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(-) Description

Title :  ISOPROPYLMALATE DEHYDROGENASE IN COMPLEX WITH ISOPROPYLMALATE
 
Authors :  J. M. Jez, S. G. Lee
Date :  30 Mar 16  (Deposition) - 11 May 16  (Release) - 06 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,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
    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): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1IPM4Ligand/Ion3-ISOPROPYLMALIC ACID
2MG4Ligand/IonMAGNESIUM ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1IPM2Ligand/Ion3-ISOPROPYLMALIC ACID
2MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1IPM2Ligand/Ion3-ISOPROPYLMALIC ACID
2MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:288 , ASP A:292 , IPM A:502 , HOH A:623 , HOH A:657 , ASP B:264binding site for residue MG A 501
2AC2SOFTWAREARG A:136 , ARG A:146 , ARG A:174 , TYR A:181 , ASP A:288 , MG A:501 , HOH A:623 , HOH A:657 , HOH A:785 , LYS B:232 , ASP B:264binding site for residue IPM A 502
3AC3SOFTWAREASP A:264 , IPM A:504 , ASP B:288 , ASP B:292 , HOH B:654 , HOH B:655binding site for residue MG A 503
4AC4SOFTWARELYS A:232 , ASN A:234 , VAL A:235 , ASP A:264 , MG A:503 , HOH A:793 , ARG B:136 , ARG B:146 , ARG B:174 , TYR B:181 , ASP B:288 , HOH B:654binding site for residue IPM A 504
5AC5SOFTWAREASP C:288 , ASP C:292 , IPM C:502 , HOH C:622 , HOH C:803 , ASP D:264binding site for residue MG C 501
6AC6SOFTWAREARG C:136 , ARG C:146 , ARG C:174 , TYR C:181 , ASP C:288 , MG C:501 , HOH C:622 , HOH C:773 , LYS D:232 , ASP D:264binding site for residue IPM C 502
7AC7SOFTWAREASP C:264 , IPM C:504 , HOH C:625 , ASP D:288 , ASP D:292 , HOH D:799binding site for residue MG C 503
8AC8SOFTWARELYS C:232 , ASP C:264 , MG C:503 , HOH C:625 , ARG D:136 , ARG D:146 , ARG D:174 , TYR D:181 , ASP D:288binding site for residue IPM C 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5J32)

(-) 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 5J32)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5J32)

(-) Exons   (0, 0)

(no "Exon" information available for 5J32)

(-) 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:369
                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeeee..hhhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhh...hhhhhhhhhh..eeeeee..hhhhh..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhh..hhhhhh..eeeeeee..hhhhh....eeee.....eeeeeeeeeehhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhh..eee.....eee......hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhh....ee.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j32 A  31 QMGRGSEFGKKRYTITLLPGDGIGPEVVSIAKNVLQQAGSLEGVEFNFREMPIGGAALDLVGVPLPEETISAAKESDAVLLGAIGGYKWDNNEKHLRPEKGLLQIRAALKVFANLRPATVLPQLVDASTLKREVAEGVDLMVVRELTGGIYFGEPRGIKTNENGEEVGFNTEVYAAHEIDRIARVAFETARKRRGKLCSVDKANVLEASILWRKRVTALASEYPDVELSHMYVDNAAMQLVRDPKQFDTIVTNNIFGDILSDEASMITGSIGMLPSASLSDSGPGLFEPIHGSAPDIAGQDKANPLATILSAAMLLKYGLGEEKAAKRIEDAVLVALNNGFRTGDIYSAGTKLVGCKEMGEEVLKSVDS 399
                                    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       350       360       370       380       390         


Chain B from PDB  Type:PROTEIN  Length:365
                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeee..hhhhhhhhhhhhhhhhhhh..eeeeeee...hhhhhhhhh...hhhhhhhhhhh.eeeeee..hhhhh..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhh..hhhhhh..eeeeeee..hhhhh....eeee.....eeeeeeeeeehhhhhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhh..eee.....eee......hhhhh......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.eehhhhh....ee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j32 B  36 SEFGKKRYTITLLPGDGIGPEVVSIAKNVLQQAGSLEGVEFNFREMPIGGAALDLVGVPLPEETISAAKESDAVLLGAIGGYKWDNNEKHLRPEKGLLQIRAALKVFANLRPATVLPQLVDASTLKREVAEGVDLMVVRELTGGIYFGEPRGIKTNENGEEVGFNTEVYAAHEIDRIARVAFETARKRRGKLCSVDKANVLEASILWRKRVTALASEYPDVELSHMYVDNAAMQLVRDPKQFDTIVTNNIFGDILSDEASMITGSIGMLPSASLSDSGPGLFEPIHGSAPDIAGQDKANPLATILSAAMLLKYGLGEEKAAKRIEDAVLVALNNGFRTGDIYSAGTKLVGCKEMGEEVLKSVDSQ 400
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395     


Chain C from PDB  Type:PROTEIN  Length:356
                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..hhhhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhh...hhhhhhhhhh..eeeeee..hhhhh..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhh..hhhhhh..eeeeeee..hhhhh....eeee.....eeeeeeeeeehhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhh..eee.....eee......hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eehhhhh....ee.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5j32 C  41 KRYTITLLPGDGIGPEVVSIAKNVLQQAGSLEGVEFNFREMPIGGAALDLVGVPLPEETISAAKESDAVLLGAIGGYKWDNNEKHLRPEKGLLQIRAALKVFANLRPATVLPQLVDASTLKREVAEGVDLMVVRELTGGIYFGEPRGIKTNENGEEVGFNTEVYAAHEIDRIARVAFETARKRRGKLCSVDKANVLEASILWRKRVTALASEYPDVELSHMYVDNAAMQLVRDPKQFDTIVTNNIFGDILSDEASMITGSIGMLPSASLSDSGPGLFEPIHGSAPDIAGQDKANPLATILSAAMLLKYGLGEEKAAKRIEDAVLVALNNGFRTGDIYSAGTKLVGCKEMGEEVLKS 396
                                    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:360
                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....eeeeeeee..hhhhhhhhhhhhhhhhhhh....eeeee..hhhhhhhhhh...hhhhhhhhhh..eeeeee..hhhhh..hhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhh..hhhhhh..eeeeeee..hhhhh....eeee.....eeeeeeeeeehhhhhhhhhhhhhhhhh...eeeeee....hhhhhhhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhh.eeeee.....eeeee....hhhhh......hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh.eehhhhh....ee.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5j32 D  38 FGKKRYTITLLPGDGIGPEVVSIAKNVLQQAGSLEGVEFNFREMPIGGAALDLVGVPLPEETISAAKESDAVLLGAIGGYKWDNNEKHLRPEKGLLQIRAALKVFANLRPATVLPQLVDASTLKREVAEGVDLMVVRELTGGIYFGEPRGIKTNENGEEVGFNTEVYAAHEIDRIARVAFETARKRRGKLCSVDKANVLEASILWRKRVTALASEYPDVELSHMYVDNAAMQLVRDPKQFDTIVTNNIFGDILSDEASMITGSIGMLPSASLSDSGPGLFEPIHGSAPDIAGQDKANPLATILSAAMLLKYGLGEEKAAKRIEDAVLVALNNGFRTGDIYSAGTKLVGCKEMGEEVLKSV 397
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397
   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 5J32)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5J32)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5J32)

(-) Gene Ontology  (15, 15)

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  1.1.1.85
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 Related Entries

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        LEU32_ARATH | P93832: 3r8w 5j33 5j34

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