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(-) Description

Title :  HUMAN GLYOXALASE II WITH CACODYLATE AND ACETATE IONS PRESENT IN THE ACTIVE SITE
 
Authors :  A. D. Cameron, M. Ridderstrom, B. Olin, B. Mannervik
Date :  10 May 99  (Deposition) - 24 Sep 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Metallo-Hydrolase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. D. Cameron, M. Ridderstrom, B. Olin, B. Mannervik
Crystal Structure Of Human Glyoxalase Ii And Its Complex With A Glutathione Thiolester Substrate Analogue.
Structure Fold. Des. V. 7 1067 1999
PubMed-ID: 10508780  |  Reference-DOI: 10.1016/S0969-2126(99)80174-9

(-) Compounds

Molecule 1 - PROTEIN (HYDROXYACYLGLUTATHIONE HYDROLASE)
    Chains: A, B
    EC Number: 3.1.2.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PKK 223-3,ACCI-DELETED
    Expression System Strain: JM 109
    Expression System Taxid: 562
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: HETEROLOGOUSLY EXPRESSED
    Synonym: GLYOXALASE II
    Tissue: LIVER

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CAC4Ligand/IonCACODYLATE ION
3CL1Ligand/IonCHLORIDE ION
4MN2Ligand/IonMANGANESE (II) ION
5ZN4Ligand/IonZINC ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:54 , HIS A:56 , HIS A:110 , ASP A:134 , ZN A:262 , CAC A:463 , HOH A:468BINDING SITE FOR RESIDUE ZN A 261
02AC2SOFTWAREASP A:58 , HIS A:59 , ASP A:134 , HIS A:173 , ZN A:261 , CAC A:463 , HOH A:468BINDING SITE FOR RESIDUE ZN A 262
03AC3SOFTWAREHIS A:56 , ASP A:58 , HIS A:110 , ASP A:134 , TYR A:145 , HIS A:173 , ZN A:261 , ZN A:262 , HOH A:468 , HOH A:506BINDING SITE FOR RESIDUE CAC A 463
04AC4SOFTWAREPHE A:137 , CYS A:141 , LYS A:143 , TYR A:175 , ARG A:249 , LYS A:252 , HOH A:471 , HOH A:507 , HOH A:521BINDING SITE FOR RESIDUE ACT A 464
05AC5SOFTWARECYS A:153 , GLU A:158BINDING SITE FOR RESIDUE CAC A 265
06AC6SOFTWAREHIS A:185 , HIS A:235 , GLU A:251 , CL A:467BINDING SITE FOR RESIDUE MN A 266
07AC7SOFTWAREMN A:266 , MN B:266BINDING SITE FOR RESIDUE CL A 467
08AC8SOFTWAREHIS B:54 , HIS B:56 , HIS B:110 , ASP B:134 , ZN B:262 , CAC B:469 , HOH B:473BINDING SITE FOR RESIDUE ZN B 261
09AC9SOFTWAREASP B:58 , HIS B:59 , ASP B:134 , HIS B:173 , ZN B:261 , CAC B:469 , HOH B:473BINDING SITE FOR RESIDUE ZN B 262
10BC1SOFTWAREHIS B:56 , ASP B:58 , HIS B:110 , ASP B:134 , HIS B:173 , TYR B:175 , ZN B:261 , ZN B:262 , HOH B:473 , HOH B:511 , HOH B:616BINDING SITE FOR RESIDUE CAC B 469
11BC2SOFTWAREPHE B:137 , CYS B:141 , TYR B:175 , ARG B:249 , LYS B:252 , HOH B:476 , HOH B:512BINDING SITE FOR RESIDUE ACT B 468
12BC3SOFTWARECYS B:153 , LYS B:154 , GLU B:158BINDING SITE FOR RESIDUE CAC B 265
13BC4SOFTWARECL A:467 , HIS B:185 , GLU B:251 , HOH B:527 , HOH B:554 , HOH B:659BINDING SITE FOR RESIDUE MN B 266
14ZNAAUTHORHIS A:54 , HIS A:56 , HIS A:110 , ASP A:134 , CAC A:463 , HOH A:468 , ASP A:58 , HIS A:59 , HIS A:173BINUCLEAR ZINC BINDING SITE IN A MOLECULE
15ZNBAUTHORHIS B:54 , HIS B:56 , HIS B:110 , ASP B:134 , CAC B:469 , HOH B:473 , ASP B:58 , HIS B:59 , HIS B:173BINUCLEAR ZINC BINDING SITE IN B MOLECULE

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QH3)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Val A:211 -Pro A:212
2Val B:211 -Pro B:212

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1QH3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1QH3)

(-) Exons   (8, 16)

Asymmetric/Biological Unit (8, 16)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003973561aENSE00001908102chr16:1877162-1876713450GLO2_HUMAN1-26260--
1.3ENST000003973563ENSE00001791655chr16:1873038-1872866173GLO2_HUMAN26-83582A:1-35
B:1-35		35
35
1.4ENST000003973564ENSE00000945924chr16:1872365-187230165GLO2_HUMAN84-105222A:36-57
B:36-57		22
22
1.5ENST000003973565ENSE00000683285chr16:1870015-1869898118GLO2_HUMAN105-144402A:57-96
B:57-96		40
40
1.6ENST000003973566ENSE00000683283chr16:1869224-1869116109GLO2_HUMAN145-181372A:97-133
B:97-133		37
37
1.7ENST000003973567ENSE00001670106chr16:1867272-1867169104GLO2_HUMAN181-215352A:133-167
B:133-167		35
35
1.8ENST000003973568ENSE00001739735chr16:1866995-1866894102GLO2_HUMAN216-249342A:168-201
B:168-201		34
34
1.9ENST000003973569ENSE00001710138chr16:1859834-185975580GLO2_HUMAN250-276272A:202-228
B:202-228		27
27
1.10bENST0000039735610bENSE00001849129chr16:1859383-1859104280GLO2_HUMAN276-308332A:228-260
B:228-260		33
33

(-) Sequences/Alignments

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:260
 aligned with GLO2_HUMAN | Q16775 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:260
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308
           GLO2_HUMAN    49 MKVEVLPALTDNYMYLVIDDETKEAAIVDPVQPQKVVDAARKHGVKLTTVLTTHHHWDHAGGNEKLVKLESGLKVYGGDDRIGALTHKITHLSTLQVGSLNVKCLATPCHTSGHICYFVSKPGGSEPPAVFTGDTLFVAGCGKFYEGTADEMCKALLEVLGRLPPDTRVYCGHEYTINNLKFARHVEPGNAAIREKLAWAKEKYSIGEPTVPSTLAEEFTYNPFMRVREKTVQQHAGETDPVTTMRAVRREKDQFKMPRD 308
               SCOP domains d1qh3a_ A: Glyoxalase II (hydroxyacylglutathione hydrolase)                                                                                                                                                                                                          SCOP domains
               CATH domains 1qh3A00 A:1-260 Metallo-beta-lactamase, chain A                                                                                                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee...eeeeeee.....eeeee....hhhhhhhhhhh.....eeeee.........hhhhhhh...eeeee.........eeee..eeeee..eeeeeeeee.....eeeeeeee.....eeeeeee...............hhhhhhhhh.........eeeee....hhhhhhhhhhh....hhhhhhhhhhhhhhhh........hhhhhh.........hhhhhhh....hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:1-35 [INCOMPLETE] Exon 1.4  PDB: A:36-57---------------------------------------Exon 1.6  PDB: A:97-133              ----------------------------------Exon 1.8  PDB: A:168-201          --------------------------Exon 1.10b  PDB: A:228-260        Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.5  PDB: A:57-96 UniProt: 105-144 ------------------------------------Exon 1.7  PDB: A:133-167           ----------------------------------Exon 1.9  PDB: A:202-228   -------------------------------- Transcript 1 (2)
                 1qh3 A   1 MKVEVLPALTDNYMYLVIDDETKEAAIVDPVQPQKVVDAARKHGVKLTTVLTTHHHWDHAGGNEKLVKLESGLKVYGGDDRIGALTHKITHLSTLQVGSLNVKCLATPCHTSGHICYFVSKPGGSEPPAVFTGDTLFVAGCGKFYEGTADEMCKALLEVLGRLPPDTRVYCGHEYTINNLKFARHVEPGNAAIREKLAWAKEKYSIGEPTVPSTLAEEFTYNPFMRVREKTVQQHAGETDPVTTMRAVRREKDQFKMPRD 260
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260


Chain B from PDB  Type:PROTEIN  Length:260
 aligned with GLO2_HUMAN | Q16775 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:260
                                    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308
           GLO2_HUMAN    49 MKVEVLPALTDNYMYLVIDDETKEAAIVDPVQPQKVVDAARKHGVKLTTVLTTHHHWDHAGGNEKLVKLESGLKVYGGDDRIGALTHKITHLSTLQVGSLNVKCLATPCHTSGHICYFVSKPGGSEPPAVFTGDTLFVAGCGKFYEGTADEMCKALLEVLGRLPPDTRVYCGHEYTINNLKFARHVEPGNAAIREKLAWAKEKYSIGEPTVPSTLAEEFTYNPFMRVREKTVQQHAGETDPVTTMRAVRREKDQFKMPRD 308
               SCOP domains d1qh3b_ B: Glyoxalase II (hydroxyacylglutathione hydrolase)                                                                                                                                                                                                          SCOP domains
               CATH domains 1qh3B00 B:1-260 Metallo-beta-lactamase, chain A                                                                                                                                                                                                                      CATH domains
           Pfam domains (1) ------Lactamase_B-1qh3B01 B:7-173                                                                                                                                            --------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ------Lactamase_B-1qh3B02 B:7-173                                                                                                                                            --------------------------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .................................................................................................................................................................................................................................................................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: B:1-35 [INCOMPLETE] Exon 1.4  PDB: B:36-57---------------------------------------Exon 1.6  PDB: B:97-133              ----------------------------------Exon 1.8  PDB: B:168-201          --------------------------Exon 1.10b  PDB: B:228-260        Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------Exon 1.5  PDB: B:57-96 UniProt: 105-144 ------------------------------------Exon 1.7  PDB: B:133-167           ----------------------------------Exon 1.9  PDB: B:202-228   -------------------------------- Transcript 1 (2)
                 1qh3 B   1 MKVEVLPALTDNYMYLVIDDETKEAAIVDPVQPQKVVDAARKHGVKLTTVLTTHHHWDHAGGNEKLVKLESGLKVYGGDDRIGALTHKITHLSTLQVGSLNVKCLATPCHTSGHICYFVSKPGGSEPPAVFTGDTLFVAGCGKFYEGTADEMCKALLEVLGRLPPDTRVYCGHEYTINNLKFARHVEPGNAAIREKLAWAKEKYSIGEPTVPSTLAEEFTYNPFMRVREKTVQQHAGETDPVTTMRAVRREKDQFKMPRD 260
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Metallo-HOrase (67)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GLO2_HUMAN | Q16775)
molecular function
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004416    hydroxyacylglutathione hydrolase activity    Catalysis of the reaction: (S)-(2-hydroxyacyl)glutathione + H2O = glutathione + a 2-hydroxy carboxylate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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:0006750    glutathione biosynthetic process    The chemical reactions and pathways resulting in the formation of 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.
    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:0006090    pyruvate metabolic process    The chemical reactions and pathways involving pyruvate, 2-oxopropanoate.
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.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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  GLO2_HUMAN | Q16775
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

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        GLO2_HUMAN | Q16775: 1qh5 2f50

(-) Related Entries Specified in the PDB File

1qh5