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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURE OF MOUSE GLYOXALASE I COMPLEXED WITH METHYL-GERFELIN

Authors :   H. Okumura, M. Kawatani, H. Osada

Date :   26 Sep 07 (Deposition) - 12 Aug 08 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Lyase, Lactoylglutathione Lyase, Glyoxalase I, Methyl- Gerfelin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Kawatani, H. Okumura, K. Honda, N. Kanoh, M. Muroi, N. Dohmae, M. Takami, M. Kitagawa, Y. Futamura, M. Imoto, H. Osada
The Identification Of An Osteoclastogenesis Inhibitor Through The Inhibition Of Glyoxalase I
Proc. Natl. Acad. Sci. Usa V. 105 11691 2008
PubMed-ID: 18695250 | Reference-DOI: 10.1073/PNAS.0712239105
(for further references see the PDB file header)

Molecule 1 - GLYOXALASE I
	Chains	:	A, B
	EC Number	:	4.4.1.5
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PRSET C
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GLO1
	Organism Common	:	MOUSE
	Organism Scientific	:	MUS MUSCULUS
	Organism Taxid	:	10090

		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	MGI	2	Ligand/Ion	METHYL 4-(2,3-DIHYDROXY-5-METHYLPHENOXY)-2-HYDROXY-6-METHYLBENZOATE
2	ZN	2	Ligand/Ion	ZINC ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:127 , GLU A:173 , GLN B:34 , GLU B:100	BINDING SITE FOR RESIDUE ZN A 301
2	AC2	SOFTWARE	GLN A:34 , GLU A:100 , HIS B:127 , GLU B:173	BINDING SITE FOR RESIDUE ZN A 401
3	AC3	SOFTWARE	HIS A:127 , MET A:158 , GLU A:173 , HOH A:546 , GLN B:34 , MET B:66 , PHE B:68 , LEU B:70 , GLU B:100	BINDING SITE FOR RESIDUE MGI A 300
4	AC4	SOFTWARE	GLN A:34 , PHE A:68 , LEU A:70 , PHE A:93 , GLU A:100 , HIS B:127 , MET B:158 , PHE B:163 , GLU B:173	BINDING SITE FOR RESIDUE MGI A 400

(no "SS Bond" information available for 2ZA0)

Asymmetric/Biological Unit

No.	Residues
1	Asp A:121	-	Pro A:122
2	Asp B:121	-	Pro B:122

(no "SAP(SNP)/Variant" information available for 2ZA0)

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_MOUSE	31-177	2	A:31-177 B:31-177
2	GLYOXALASE_I_1	PS00934	Glyoxalase I signature 1.	LGUL_MOUSE	34-55	2	A:34-55 B:34-55
3	GLYOXALASE_I_2	PS00935	Glyoxalase I signature 2.	LGUL_MOUSE	118-134	2	A:118-134 B:118-134

(no "Exon" information available for 2ZA0)

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:180
 aligned with A5GZX3_MOUSE | A5GZX3 from UniProtKB/TrEMBL  Length:184

    Alignment length:180
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183
         A5GZX3_MOUSE     4 PQPASSGLTDETAFSCCSDPDPSTKDFLLQQTMLRIKDPKKSLDFYTRVLGLTLLQKLDFPAMKFSLYFLAYEDKNDIPKDKSEKTAWTFSRKATLELTHNWGTEDDETQSYHNGNSDPRGFGHIGIAVPDVYSACKRFEELGVKFVKKPDDGKMKGLAFIQDPDGYWIEILNPNKIATI 183
               SCOP domains d2za0a_ A: automated matches                                                                                                                                                         SCOP domains
               CATH domains 2za0A00 A:4-183 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhh....hhhhh..eeeeeeee..hhhhhhhhhhhh...eeeeeeeehhh.eeeeeee..hhhhh..hhhhhhhhhh....eeeeeee.hhhhh..............eeeeeee..hhhhhhhhhhhh...eee..........eeee.....eeeee...hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2za0 A   4 PQPASSGLTDETAFSCCSDPDPSTKDFLLQQTMLRIKDPKKSLDFYTRVLGLTLLQKLDFPAMKFSLYFLAYEDKNDIPKDKSEKTAWTFSRKATLELTHNWGTEDDETQSYHNGNSDPRGFGHIGIAVPDVYSACKRFEELGVKFVKKPDDGKMKGLAFIQDPDGYWIEILNPNKIATI 183
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183

Chain A from PDB  Type:PROTEIN  Length:180
 aligned with LGUL_MOUSE | Q9CPU0 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:180
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183
           LGUL_MOUSE     4 PQPASSGLTDETAFSCCSDPDPSTKDFLLQQTMLRIKDPKKSLDFYTRVLGLTLLQKLDFPAMKFSLYFLAYEDKNDIPKDKSEKTAWTFSRKATLELTHNWGTEDDETQSYHNGNSDPRGFGHIGIAVPDVYSACKRFEELGVKFVKKPDDGKMKGLAFIQDPDGYWIEILNPNKIATI 183
               SCOP domains d2za0a_ A: automated matches                                                                                                                                                         SCOP domains
               CATH domains 2za0A00 A:4-183 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                                                      CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhhhh....hhhhh..eeeeeeee..hhhhhhhhhhhh...eeeeeeeehhh.eeeeeee..hhhhh..hhhhhhhhhh....eeeeeee.hhhhh..............eeeeeee..hhhhhhhhhhhh...eee..........eeee.....eeeee...hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) ---------------------------VOC  PDB: A:31-177 UniProt: 31-177                                                                                                                 ------ PROSITE (1)
                PROSITE (2) ------------------------------GLYOXALASE_I_1        --------------------------------------------------------------GLYOXALASE_I_2   ------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2za0 A   4 PQPASSGLTDETAFSCCSDPDPSTKDFLLQQTMLRIKDPKKSLDFYTRVLGLTLLQKLDFPAMKFSLYFLAYEDKNDIPKDKSEKTAWTFSRKATLELTHNWGTEDDETQSYHNGNSDPRGFGHIGIAVPDVYSACKRFEELGVKFVKKPDDGKMKGLAFIQDPDGYWIEILNPNKIATI 183
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183

Chain B from PDB  Type:PROTEIN  Length:176
 aligned with A5GZX3_MOUSE | A5GZX3 from UniProtKB/TrEMBL  Length:184

    Alignment length:176
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178      
         A5GZX3_MOUSE     9 SGLTDETAFSCCSDPDPSTKDFLLQQTMLRIKDPKKSLDFYTRVLGLTLLQKLDFPAMKFSLYFLAYEDKNDIPKDKSEKTAWTFSRKATLELTHNWGTEDDETQSYHNGNSDPRGFGHIGIAVPDVYSACKRFEELGVKFVKKPDDGKMKGLAFIQDPDGYWIEILNPNKIATII 184
               SCOP domains d2za0b_ B: automated matches                                                                                                                                                     SCOP domains
               CATH domains 2za0B00 B:9-184 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                                                  CATH domains
           Pfam domains (1) ----------------------Glyoxalase-2za0B01 B:31-174                                                                                                                     ---------- Pfam domains (1)
           Pfam domains (2) ----------------------Glyoxalase-2za0B02 B:31-174                                                                                                                     ---------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhh....hhhhh..eeeeeeee..hhhhhhhhhhhh...eeeeeeeehhh.eeeeeee..hhhhh..hhhhhhhhhh....eeeeeee.hhhhh..............eeeeeee..hhhhhhhhhhhh...eee..........eeee.....eeeee...hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2za0 B   9 SGLTDETAFSCCSDPDPSTKDFLLQQTMLRIKDPKKSLDFYTRVLGLTLLQKLDFPAMKFSLYFLAYEDKNDIPKDKSEKTAWTFSRKATLELTHNWGTEDDETQSYHNGNSDPRGFGHIGIAVPDVYSACKRFEELGVKFVKKPDDGKMKGLAFIQDPDGYWIEILNPNKIATII 184
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178

Chain B from PDB  Type:PROTEIN  Length:176
 aligned with LGUL_MOUSE | Q9CPU0 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:176
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178      
           LGUL_MOUSE     9 SGLTDETAFSCCSDPDPSTKDFLLQQTMLRIKDPKKSLDFYTRVLGLTLLQKLDFPAMKFSLYFLAYEDKNDIPKDKSEKTAWTFSRKATLELTHNWGTEDDETQSYHNGNSDPRGFGHIGIAVPDVYSACKRFEELGVKFVKKPDDGKMKGLAFIQDPDGYWIEILNPNKIATII 184
               SCOP domains d2za0b_ B: automated matches                                                                                                                                                     SCOP domains
               CATH domains 2za0B00 B:9-184 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1                                                                                                                  CATH domains
           Pfam domains (1) ----------------------Glyoxalase-2za0B01 B:31-174                                                                                                                     ---------- Pfam domains (1)
           Pfam domains (2) ----------------------Glyoxalase-2za0B02 B:31-174                                                                                                                     ---------- Pfam domains (2)
         Sec.struct. author ...hhhhhhhh....hhhhh..eeeeeeee..hhhhhhhhhhhh...eeeeeeeehhh.eeeeeee..hhhhh..hhhhhhhhhh....eeeeeee.hhhhh..............eeeeeee..hhhhhhhhhhhh...eee..........eeee.....eeeee...hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------VOC  PDB: B:31-177 UniProt: 31-177                                                                                                                 ------- PROSITE (1)
                PROSITE (2) -------------------------GLYOXALASE_I_1        --------------------------------------------------------------GLYOXALASE_I_2   -------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2za0 B   9 SGLTDETAFSCCSDPDPSTKDFLLQQTMLRIKDPKKSLDFYTRVLGLTLLQKLDFPAMKFSLYFLAYEDKNDIPKDKSEKTAWTFSRKATLELTHNWGTEDDETQSYHNGNSDPRGFGHIGIAVPDVYSACKRFEELGVKFVKKPDDGKMKGLAFIQDPDGYWIEILNPNKIATII 184
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Roll (3276)

Topology: 2,3-Dihydroxybiphenyl 1,2-Dioxygenase; domain 1 (113)

Homologous Superfamily: 2,3-Dihydroxybiphenyl 1,2-Dioxygenase, domain 1 (106)

Mouse (Mus musculus) (1)

1a	2za0B00	B:9-184
1b	2za0A00	A:4-183

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Glyoxalase (58)

Family: Glyoxalase (34)

Mus musculus (Mouse) (1)

1a	Glyoxalase-2za0B01	B:31-174
1b	Glyoxalase-2za0B02	B:31-174

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (LGUL_MOUSE | Q9CPU0)

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:0019243	methylglyoxal catabolic process to D-lactate via S-lactoyl-glutathione	The chemical reactions and pathways resulting in the breakdown of methylglyoxal, CH3-CO-CHO, into D-lactate via the intermediate S-lactoyl-glutathione. Glutathione is used in the first step of the pathway and then regenerated in the second step.
	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: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: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.

Chain A,B (A5GZX3_MOUSE | A5GZX3)

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.
cellular component
	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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		Asp A:121 - Pro A:122	[ RasMol ]
		Asp B:121 - Pro B:122	[ RasMol ]

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UniProtKB/Swiss-Prot
	LGUL_MOUSE \| Q9CPU0	:	4kyh 4kyk 4opn 4pv5 4x2a

1fro	HUMAN GLYOXALASE I WITH BENZYL-GLUTATHIONE INHIBITOR
1qin	HUMAN GLYOXALASE I COMPLEXED WITH S-(N-HYDROXY-N-P- IODOPHENYLCARBAMOYL)GLUTATHIONE
1qip	HUMAN GLYOXALASE I COMPLEXED WITH S-(P- NITROBENZYLOXYCARBONYL)GLUTATHIONE

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 (0, 0)

PROSITE Motifs (3, 6)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 2)

CATH Domains (1, 2)

Pfam Domains (1, 2)

Gene Ontology (12, 21)

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