1S89 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   H98N MUTANT OF METHYLGLYOXAL SYNTHASE FROM E. COLI COMPLEXED WITH PHOSPHOGLYCOLIC ACID

Authors :   G. T. Marks, D. H. Harrison, M. Susler

Date :   31 Jan 04 (Deposition) - 30 Mar 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.22

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

Keywords :   Glycolytic Bypass, Methylglyoxal, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. T. Marks, M. Susler, D. H. Harrison
Mutagenic Studies On Histidine 98 Of Methylglyoxal Synthase: Effects On Mechanism And Conformational Change.
Biochemistry V. 43 3802 2004
PubMed-ID: 15049687 | Reference-DOI: 10.1021/BI035838O
(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	:	PET-16B
	Expression System Strain	:	ML1
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MGSA, B0963, Z1314, ECS1047, SF0965, S1031
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	MGS

		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 , PRO A:67 , ASP A:71 , ASN A:98 , HOH A:215 , ARG F:150	BINDING SITE FOR RESIDUE PGA A 201
2	AC2	SOFTWARE	VAL B:17 , ALA B:18 , HIS B:19 , LYS B:23 , THR B:45 , THR B:47 , THR B:48 , SER B:65 , GLY B:66 , PRO B:67 , ASP B:71 , ASN B:98 , HOH B:217 , ARG E:150	BINDING SITE FOR RESIDUE PGA B 202
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 , ASN C:98 , HOH C:224 , ARG D:150	BINDING SITE FOR RESIDUE PGA C 203
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 , PRO D:67 , ASP D:71 , ASN D:98 , HOH D:212	BINDING SITE FOR RESIDUE PGA D 204
5	AC5	SOFTWARE	ARG B:150 , VAL E:17 , ALA E:18 , LYS E:23 , THR E:45 , THR E:47 , THR E:48 , SER E:65 , GLY E:66 , PRO E:67 , ASP E:71 , ASN E:98 , HOH E:210	BINDING SITE FOR RESIDUE PGA E 205
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 , PRO F:67 , ASP F:71 , ASN F:98 , HOH F:218	BINDING SITE FOR RESIDUE PGA F 206

(no "SS Bond" information available for 1S89)

(no "Cis Peptide Bond" information available for 1S89)

(no "SAP(SNP)/Variant" information available for 1S89)

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 1S89)

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 d1s89a_ A: Methylglyoxal synthase, MgsA                                                                                                                  SCOP domains
               CATH domains 1s89A00 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.hhhhhhhhhhhhhhh..eeeeeehhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------METHYLGLY------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s89 A   1 MELTTRTLPARKHIALVAHDHCKQMLMSWVERHQPLLEQHVLYATGTTGNLISRATGMNVNAMLSGPMGGDQQVGALISEGKIDVLIFFWDPLNAVPNDPDVKALLRLATVWNIPVATNVATADFIIQSPHFNDAVDILIPDYQRYLADRLK 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain B 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 d1s89b_ B: Methylglyoxal synthase, MgsA                                                                                                                  SCOP domains
               CATH domains 1s89B00 B: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
                 1s89 B   1 MELTTRTLPARKHIALVAHDHCKQMLMSWVERHQPLLEQHVLYATGTTGNLISRATGMNVNAMLSGPMGGDQQVGALISEGKIDVLIFFWDPLNAVPNDPDVKALLRLATVWNIPVATNVATADFIIQSPHFNDAVDILIPDYQRYLADRLK 152
                                    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 d1s89c_ C: Methylglyoxal synthase, MgsA                                                                                                                  SCOP domains
               CATH domains 1s89C00 C:1-152  [code=3.40.50.1380, no name defined]                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeee...hhhhhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhh..eeeeeehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------METHYLGLY------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s89 C   1 MELTTRTLPARKHIALVAHDHCKQMLMSWVERHQPLLEQHVLYATGTTGNLISRATGMNVNAMLSGPMGGDQQVGALISEGKIDVLIFFWDPLNAVPNDPDVKALLRLATVWNIPVATNVATADFIIQSPHFNDAVDILIPDYQRYLADRLK 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 d1s89d_ D: Methylglyoxal synthase, MgsA                                                                                                                  SCOP domains
               CATH domains 1s89D00 D:1-152  [code=3.40.50.1380, no name defined]                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeeehhhhhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhhh.eeeeeehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------METHYLGLY------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s89 D   1 MELTTRTLPARKHIALVAHDHCKQMLMSWVERHQPLLEQHVLYATGTTGNLISRATGMNVNAMLSGPMGGDQQVGALISEGKIDVLIFFWDPLNAVPNDPDVKALLRLATVWNIPVATNVATADFIIQSPHFNDAVDILIPDYQRYLADRLK 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 d1s89e_ E: Methylglyoxal synthase, MgsA                                                                                                                  SCOP domains
               CATH domains 1s89E00 E:1-152  [code=3.40.50.1380, no name defined]                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee....eeeeeehhhhhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhh..eee..hhhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhh...ee.hhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------METHYLGLY------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s89 E   1 MELTTRTLPARKHIALVAHDHCKQMLMSWVERHQPLLEQHVLYATGTTGNLISRATGMNVNAMLSGPMGGDQQVGALISEGKIDVLIFFWDPLNAVPNDPDVKALLRLATVWNIPVATNVATADFIIQSPHFNDAVDILIPDYQRYLADRLK 152
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150

Chain F 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 d1s89f_ F: Methylglyoxal synthase, MgsA                                                                                                                  SCOP domains
               CATH domains 1s89F00 F:1-152  [code=3.40.50.1380, no name defined]                                                                                                    CATH domains
           Pfam domains (1) ------------------------MGS-1s89F01 F:25-118                                                                          ---------------------------------- Pfam domains (1)
           Pfam domains (2) ------------------------MGS-1s89F02 F:25-118                                                                          ---------------------------------- Pfam domains (2)
           Pfam domains (3) ------------------------MGS-1s89F03 F:25-118                                                                          ---------------------------------- Pfam domains (3)
           Pfam domains (4) ------------------------MGS-1s89F04 F:25-118                                                                          ---------------------------------- Pfam domains (4)
           Pfam domains (5) ------------------------MGS-1s89F05 F:25-118                                                                          ---------------------------------- Pfam domains (5)
           Pfam domains (6) ------------------------MGS-1s89F06 F:25-118                                                                          ---------------------------------- Pfam domains (6)
         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
                 1s89 F   1 MELTTRTLPARKHIALVAHDHCKQMLMSWVERHQPLLEQHVLYATGTTGNLISRATGMNVNAMLSGPMGGDQQVGALISEGKIDVLIFFWDPLNAVPNDPDVKALLRLATVWNIPVATNVATADFIIQSPHFNDAVDILIPDYQRYLADRLK 152
                                    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	d1s89a_	A:
1b	d1s89b_	B:
1c	d1s89c_	C:
1d	d1s89d_	D:
1e	d1s89e_	E:
1f	d1s89f_	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. (6)

1a	1s89A00	A:1-152
1b	1s89B00	B:1-152
1c	1s89C00	C:1-152
1d	1s89D00	D:1-152
1e	1s89E00	E:1-152
1f	1s89F00	F:1-152

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Family: MGS (13)

Escherichia coli (strain K12) (4)

1a	MGS-1s89F01	F:25-118
1b	MGS-1s89F02	F:25-118
1c	MGS-1s89F03	F:25-118
1d	MGS-1s89F04	F:25-118
1e	MGS-1s89F05	F:25-118
1f	MGS-1s89F06	F:25-118

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

1s8a	H98Q MUTANT OF METHYLGLYOXAL SYNTHASE FROM E. COLI COMPLEXED WITH PHOSPHOGLYCOLIC ACID

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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