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(-) Description

Title :  CRYSTAL STRUCTURE OF GLUTATHIONE REDUCTASE GLR1 FROM THE YEAST SACCHAROMYCES CEREVISIAE
 
Authors :  J. Yu, C. Z. Zhou
Date :  19 Jul 06  (Deposition) - 12 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Glutathione Reductase Complexed With Fad, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Yu, C. Z. Zhou
Crystal Structure Of Glutathione Reductase Glr1 From The Yeast Saccharomyces Cerevisiae.
Proteins V. 68 972 2007
PubMed-ID: 17554778  |  Reference-DOI: 10.1002/PROT.21354

(-) Compounds

Molecule 1 - GLUTATHIONE REDUCTASE
    Chains: A, B
    EC Number: 1.8.1.7
    Engineered: YES
    Expression System: PICHIA PASTORIS
    Expression System Plasmid: PPIC9K
    Expression System Strain: GS115
    Expression System Taxid: 4922
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 13-491
    Organism Common: BAKER'S YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 4932
    Synonym: GR, GRASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 19)

Asymmetric/Biological Unit (5, 19)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2GOL11Ligand/IonGLYCEROL
3GSH2Ligand/IonGLUTATHIONE
4NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
5PO42Ligand/IonPHOSPHATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:258 , ASN A:278 , LYS B:260 , VAL B:262BINDING SITE FOR RESIDUE NAG A 1301
02AC2SOFTWARELYS A:260 , ARG B:228 , LEU B:258 , ASN B:278 , HOH B:6196BINDING SITE FOR RESIDUE NAG B 1303
03AC3SOFTWAREVAL A:36 , ALA A:37 , ARG A:40 , ARG A:350 , HOH A:6113BINDING SITE FOR RESIDUE PO4 A 5001
04AC4SOFTWAREVAL B:36 , ALA B:37 , ARG B:40 , ILE B:346 , ARG B:350 , HOH B:6111 , HOH B:6334BINDING SITE FOR RESIDUE PO4 B 5002
05AC5SOFTWAREGLY A:30 , GLY A:32 , SER A:33 , GLY A:34 , VAL A:52 , GLU A:53 , ALA A:54 , GLY A:59 , THR A:60 , CYS A:61 , VAL A:64 , GLY A:65 , CYS A:66 , LYS A:69 , GLY A:137 , TRP A:138 , ALA A:139 , ALA A:167 , THR A:168 , GLY A:169 , TYR A:207 , ARG A:295 , GLY A:333 , ASP A:334 , GLU A:340 , LEU A:341 , THR A:342 , PRO A:343 , HOH A:6015 , HOH A:6018 , HOH A:6027 , HOH A:6041 , HOH A:6046 , HOH A:6122 , HOH A:6136 , HIS B:472 , PRO B:473BINDING SITE FOR RESIDUE FAD A 1001
06AC6SOFTWAREHIS A:472 , PRO A:473 , GLY B:30 , GLY B:32 , SER B:33 , GLY B:34 , VAL B:52 , GLU B:53 , ALA B:54 , GLY B:59 , THR B:60 , CYS B:61 , VAL B:64 , GLY B:65 , CYS B:66 , LYS B:69 , GLY B:137 , TRP B:138 , ALA B:139 , ALA B:167 , THR B:168 , GLY B:169 , TYR B:207 , ARG B:295 , HIS B:298 , GLY B:333 , ASP B:334 , GLU B:340 , LEU B:341 , THR B:342 , PRO B:343 , HOH B:6017 , HOH B:6020 , HOH B:6025 , HOH B:6036 , HOH B:6042 , HOH B:6082 , HOH B:6191BINDING SITE FOR RESIDUE FAD B 2001
07AC7SOFTWAREGLU A:238 , CYS A:239 , ASN A:242 , THR A:243 , ASN A:405 , ARG A:423 , LYS A:425 , HOH A:6012 , HOH A:6247 , HOH A:6369BINDING SITE FOR RESIDUE GSH A 3001
08AC8SOFTWAREGLU B:238 , CYS B:239 , THR B:243 , LYS B:390 , ASN B:405 , LYS B:425 , HOH B:6011 , HOH B:6240 , HOH B:6252BINDING SITE FOR RESIDUE GSH B 4001
09AC9SOFTWAREGLY A:204 , ALA A:205 , ILE A:227 , ARG A:228 , ARG A:234 , HOH A:6194 , HOH A:6375BINDING SITE FOR RESIDUE GOL A 6001
10BC1SOFTWARETYR B:321 , ASN B:323 , ARG B:355 , ARG B:363 , ASN B:364BINDING SITE FOR RESIDUE GOL B 6002
11BC2SOFTWAREGLY B:204 , ALA B:205 , ILE B:227 , ARG B:228 , ARG B:234 , HOH B:6046 , HOH B:6257BINDING SITE FOR RESIDUE GOL B 6003
12BC3SOFTWAREILE B:178 , ARG B:228 , LYS B:260 , ILE B:261 , HOH B:6106BINDING SITE FOR RESIDUE GOL B 6004
13BC4SOFTWAREILE A:178 , ARG A:228 , LYS A:260 , ILE A:261 , HOH A:6100BINDING SITE FOR RESIDUE GOL A 6005
14BC5SOFTWARELYS A:250 , LYS A:419 , SER A:420 , PRO A:421 , HOH A:6034 , LYS B:143BINDING SITE FOR RESIDUE GOL A 6006
15BC6SOFTWARETHR B:243 , ASP B:246 , HIS B:247 , LYS B:250 , HOH B:6032 , HOH B:6120 , HOH B:6128BINDING SITE FOR RESIDUE GOL B 6007
16BC7SOFTWARETYR A:321 , ASN A:323 , ARG A:355 , ASN A:364 , HOH A:6195BINDING SITE FOR RESIDUE GOL A 6008
17BC8SOFTWAREASP B:186 , ASP B:188 , ARG B:192 , HOH B:6126BINDING SITE FOR RESIDUE GOL B 6009
18BC9SOFTWAREGLN B:315 , VAL B:336 , GLY B:337 , LYS B:338BINDING SITE FOR RESIDUE GOL B 6010
19CC1SOFTWAREASP A:186 , ASP A:188 , ARG A:192 , HOH A:6110BINDING SITE FOR RESIDUE GOL A 6011

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:61 -A:66
2B:61 -B:66

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1His A:379 -Pro A:380
2His A:472 -Pro A:473
3His B:379 -Pro B:380
4His B:472 -Pro B:473

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PYRIDINE_REDOX_1PS00076 Pyridine nucleotide-disulphide oxidoreductases class-I active site.GSHR_YEAST58-68
 		  2A:58-68
B:58-68

(-) Exons   (1, 2)

Asymmetric/Biological Unit (1, 2)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YPL091W1YPL091W.1XVI:375499-3769501452GSHR_YEAST1-4834832A:22-483 (gaps)
B:22-483 (gaps)		462
462

(-) 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:461
 aligned with GSHR_YEAST | P41921 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:462
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481  
           GSHR_YEAST    22 KHYDYLVIGGGSGGVASARRAASYGAKTLLVEAKALGGTCVNVGCVPKKVMWYASDLATRVSHANEYGLYQNLPLDKEHLTFNWPEFKQKRDAYVHRLNGIYQKNLEKEKVDVVFGWARFNKDGNVEVQKRDNTTEVYSANHILVATGGKAIFPENIPGFELGTDSDGFFRLEEQPKKVVVVGAGYIGIELAGVFHGLGSETHLVIRGETVLRKFDECIQNTITDHYVKEGINVHKLSKIVKVEKNVETDKLKIHMNDSKSIDDVDELIWTIGRKSHLGMGSENVGIKLNSHDQIIADEYQNTNVPNIYSLGDVVGKVELTPVAIAAGRKLSNRLFGPEKFRNDKLDYENVPSVIFSHPEAGSIGISEKEAIEKYGKENIKVYNSKFTAMYYAMLSEKSPTRYKIVCAGPNEKVVGLHIVGDSSAEILQGFGVAIKMGATKADFDNCVAIHPTSAEELVTMR 483
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2hqmA01 A:22-172,A:294-370  [code=3.50.50.60, no name defined]                                                                                         2hqmA02 A:173-293  [code=3.50.50.60, no name defined]                                                                    2hqmA01 A:22-172,A:294-370  [code=3.50.50.60, no name defined]               2hqmA03 A:371-483  [code=3.30.390.30, no name defined]                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh.............hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee.....eeeee.....eeeeeeeeee...eee.......hhhhh.hhhhhhhh.....eeeee..hhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhhh.eee....eeeeee..-...eeeee....eeeee.eeee...eee....hhhhhh.....................eee.hhhh....hhhhhhhhhhhhhhhhhhhhhhh..........eee.....eeeee.hhhhhhhhhh...eeeeeeee.hhhhhhh.....eeeeeeee....eeeeeeee..hhhhhhhhhhhhhhh..hhhhhhh.......hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------PYRIDINE_RE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:22-483 (gaps) UniProt: 1-483 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                     Transcript 1
                 2hqm A  22 KHYDYLVIGGGSGGVASARRAASYGAKTLLVEAKALGGTCVNVGCVPKKVMWYASDLATRVSHANEYGLYQNLPLDKEHLTFNWPEFKQKRDAYVHRLNGIYQKNLEKEKVDVVFGWARFNKDGNVEVQKRDNTTEVYSANHILVATGGKAIFPENIPGFELGTDSDGFFRLEEQPKKVVVVGAGYIGIELAGVFHGLGSETHLVIRGETVLRKFDECIQNTITDHYVKEGINVHKLSKIVKVEKNV-TDKLKIHMNDSKSIDDVDELIWTIGRKSHLGMGSENVGIKLNSHDQIIADEYQNTNVPNIYSLGDVVGKVELTPVAIAAGRKLSNRLFGPEKFRNDKLDYENVPSVIFSHPEAGSIGISEKEAIEKYGKENIKVYNSKFTAMYYAMLSEKSPTRYKIVCAGPNEKVVGLHIVGDSSAEILQGFGVAIKMGATKADFDNCVAIHPTSAEELVTMR 483
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261      |271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481  
                                                                                                                                                                                                                                                                                268 |                                                                                                                                                                                                                     
                                                                                                                                                                                                                                                                                  270                                                                                                                                                                                                                     


Chain B from PDB  Type:PROTEIN  Length:461
 aligned with GSHR_YEAST | P41921 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:462
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481  
           GSHR_YEAST    22 KHYDYLVIGGGSGGVASARRAASYGAKTLLVEAKALGGTCVNVGCVPKKVMWYASDLATRVSHANEYGLYQNLPLDKEHLTFNWPEFKQKRDAYVHRLNGIYQKNLEKEKVDVVFGWARFNKDGNVEVQKRDNTTEVYSANHILVATGGKAIFPENIPGFELGTDSDGFFRLEEQPKKVVVVGAGYIGIELAGVFHGLGSETHLVIRGETVLRKFDECIQNTITDHYVKEGINVHKLSKIVKVEKNVETDKLKIHMNDSKSIDDVDELIWTIGRKSHLGMGSENVGIKLNSHDQIIADEYQNTNVPNIYSLGDVVGKVELTPVAIAAGRKLSNRLFGPEKFRNDKLDYENVPSVIFSHPEAGSIGISEKEAIEKYGKENIKVYNSKFTAMYYAMLSEKSPTRYKIVCAGPNEKVVGLHIVGDSSAEILQGFGVAIKMGATKADFDNCVAIHPTSAEELVTMR 483
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 2hqmB01 B:22-172,B:294-370  [code=3.50.50.60, no name defined]                                                                                         2hqmB02 B:173-293  [code=3.50.50.60, no name defined]                                                                    2hqmB01 B:22-172,B:294-370  [code=3.50.50.60, no name defined]               2hqmB03 B:371-483  [code=3.30.390.30, no name defined]                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee..hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee.....eeeee.....eeeeeeeeee...eee.......hhhhh.hhhhhhhh.....eeeee..hhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhhh.eee....eeeeee..-...eeeee....eeeee.eeee...eee....hhhhh......................eee.hhhh....hhhhhhhhhhhhhhhhhhhhhhh..........eee.....eeeee.hhhhhhhhhh...eeeeeeee.hhhhhhh.....eeeeeeee....eeeeeeee..hhhhhhhhhhhhhhh..hhhhhhh.......hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------PYRIDINE_RE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:22-483 (gaps) UniProt: 1-483 [INCOMPLETE]                                                                                                                                                                                                                                                                                                                                                                                                                     Transcript 1
                 2hqm B  22 KHYDYLVIGGGSGGVASARRAASYGAKTLLVEAKALGGTCVNVGCVPKKVMWYASDLATRVSHANEYGLYQNLPLDKEHLTFNWPEFKQKRDAYVHRLNGIYQKNLEKEKVDVVFGWARFNKDGNVEVQKRDNTTEVYSANHILVATGGKAIFPENIPGFELGTDSDGFFRLEEQPKKVVVVGAGYIGIELAGVFHGLGSETHLVIRGETVLRKFDECIQNTITDHYVKEGINVHKLSKIVKVEKNV-TDKLKIHMNDSKSIDDVDELIWTIGRKSHLGMGSENVGIKLNSHDQIIADEYQNTNVPNIYSLGDVVGKVELTPVAIAAGRKLSNRLFGPEKFRNDKLDYENVPSVIFSHPEAGSIGISEKEAIEKYGKENIKVYNSKFTAMYYAMLSEKSPTRYKIVCAGPNEKVVGLHIVGDSSAEILQGFGVAIKMGATKADFDNCVAIHPTSAEELVTMR 483
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261      |271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481  
                                                                                                                                                                                                                                                                                268 |                                                                                                                                                                                                                     
                                                                                                                                                                                                                                                                                  270
   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  (0, 0)

(no "SCOP Domain" information available for 2HQM)

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HQM)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GSHR_YEAST | P41921)
molecular function
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0004362    glutathione-disulfide reductase activity    Catalysis of the reaction: 2 glutathione + NADP+ = glutathione disulfide + NADPH + H+.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016668    oxidoreductase activity, acting on a sulfur group of donors, NAD(P) as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a sulfur-containing group acts as a hydrogen or electron donor and reduces NAD or NADP.
biological process
    GO:0045454    cell redox homeostasis    Any process that maintains the redox environment of a cell or compartment within a cell.
    GO:0098869    cellular oxidant detoxification    Any process carried out at the cellular level that reduces or removes the toxicity superoxide radicals or hydrogen peroxide.
    GO:0034599    cellular response to oxidative stress    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    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:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0010731    protein glutathionylation    The protein modification process in which a glutathione molecule is added to a protein amino acid through a disulfide linkage.
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:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2HQM)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2HQM)