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(-) Description

Title :  CRYSTAL STRUCTURE OF YEAST METHYLGLYOXAL/ISOVALERALDEHYDE REDUCTASE GRE2 COMPLEXED WITH NADPH
 
Authors :  P. C. Guo, Z. Z. Bao, W. F. Li, C. Z. Zhou
Date :  17 Mar 14  (Deposition) - 22 Oct 14  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Rossmann Fold, Reductase, Nadph Binding, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. C. Guo, Z. Z. Bao, X. X. Ma, Q. Xia, W. F. Li
Structural Insights Into The Cofactor-Assisted Substrate Recognition Of Yeast Methylglyoxal/Isovaleraldehyde Reductase Gre2
Biochim. Biophys. Acta V. 1844 1486 2014
PubMed-ID: 24879127  |  Reference-DOI: 10.1016/J.BBAPAP.2014.05.008

(-) Compounds

Molecule 1 - NADPH-DEPENDENT METHYLGLYOXAL REDUCTASE GRE2
    Chains: A, B, C, D
    EC Number: 1.1.1.283, 1.1.1.265
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GRE2, YOL151W
    Organism Common: YEAST
    Organism Scientific: SACCHAROMYCES CEREVISIAE
    Organism Taxid: 559292
    Strain: S288C
    Synonym: 3-METHYLBUTANAL REDUCTASE, GENES DE RESPUESTA A ESTRES PROTEIN 2, ISOVALERALDEHYDE REDUCTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1NDP-1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1NDP-1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:7 , ASN A:9 , GLY A:10 , PHE A:11 , ILE A:12 , ARG A:32 , LYS A:36 , ASP A:57 , ILE A:58 , THR A:81 , ALA A:82 , SER A:83 , PRO A:84 , PHE A:85 , THR A:125 , SER A:126 , SER A:127 , TYR A:165 , LYS A:169 , PRO A:196 , VAL A:197 , TYR A:198 , VAL A:199 , SER A:216 , HOH A:532BINDING SITE FOR RESIDUE NDP A 401
2AC2SOFTWAREGLY B:7 , ASN B:9 , GLY B:10 , PHE B:11 , ILE B:12 , ARG B:32 , LYS B:36 , ASP B:57 , ILE B:58 , THR B:81 , ALA B:82 , SER B:83 , PRO B:84 , PHE B:85 , THR B:125 , SER B:126 , SER B:127 , TYR B:165 , LYS B:169 , PRO B:196 , VAL B:197 , TYR B:198 , VAL B:199 , SER B:216 , HOH B:511 , HOH B:513BINDING SITE FOR RESIDUE NDP B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4PVD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PVD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4PVD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4PVD)

(-) Exons   (0, 0)

(no "Exon" information available for 4PVD)

(-) Sequences/Alignments

Asymmetric 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:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh.....eeeee.........hhhhhhhhh..eeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhh.hhhhh.....ee..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee.eee....hhhhh....hhhhhhhhhhh...........eeeeeehhhhhhhhhhhhhh......eeee..eeeehhhhhhhhhhhh.......................ee.hhhhhhhhh....hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pvd A   1 MSVFVSGANGFIAQHIVDLLLKEDYKVIGSARSQEKAENLTEAFGNNPKFSMEVVPDISKLDAFDHVFQKHGKDIKIVLHTASPFCFDITDSERDLLIPAVNGVKGILHSIKKYAADSVERVVLTSSYAAVFDMAKENDKSLTFNEESWNPATWESCQSDPVNAYCGSKKFAEKAAWEFLEENRDSVKFELTAVNPVYVFGPQMFDKDVKKHLNTSCELVNSLMHLSPEDKIPELFGGYIDVRDVAKAHLVAFQKRETIGQRLIVSEARFTMQDVLDILNEDFPVLKGNIPVGKPGSGATHNTLGATLDNKKSKKLLGFKFRNLKETIDDTASQILKFEGRI 342
                                    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       270       280       290       300       310       320       330       340  


Chain B from PDB  Type:PROTEIN  Length:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh.....eeeee.........hhhhhhhhh..eeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeee.hhhhh.hhhhh.....eee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee.eee....hhhhh....hhhhhhhhhhhh..........eeeeeehhhhhhhhhhhhhh......eeee..eeeehhhhhhhhhhhh.......................eeehhhhhhhhh....hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pvd B   1 MSVFVSGANGFIAQHIVDLLLKEDYKVIGSARSQEKAENLTEAFGNNPKFSMEVVPDISKLDAFDHVFQKHGKDIKIVLHTASPFCFDITDSERDLLIPAVNGVKGILHSIKKYAADSVERVVLTSSYAAVFDMAKENDKSLTFNEESWNPATWESCQSDPVNAYCGSKKFAEKAAWEFLEENRDSVKFELTAVNPVYVFGPQMFDKDVKKHLNTSCELVNSLMHLSPEDKIPELFGGYIDVRDVAKAHLVAFQKRETIGQRLIVSEARFTMQDVLDILNEDFPVLKGNIPVGKPGSGATHNTLGATLDNKKSKKLLGFKFRNLKETIDDTASQILKFEGRI 342
                                    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       270       280       290       300       310       320       330       340  


Chain C from PDB  Type:PROTEIN  Length:308
                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee....hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh.....eeeee.........hhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhh.....eeeee.hhhhh...hhhhh...ee..........hhhhhhhhhhhhhhh.....eeeeeee.eee....hhhhh...hhhhhhh..........eeeeeehhhhhhhhhhhhhh......eeee..eeeehhhhhhhhhhhh.......................ee.hhhhhhhhh....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pvd C   1 MSVFVSGANGFIAQHIVDLLLKEDYKVIGSARSQEKAENLTEAFGNNPKFSMEVVPDISKLDAFDHVFQKHGKDIKIVLHTASPLIPAVNGVKGILHSIKKYAADSVERVVLTSSYAAVFDMAKENDKSLTFNEESWNPATKKFAEKAAWEFLEENRDSVKFELTAVNPVYVFGPQMFDKDVKKELVNSLMHLSPEDKIPELFGGYIDVRDVAKAHLVAFQKRETIGQRLIVSEARFTMQDVLDILNEDFPVLKGNIPVGKPGSGATHNTLGATLDNKKSKKLLGFKFRNLKETIDDTASQILKFEGR 341
                                    10        20        30        40        50        60        70        80   ||  102       112       122       132       142       152||     177       187       197       207   ||  223       233       243       253       263       273       283       293       303       313       323       333        
                                                                                                              84|                                                     153|                                       211|                                                                                                                           
                                                                                                               97                                                      169                                        218                                                                                                                           


Chain D from PDB  Type:PROTEIN  Length:305
                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh.....eeeee.........hhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhh.....eeeee.hhhhh.........ee......hhhhhhhhhhhhhhh......eeeeeee.eee....hhhhh...hhhhhhhh..........eeeeeehhhhhhhhhhhhhh......eeee..eeeehhhhhhhhhhhh.......................ee.hhhhhhhhh....hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pvd D   1 MSVFVSGANGFIAQHIVDLLLKEDYKVIGSARSQEKAENLTEAFGNNPKFSMEVVPDISKLDAFDHVFQKHGKDIKIVLHTASPLLIPAVNGVKGILHSIKKYAADSVERVVLTSSYAAVFDKENDKSLTFNNPATSKKFAEKAAWEFLEENRDSVKFELTAVNPVYVFGPQMFDKDVKKCELVNSLMHLSPEDKIPELFGGYIDVRDVAKAHLVAFQKRETIGQRLIVSEARFTMQDVLDILNEDFPVLKGNIPVGKPGSGATHNTLGATLDNKKSKKLLGFKFRNLKETIDDTASQILKFEGR 341
                                    10        20        30        40        50        60        70        80   ||  101       111       121       131 ||    143 ||  ||171       181       191       201       211|      226       236       246       256       266       276       286       296       306       316       326       336     
                                                                                                              84|                                  133|      145|  ||                                        211|                                                                                                                            
                                                                                                               96                                   136       150  ||                                         217                                                                                                                            
                                                                                                                                                                 153|                                                                                                                                                                        
                                                                                                                                                                  168
   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 4PVD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4PVD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4PVD)

(-) Gene Ontology  (11, 11)

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        GRE2_YEAST | Q12068: 4pvc

(-) Related Entries Specified in the PDB File

4pvc