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(-) Description

Title :  ISOPROPYLMALATE DEHYDROGENASE K232M MUTANT
 
Authors :  S. G. Lee, J. M. Jez
Date :  30 Mar 16  (Deposition) - 11 May 16  (Release) - 06 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.83
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Dehydrogenase, Leucine Biosynthesis, Glucosinolate Biosynthesis, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. G. Lee, R. Nwumeh, J. M. Jez
Structure And Mechanism Of Isopropylmalate Dehydrogenase From Arabidopsis Thaliana: Insights On Leucine And Aliphati Glucosinolate Biosynthesis.
J. Biol. Chem. V. 291 13421 2016
PubMed-ID: 27137927  |  Reference-DOI: 10.1074/JBC.M116.730358

(-) Compounds

Molecule 1 - 3-ISOPROPYLMALATE DEHYDROGENASE 2, CHLOROPLASTIC
    Chains: A, B, C, D
    EC Number: 1.1.1.85
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: IMDH2, IMDH, AT1G80560, T21F11.11
    Mutation: YES
    Organism Common: MOUSE-EAR CRESS
    Organism Scientific: ARABIDOPSIS THALIANA
    Organism Taxid: 3702
    Synonym: IMDH 2,BETA-IPM DEHYDROGENASE 2

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
2SO46Ligand/IonSULFATE ION
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SO44Ligand/IonSULFATE ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2SO42Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:288 , ASP A:292 , HOH A:691 , HOH A:714 , HOH A:778 , ASP C:264binding site for residue MG A 501
02AC2SOFTWAREGLY A:302 , HIS A:321 , ASN A:334binding site for residue SO4 A 502
03AC3SOFTWARELYS A:130 , GLN A:134 , HOH A:612 , HOH A:659 , HOH A:757 , LYS B:354binding site for residue SO4 A 503
04AC4SOFTWAREARG A:136 , ARG A:146 , ARG A:174 , HOH A:610 , HOH A:691 , HOH A:714binding site for residue SO4 A 504
05AC5SOFTWAREASP B:288 , ASP B:292 , HOH B:662 , HOH B:665 , HOH B:753 , ASP D:264binding site for residue MG B 501
06AC6SOFTWAREARG B:136 , ARG B:146 , ARG B:174 , HOH B:611 , HOH B:662 , HOH B:665 , HOH B:800binding site for residue SO4 B 502
07AC7SOFTWAREASP A:264 , ASP C:288 , ASP C:292 , HOH C:644 , HOH C:656 , HOH C:789binding site for residue MG C 501
08AC8SOFTWAREARG C:136 , ARG C:146 , ARG C:174 , HOH C:607 , HOH C:644 , HOH C:656binding site for residue SO4 C 502
09AC9SOFTWAREASP B:264 , ASP D:288 , ASP D:292 , HOH D:663 , HOH D:674 , HOH D:745binding site for residue MG D 501
10AD1SOFTWAREARG D:136 , ARG D:146 , ARG D:174 , HOH D:606 , HOH D:663 , HOH D:674binding site for residue SO4 D 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5J34)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:184 -Pro A:185
2Glu B:184 -Pro B:185
3Glu C:184 -Pro C:185
4Glu D:184 -Pro D:185

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5J34)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J34)

(-) Exons   (0, 0)

(no "Exon" information available for 5J34)

(-) 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:359
                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh....hhhhhhhhhh..eeeeee..hhhhh..hhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhh..hhhhhh..eeeeeee...........eeee.....eeeeeeeeeehhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhh..eee.....eee......hhhhh......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.eehhhhh....ee.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j34 A  41 KRYTITLLPGDGIGPEVVSIAKNVLQQAGSLEGVEFNFREMPIGGAALDLVGVPLPEETISAAKESDAVLLGAIGGYKWDNNEKHLRPEKGLLQIRAALKVFANLRPATVLPQLVDASTLKREVAEGVDLMVVRELTGGIYFGEPRGIKTNENGEEVGFNTEVYAAHEIDRIARVAFETARKRRGKLCSVDMANVLEASILWRKRVTALASEYPDVELSHMYVDNAAMQLVRDPKQFDTIVTNNIFGDILSDEASMITGSIGMLPSASLSDSGPGLFEPIHGSAPDIAGQDKANPLATILSAAMLLKYGLGEEKAAKRIEDAVLVALNNGFRTGDIYSAGTKLVGCKEMGEEVLKSVDS 399
                                    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       350       360       370       380       390         


Chain B from PDB  Type:PROTEIN  Length:359
                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..hhhhhhhhhhhhhhhhhhh...eeeeee..hhhhhhhhh....hhhhhhhhhhh.eeeeee..hhhhh..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhh..hhhhhh..eeeeeee...........eeee.....eeeeeeeeeehhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhh.eeeee.....eeeee....hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhh....ee.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j34 B  41 KRYTITLLPGDGIGPEVVSIAKNVLQQAGSLEGVEFNFREMPIGGAALDLVGVPLPEETISAAKESDAVLLGAIGGYKWDNNEKHLRPEKGLLQIRAALKVFANLRPATVLPQLVDASTLKREVAEGVDLMVVRELTGGIYFGEPRGIKTNENGEEVGFNTEVYAAHEIDRIARVAFETARKRRGKLCSVDMANVLEASILWRKRVTALASEYPDVELSHMYVDNAAMQLVRDPKQFDTIVTNNIFGDILSDEASMITGSIGMLPSASLSDSGPGLFEPIHGSAPDIAGQDKANPLATILSAAMLLKYGLGEEKAAKRIEDAVLVALNNGFRTGDIYSAGTKLVGCKEMGEEVLKSVDS 399
                                    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       350       360       370       380       390         


Chain C from PDB  Type:PROTEIN  Length:359
                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh....hhhhhhhhhhh.eeeeee..hhhhh..hhhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhh..hhhhhh..eeeeeee...........eeee.....eeeeeeeeeehhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhh.eeeee.....eeeee....hhhhh......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.eehhhhh....ee.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j34 C  41 KRYTITLLPGDGIGPEVVSIAKNVLQQAGSLEGVEFNFREMPIGGAALDLVGVPLPEETISAAKESDAVLLGAIGGYKWDNNEKHLRPEKGLLQIRAALKVFANLRPATVLPQLVDASTLKREVAEGVDLMVVRELTGGIYFGEPRGIKTNENGEEVGFNTEVYAAHEIDRIARVAFETARKRRGKLCSVDMANVLEASILWRKRVTALASEYPDVELSHMYVDNAAMQLVRDPKQFDTIVTNNIFGDILSDEASMITGSIGMLPSASLSDSGPGLFEPIHGSAPDIAGQDKANPLATILSAAMLLKYGLGEEKAAKRIEDAVLVALNNGFRTGDIYSAGTKLVGCKEMGEEVLKSVDS 399
                                    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       350       360       370       380       390         


Chain D from PDB  Type:PROTEIN  Length:359
                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhh....hhhhhhhhhhh.eeeeee..hhhhh..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhh..hhhhhh..eeeeeee...........eeee.....eeeeeeeeeehhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhh..eee.....eee......hhhhh......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.eehhhhh....ee.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j34 D  41 KRYTITLLPGDGIGPEVVSIAKNVLQQAGSLEGVEFNFREMPIGGAALDLVGVPLPEETISAAKESDAVLLGAIGGYKWDNNEKHLRPEKGLLQIRAALKVFANLRPATVLPQLVDASTLKREVAEGVDLMVVRELTGGIYFGEPRGIKTNENGEEVGFNTEVYAAHEIDRIARVAFETARKRRGKLCSVDMANVLEASILWRKRVTALASEYPDVELSHMYVDNAAMQLVRDPKQFDTIVTNNIFGDILSDEASMITGSIGMLPSASLSDSGPGLFEPIHGSAPDIAGQDKANPLATILSAAMLLKYGLGEEKAAKRIEDAVLVALNNGFRTGDIYSAGTKLVGCKEMGEEVLKSVDS 399
                                    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       350       360       370       380       390
   Legend:   → Mismatch (orange background)
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  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 5J34)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J34)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J34)

(-) Gene Ontology  (15, 15)

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 Related Entries

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

UniProtKB/Swiss-Prot
        LEU32_ARATH | P93832: 3r8w 5j32 5j33

(-) Related Entries Specified in the PDB File

5j32 5j33