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Asym./Biol. Unit (Jmol Viewer)

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Title :   HUMAN GLYOXALASE I WITH AN N-HYDROXYPYRIDONE INHIBITOR

Authors :   T. A. Fukami, M. Irie, T. Matsuura

Date :   02 Nov 12 (Deposition) - 06 Nov 13 (Release) - 06 Nov 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A,B

Keywords :   Glyoxalase, Lyase-Lyase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. Koyano, T. Aoki, S. Yamamoto, T. Kobayashi, T. Miura, K. Ohara, T. A. Fukami, M. Irie, H. Sakamoto
N-Hydroxypyridone-Based Glyoxalase I Inhibitors Mimicking Binding Interactions Of The Substrate
To Be Published
PubMed: search

Molecule 1 - LACTOYLGLUTATHIONE LYASE
	Chains	:	A, B
	EC Number	:	4.4.1.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-15B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GLO1
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	ALDOKETOMUTASE, GLYOXALASE I, GLX I, KETONE-ALDEHYDE MUTASE, METHYLGLYOXALASE, S-D-LACTOYLGLUTATHIONE METHYLGLYOXAL LYASE

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	HPW	2	Ligand/Ion	N-[3-(1-HYDROXY-6-OXO-4-PHENYL-1,6-DIHYDRO-PYRIDIN-2-YL)-5-METHANESULFONYLAMINO-PHENYL]-METHANESULFONAMIDE
2	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLN A:33 , GLU A:99 , HIS B:126 , GLU B:172 , HPW B:301	BINDING SITE FOR RESIDUE ZN A 201
2	AC2	SOFTWARE	HIS A:126 , GLU A:172 , HPW A:203 , GLN B:33 , GLU B:99	BINDING SITE FOR RESIDUE ZN A 202
3	AC3	SOFTWARE	HIS A:126 , LYS A:150 , LYS A:156 , MET A:157 , LEU A:160 , GLU A:172 , MET A:179 , ZN A:202 , HOH A:308 , GLN B:33 , MET B:35 , PHE B:67 , LEU B:69 , PHE B:71 , GLU B:99 , HOH B:409	BINDING SITE FOR RESIDUE HPW A 203
4	AC4	SOFTWARE	GLN A:33 , MET A:35 , PHE A:67 , LEU A:69 , ILE A:88 , GLU A:99 , ZN A:201 , HIS B:126 , MET B:157 , GLU B:172 , MET B:179 , ALA B:180 , HOH B:440 , HOH B:463 , HOH B:484	BINDING SITE FOR RESIDUE HPW B 301

(no "SS Bond" information available for 3W0U)

Asymmetric/Biological Unit

No.	Residues
1	Asp A:120	-	Pro A:121
2	Asp B:120	-	Pro B:121

Asymmetric/Biological Unit (2, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_031078	C	19	Y	LGUL_HUMAN	Polymorphism	17855424	A/B	C	18	Y
2	UniProt	VAR_013481	E	111	A	LGUL_HUMAN	Polymorphism	4746	A/B	E	110	A

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	VOC	PS51819	Vicinal oxygen chelate (VOC) domain profile.	LGUL_HUMAN	31-177	2	A:30-176 B:30-176
2	GLYOXALASE_I_1	PS00934	Glyoxalase I signature 1.	LGUL_HUMAN	34-55	2	A:33-54 B:33-54
3	GLYOXALASE_I_2	PS00935	Glyoxalase I signature 2.	LGUL_HUMAN	118-134	2	A:117-133 B:117-133

Asymmetric/Biological Unit (6, 12)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1	ENST00000373365	1	ENSE00001460407	chr6:38670917-38670747	171	LGUL_HUMAN	1-28	28	2	A:8-27 B:8-27	20 20
1.2	ENST00000373365	2	ENSE00000750279	chr6:38654750-38654668	83	LGUL_HUMAN	29-56	28	2	A:28-55 B:28-55	28 28
1.3	ENST00000373365	3	ENSE00000750268	chr6:38652290-38652150	141	LGUL_HUMAN	56-103	48	2	A:55-102 B:55-102	48 48
1.4b	ENST00000373365	4b	ENSE00000750246	chr6:38650651-38650584	68	LGUL_HUMAN	103-126	24	2	A:102-125 B:102-125	24 24
1.5	ENST00000373365	5	ENSE00002145874	chr6:38649877-38649788	90	LGUL_HUMAN	126-156	31	2	A:125-155 B:125-155	31 31
1.6	ENST00000373365	6	ENSE00002199029	chr6:38645159-38643719	1441	LGUL_HUMAN	156-184	29	2	A:155-182 B:155-182	28 28

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:175
 aligned with LGUL_HUMAN | Q04760 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:175
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178     
           LGUL_HUMAN     9 GGLTDEAALSCCSDADPSTKDFLLQQTMLRVKDPKKSLDFYTRVLGMTLIQKCDFPIMKFSLYFLAYEDKNDIPKEKDEKIAWALSRKATLELTHNWGTEDDETQSYHNGNSDPRGFGHIGIAVPDVYSACKRFEELGVKFVKKPDDGKMKGLAFIQDPDGYWIEILNPNKMATL 183
               SCOP domains d3w0ua_ A: automated matches                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh....hhhhh..eeeeeeee..hhhhhhhhhhhh...eeeeeeee....eeeeeee..hhhhh..hhhhhhhhhh....eeeeeee.hhhhh..............eeeeeee..hhhhhhhhhhhh...eee..........eeee.....eeeeehhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------Y-------------------------------------------------------------------------------------------A------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------------------VOC  PDB: A:30-176 UniProt: 31-177                                                                                                                 ------ PROSITE (1)
                PROSITE (2) -------------------------GLYOXALASE_I_1        --------------------------------------------------------------GLYOXALASE_I_2   ------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: A:8-2Exon 1.2  PDB: A:28-55      ----------------------------------------------Exon 1.4b  PDB: A:102-12-----------------------------Exon 1.6  PDB: A:155-182     Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.3  PDB: A:55-102 UniProt: 56-103         ----------------------Exon 1.5  PDB: A:125-155       --------------------------- Transcript 1 (2)
                 3w0u A   8 GGLTDEAALSCCSDADPSTKDFLLQQTMLRVKDPKKSLDFYTRVLGMTLIQKCDFPIMKFSLYFLAYEDKNDIPKEKDEKIAWALSRKATLELTHNWGTEDDETQSYHNGNSDPRGFGHIGIAVPDVYSACKRFEELGVKFVKKPDDGKMKGLAFIQDPDGYWIEILNPNKMATL 182
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177

Chain B from PDB  Type:PROTEIN  Length:175
 aligned with LGUL_HUMAN | Q04760 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:175
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178     
           LGUL_HUMAN     9 GGLTDEAALSCCSDADPSTKDFLLQQTMLRVKDPKKSLDFYTRVLGMTLIQKCDFPIMKFSLYFLAYEDKNDIPKEKDEKIAWALSRKATLELTHNWGTEDDETQSYHNGNSDPRGFGHIGIAVPDVYSACKRFEELGVKFVKKPDDGKMKGLAFIQDPDGYWIEILNPNKMATL 183
               SCOP domains d3w0ub_ B: automated matches                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh.....hhhhh..eeeeeeee..hhhhhhhhhhhh...eeeeeeee....eeeeeee..hhhhh..hhhhhhhhhh....eeeeeee.hhhhh..............eeeeeee..hhhhhhhhhhhh...eee..........eeee.....eeeeehhhhh... Sec.struct. author
                 SAPs(SNPs) ----------Y-------------------------------------------------------------------------------------------A------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ----------------------VOC  PDB: B:30-176 UniProt: 31-177                                                                                                                 ------ PROSITE (1)
                PROSITE (2) -------------------------GLYOXALASE_I_1        --------------------------------------------------------------GLYOXALASE_I_2   ------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: B:8-2Exon 1.2  PDB: B:28-55      ----------------------------------------------Exon 1.4b  PDB: B:102-12-----------------------------Exon 1.6  PDB: B:155-182     Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.3  PDB: B:55-102 UniProt: 56-103         ----------------------Exon 1.5  PDB: B:125-155       --------------------------- Transcript 1 (2)
                 3w0u B   8 GGLTDEAALSCCSDADPSTKDFLLQQTMLRVKDPKKSLDFYTRVLGMTLIQKCDFPIMKFSLYFLAYEDKNDIPKEKDEKIAWALSRKATLELTHNWGTEDDETQSYHNGNSDPRGFGHIGIAVPDVYSACKRFEELGVKFVKKPDDGKMKGLAFIQDPDGYWIEILNPNKMATL 182
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177

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 '\|'

(no "CATH Domain" information available for 3W0U)

(no "Pfam Domain" information available for 3W0U)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (LGUL_HUMAN | Q04760)

molecular function
	GO:0004462	lactoylglutathione lyase activity	Catalysis of the reaction: (R)-S-lactoylglutathione = glutathione + methylglyoxal.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0006749	glutathione metabolic process	The chemical reactions and pathways involving glutathione, the tripeptide glutamylcysteinylglycine, which acts as a coenzyme for some enzymes and as an antioxidant in the protection of sulfhydryl groups in enzymes and other proteins; it has a specific role in the reduction of hydrogen peroxide (H2O2) and oxidized ascorbate, and it participates in the gamma-glutamyl cycle.
	GO:0009438	methylglyoxal metabolic process	The chemical reactions and pathways involving methylglyoxal, CH3-CO-CHO, the aldehyde of pyruvic acid.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0030316	osteoclast differentiation	The process in which a relatively unspecialized monocyte acquires the specialized features of an osteoclast. An osteoclast is a specialized phagocytic cell associated with the absorption and removal of the mineralized matrix of bone tissue.
	GO:0006090	pyruvate metabolic process	The chemical reactions and pathways involving pyruvate, 2-oxopropanoate.
	GO:0006357	regulation of transcription from RNA polymerase II promoter	Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
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.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Asp A:120 - Pro A:121	[ RasMol ]
		Asp B:120 - Pro B:121	[ RasMol ]

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	3w0u
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	LGUL_HUMAN \| Q04760	:	1bh5 1fro 1qin 1qip 3vw9 3w0t

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 4)

PROSITE Motifs (3, 6)

Exons (6, 12)

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SCOP Domains (1, 2)

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Gene Ontology (14, 14)

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