLNAVPHDPDVKALLRLATVWNIPVATNVATADFIIQSPHFNDAVDILIPDYQRYLADRL 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain C from PDB  Type:PROTEIN  Length:152
 aligned with MGSA_ECOLI | P0A731 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  
           MGSA_ECOLI     1 MELTTRTLPARKHIALVAHDHCKQMLMSWVERHQPLLEQHVLYATGTTGNLISRATGMNVNAMLSGPMGGDQQVGALISEGKIDVLIFFWDPLNAVPHDPDVKALLRLATVWNIPVATNVATADFIIQSPHFNDAVDILIPDYQRYLADRLK 152
               SCOP domains d1eghc_ C: Methylglyoxal synthase, MgsA                                                                                                                  SCOP domains
               CATH domains 1eghC00 C:1-152  [code=3.40.50.1380, no name defined]                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeee...hhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------METHYLGLY------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1egh C   1 MELTTRTLPARKHIALVAHDHCKQMLMSWVERHQPLLEQHVLYATGTTGNLISRATGMNVNAMLSGPMGGDQQVGALISEGKIDVLIFFWDPLNAVPHDPDVKALLRLATVWNIPVATNVATADFIIQSPHFNDAVDILIPDYQRYLADRLK 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain D from PDB  Type:PROTEIN  Length:152
 aligned with MGSA_ECOLI | P0A731 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  
           MGSA_ECOLI     1 MELTTRTLPARKHIALVAHDHCKQMLMSWVERHQPLLEQHVLYATGTTGNLISRATGMNVNAMLSGPMGGDQQVGALISEGKIDVLIFFWDPLNAVPHDPDVKALLRLATVWNIPVATNVATADFIIQSPHFNDAVDILIPDYQRYLADRLK 152
               SCOP domains d1eghd_ D: Methylglyoxal synthase, MgsA                                                                                                                  SCOP domains
               CATH domains 1eghD00 D:1-152  [code=3.40.50.1380, no name defined]                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeee...hhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------METHYLGLY------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1egh D   1 MELTTRTLPARKHIALVAHDHCKQMLMSWVERHQPLLEQHVLYATGTTGNLISRATGMNVNAMLSGPMGGDQQVGALISEGKIDVLIFFWDPLNAVPHDPDVKALLRLATVWNIPVATNVATADFIIQSPHFNDAVDILIPDYQRYLADRLK 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain E from PDB  Type:PROTEIN  Length:152
 aligned with MGSA_ECOLI | P0A731 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150  
           MGSA_ECOLI     1 MELTTRTLPARKHIALVAHDHCKQMLMSWVERHQPLLEQHVLYATGTTGNLISRATGMNVNAMLSGPMGGDQQVGALISEGKIDVLIFFWDPLNAVPHDPDVKALLRLATVWNIPVATNVATADFIIQSPHFNDAVDILIPDYQRYLADRLK 152
               SCOP domains d1eghe_ E: Methylglyoxal synthase, MgsA                                                                                                                  SCOP domains
               CATH domains 1eghE00 E:1-152  [code=3.40.50.1380, no name defined]                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeee...hhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhh..eeeeeehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------METHYLGLY------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1egh E   1 MELTTRTLPARKHIALVAHDHCKQMLMSWVERHQPLLEQHVLYATGTTGNLISRATGMNVNAMLSGPMGGDQQVGALISEGKIDVLIFFWDPLNAVPHDPDVKALLRLATVWNIPVATNVATADFIIQSPHFNDAVDILIPDYQRYLADRLK 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain F from PDB  Type:PROTEIN  Length:151
 aligned with MGSA_ECOLI | P0A731 from UniProtKB/Swiss-Prot  Length:152

    Alignment length:151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150 
           MGSA_ECOLI     1 MELTTRTLPARKHIALVAHDHCKQMLMSWVERHQPLLEQHVLYATGTTGNLISRATGMNVNAMLSGPMGGDQQVGALISEGKIDVLIFFWDPLNAVPHDPDVKALLRLATVWNIPVATNVATADFIIQSPHFNDAVDILIPDYQRYLADRL 151
               SCOP domains d1eghf_ F: Methylglyoxal synthase, MgsA                                                                                                                 SCOP domains
               CATH domains 1eghF00 F:1-151  [code=3.40.50.1380, no name defined]                                                                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeee...hhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------METHYLGLY------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1egh F   1 MELTTRTLPARKHIALVAHDHCKQMLMSWVERHQPLLEQHVLYATGTTGNLISRATGMNVNAMLSGPMGGDQQVGALISEGKIDVLIFFWDPLNAVPHDPDVKALLRLATVWNIPVATNVATADFIIQSPHFNDAVDILIPDYQRYLADRL 151
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

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/Biological 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)

Escherichia coli [TaxId: 562] (5)

1a	d1egha_	A:
1b	d1eghb_	B:
1c	d1eghc_	C:
1d	d1eghd_	D:
1e	d1eghe_	E:
1f	d1eghf_	F:

Asymmetric/Biological 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)

Escherichia coli. Organism_taxid: 562. (7)

1a	1eghB00	B:1-151
1b	1eghF00	F:1-151
1c	1eghA00	A:1-152
1d	1eghC00	C:1-152
1e	1eghD00	D:1-152
1f	1eghE00	E:1-152

(no "Pfam Domain" information available for 1EGH)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D,E,F (MGSA_ECOLI | P0A731)

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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1egh)

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	MGSA_ECOLI \| P0A731	:	1b93 1ik4 1s89 1s8a

1b93	1B93 CONTAINS THE SAME PROTEIN COMPLEXED WITH INORGANIC PHOSPHATE AND FORMATE

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