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(-) Description

Title :  CRYSTAL STRUCTURE OF SACCHAROMYCES CEREVESIAE MITOCHONDRIAL NADP(+)-DEPENDENT ISOCITRATE DEHYDROGENASE IN COMPLEX WITH ISOCITRATE
 
Authors :  Y. J. Peng, J. P. Ding
Date :  28 Jun 07  (Deposition) - 01 Jul 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Rossmann Fold, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. J. Peng, C. Zhong, W. Huang, J. P. Ding
Structural Studies Of Saccharomyces Cerevesiae Mitochondria Nadp-Dependent Isocitrate Dehydrogenase In Different Enzymatic States Reveal Substantial Conformational Changes During The Catalytic Reaction
Protein Sci. V. 17 1542 2008
PubMed-ID: 18552125  |  Reference-DOI: 10.1110/PS.035675.108

(-) Compounds

Molecule 1 - ISOCITRATE DEHYDROGENASE [NADP]
    ChainsA, B, C, D, E, F
    EC Number1.1.1.42
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET-3E-HIS
    Expression System StrainBL21 (DE3) PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneIDP1
    Organism CommonYEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    StrainYPH499
    SynonymIDP1P, OXALOSUCCINATE DECARBOXYLASE, IDH, NADP+, -SPECIFIC ICDH, IDP

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)AB    
Biological Unit 2 (1x)  CD  
Biological Unit 3 (1x)    EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1ICT6Ligand/IonISOCITRIC ACID
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1ICT2Ligand/IonISOCITRIC ACID
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ICT2Ligand/IonISOCITRIC ACID
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1ICT2Ligand/IonISOCITRIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:78 , SER A:95 , ASN A:97 , ARG A:101 , ARG A:110 , ARG A:133 , TYR A:140 , ASP A:277 , LYS B:214 , ASP B:254BINDING SITE FOR RESIDUE ICT A 2101
2AC2SOFTWARELYS A:214 , ASP A:254 , THR B:78 , SER B:95 , ASN B:97 , ARG B:101 , ARG B:110 , ARG B:133 , TYR B:140 , ASP B:277 , HOH B:2305BINDING SITE FOR RESIDUE ICT B 2102
3AC3SOFTWARETHR C:78 , SER C:95 , ASN C:97 , ARG C:101 , ARG C:110 , ARG C:133 , TYR C:140 , ASP C:277 , HOH C:2131 , LYS D:214 , ILE D:217 , ASP D:254BINDING SITE FOR RESIDUE ICT C 2103
4AC4SOFTWAREHOH C:2195 , SER D:95 , ASN D:97 , ARG D:101 , ARG D:110 , ARG D:133 , ASP D:277 , HOH D:2135 , HOH D:2139 , HOH D:2254BINDING SITE FOR RESIDUE ICT D 2104
5AC5SOFTWARETHR E:78 , SER E:95 , ASN E:97 , ARG E:101 , ARG E:110 , ARG E:133 , TYR E:140 , ASP E:277 , HOH E:2108 , LYS F:214 , ASP F:254 , HOH F:2141BINDING SITE FOR RESIDUE ICT E 2105
6AC6SOFTWAREILE E:217 , ASP E:254 , THR F:78 , SER F:95 , ASN F:97 , ARG F:101 , ARG F:110 , ARG F:133 , ASP F:277 , HOH F:2126BINDING SITE FOR RESIDUE ICT F 2106

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2QFW)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2QFW)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 6)

Asymmetric Unit (1, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IDH_IMDHPS00470 Isocitrate and isopropylmalate dehydrogenases signature.IDHP_YEAST288-307
 
 
 
 
 
  6A:273-292
B:273-292
C:273-292
D:273-292
E:273-292
F:273-292
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IDH_IMDHPS00470 Isocitrate and isopropylmalate dehydrogenases signature.IDHP_YEAST288-307
 
 
 
 
 
  2A:273-292
B:273-292
-
-
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IDH_IMDHPS00470 Isocitrate and isopropylmalate dehydrogenases signature.IDHP_YEAST288-307
 
 
 
 
 
  2-
-
C:273-292
D:273-292
-
-
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1IDH_IMDHPS00470 Isocitrate and isopropylmalate dehydrogenases signature.IDHP_YEAST288-307
 
 
 
 
 
  2-
-
-
-
E:273-292
F:273-292

(-) Exons   (0, 0)

(no "Exon" information available for 2QFW)

(-) 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:407
 aligned with IDHP_YEAST | P21954 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:407
                                    27        37        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       407       417       
           IDHP_YEAST    18 SKIKVKQPVVELDGDEMTRIIWDKIKKKLILPYLDVDLKYYDLSVESRDATSDKITQDAAEAIKKYGVGIKCATITPDEARVKEFNLHKMWKSPNGTIRNILGGTVFREPIVIPRIPRLVPRWEKPIIIGRHAHGDQYKATDTLIPGPGSLELVYKPSDPTTAQPQTLKVYDYKGSGVAMAMYNTDESIEGFAHSSFKLAIDKKLNLFLSTKNTILKKYDGRFKDIFQEVYEAQYKSKFEQLGIHYEHRLIDDMVAQMIKSKGGFIMALKNYDGDVQSDIVAQGFGSLGLMTSILVTPDGKTFESEAAHGTVTRHYRKYQKGEETSTNSIASIFAWSRGLLKRGELDNTPALCKFANILESATLNTVQQDGIMTKDLALACGNNERSAYVTTEEFLDAVEKRLQKEI 424
               SCOP domains d2qfwa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 2qfwA00 A:3-409 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....eeeee.hhhhhhhhhhhhhhhh...ee..eeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee..............eeeeeeee..hhhhh.eeeee...eeeeeeeee........eeeeeeee...eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhh....eeeeee......eeee.....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qfw A   3 SKIKVKQPVVELDGDEMTRIIWDKIKKKLILPYLDVDLKYYDLSVESRDATSDKITQDAAEAIKKYGVGIKCATITPDEARVKEFNLHKMWKSPNGTIRNILGGTVFREPIVIPRIPRLVPRWEKPIIIGRHAHGDQYKATDTLIPGPGSLELVYKPSDPTTAQPQTLKVYDYKGSGVAMAMYNTDESIEGFAHSSFKLAIDKKLNLFLSTKNTILKKYDGRFKDIFQEVYEAQYKSKFEQLGIHYEHRLIDDMVAQMIKSKGGFIMALKNYDGDVQSDIVAQGFGSLGLMTSILVTPDGKTFESEAAHGTVTRHYRKYQKGEETSTNSIASIFAWSRGLLKRGELDNTPALCKFANILESATLNTVQQDGIMTKDLALACGNNERSAYVTTEEFLDAVEKRLQKEI 409
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       

Chain B from PDB  Type:PROTEIN  Length:408
 aligned with IDHP_YEAST | P21954 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:408
                                    28        38        48        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       318       328       338       348       358       368       378       388       398       408       418        
           IDHP_YEAST    19 KIKVKQPVVELDGDEMTRIIWDKIKKKLILPYLDVDLKYYDLSVESRDATSDKITQDAAEAIKKYGVGIKCATITPDEARVKEFNLHKMWKSPNGTIRNILGGTVFREPIVIPRIPRLVPRWEKPIIIGRHAHGDQYKATDTLIPGPGSLELVYKPSDPTTAQPQTLKVYDYKGSGVAMAMYNTDESIEGFAHSSFKLAIDKKLNLFLSTKNTILKKYDGRFKDIFQEVYEAQYKSKFEQLGIHYEHRLIDDMVAQMIKSKGGFIMALKNYDGDVQSDIVAQGFGSLGLMTSILVTPDGKTFESEAAHGTVTRHYRKYQKGEETSTNSIASIFAWSRGLLKRGELDNTPALCKFANILESATLNTVQQDGIMTKDLALACGNNERSAYVTTEEFLDAVEKRLQKEIKS 426
               SCOP domains d2qfwb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 2qfwB00 B:4-411 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .ee....eeeee.hhhhhhhhhhhhhhhh...ee..eeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhh.......hhhhhhhhhhh.eeeeee..............eeeeeeee..hhhhhheeeee...eeeeeeeee........eeeeeeee...eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhh....eeeeee......eeeee....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2qfw B   4 KIKVKQPVVELDGDEMTRIIWDKIKKKLILPYLDVDLKYYDLSVESRDATSDKITQDAAEAIKKYGVGIKCATITPDEARVKEFNLHKMWKSPNGTIRNILGGTVFREPIVIPRIPRLVPRWEKPIIIGRHAHGDQYKATDTLIPGPGSLELVYKPSDPTTAQPQTLKVYDYKGSGVAMAMYNTDESIEGFAHSSFKLAIDKKLNLFLSTKNTILKKYDGRFKDIFQEVYEAQYKSKFEQLGIHYEHRLIDDMVAQMIKSKGGFIMALKNYDGDVQSDIVAQGFGSLGLMTSILVTPDGKTFESEAAHGTVTRHYRKYQKGEETSTNSIASIFAWSRGLLKRGELDNTPALCKFANILESATLNTVQQDGIMTKDLALACGNNERSAYVTTEEFLDAVEKRLQKEIKS 411
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403        

Chain C from PDB  Type:PROTEIN  Length:410
 aligned with IDHP_YEAST | P21954 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:410
                                    27        37        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       407       417       427
           IDHP_YEAST    18 SKIKVKQPVVELDGDEMTRIIWDKIKKKLILPYLDVDLKYYDLSVESRDATSDKITQDAAEAIKKYGVGIKCATITPDEARVKEFNLHKMWKSPNGTIRNILGGTVFREPIVIPRIPRLVPRWEKPIIIGRHAHGDQYKATDTLIPGPGSLELVYKPSDPTTAQPQTLKVYDYKGSGVAMAMYNTDESIEGFAHSSFKLAIDKKLNLFLSTKNTILKKYDGRFKDIFQEVYEAQYKSKFEQLGIHYEHRLIDDMVAQMIKSKGGFIMALKNYDGDVQSDIVAQGFGSLGLMTSILVTPDGKTFESEAAHGTVTRHYRKYQKGEETSTNSIASIFAWSRGLLKRGELDNTPALCKFANILESATLNTVQQDGIMTKDLALACGNNERSAYVTTEEFLDAVEKRLQKEIKSI 427
               SCOP domains d2qfwc_ C: automated matches                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2qfwC00 C:3-412 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                                                                              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....eeeee.hhhhhhhhhhhhhhhh...ee..eeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhhh......hhhhhhhhhhh.eeeeee..............eeeeeeee..hhhhhheeeee...eeeeeeeee........eeeeeeee...eeeeeeeeehhhhhhhhhhhhhhhhhh...eeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhh....eeeeee......eeee.....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qfw C   3 SKIKVKQPVVELDGDEMTRIIWDKIKKKLILPYLDVDLKYYDLSVESRDATSDKITQDAAEAIKKYGVGIKCATITPDEARVKEFNLHKMWKSPNGTIRNILGGTVFREPIVIPRIPRLVPRWEKPIIIGRHAHGDQYKATDTLIPGPGSLELVYKPSDPTTAQPQTLKVYDYKGSGVAMAMYNTDESIEGFAHSSFKLAIDKKLNLFLSTKNTILKKYDGRFKDIFQEVYEAQYKSKFEQLGIHYEHRLIDDMVAQMIKSKGGFIMALKNYDGDVQSDIVAQGFGSLGLMTSILVTPDGKTFESEAAHGTVTRHYRKYQKGEETSTNSIASIFAWSRGLLKRGELDNTPALCKFANILESATLNTVQQDGIMTKDLALACGNNERSAYVTTEEFLDAVEKRLQKEIKSI 412
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412

Chain D from PDB  Type:PROTEIN  Length:412
 aligned with IDHP_YEAST | P21954 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:412
                                    25        35        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       405       415       425  
           IDHP_YEAST    16 AFSKIKVKQPVVELDGDEMTRIIWDKIKKKLILPYLDVDLKYYDLSVESRDATSDKITQDAAEAIKKYGVGIKCATITPDEARVKEFNLHKMWKSPNGTIRNILGGTVFREPIVIPRIPRLVPRWEKPIIIGRHAHGDQYKATDTLIPGPGSLELVYKPSDPTTAQPQTLKVYDYKGSGVAMAMYNTDESIEGFAHSSFKLAIDKKLNLFLSTKNTILKKYDGRFKDIFQEVYEAQYKSKFEQLGIHYEHRLIDDMVAQMIKSKGGFIMALKNYDGDVQSDIVAQGFGSLGLMTSILVTPDGKTFESEAAHGTVTRHYRKYQKGEETSTNSIASIFAWSRGLLKRGELDNTPALCKFANILESATLNTVQQDGIMTKDLALACGNNERSAYVTTEEFLDAVEKRLQKEIKSI 427
               SCOP domains d2qfwd_ D: automated matches                                                                                                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains 2qfwD00 D:1-412 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....ee....eeeee.hhhhhhhhhhhhhhhh...ee..eeeee.hhhhhhhhhhhhhhhhhhhhhhhheeee......hhhhhhhh.......hhhhhhhhhhh.eeeeee..............eeeeeeee..hhhhhheeeee...eeeeeeeee........eeeeeeee...eeeeeeeeehhhhhhhhhhhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhh....eeeeee......eeeee....hhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qfw D   1 AFSKIKVKQPVVELDGDEMTRIIWDKIKKKLILPYLDVDLKYYDLSVESRDATSDKITQDAAEAIKKYGVGIKCATITPDEARVKEFNLHKMWKSPNGTIRNILGGTVFREPIVIPRIPRLVPRWEKPIIIGRHAHGDQYKATDTLIPGPGSLELVYKPSDPTTAQPQTLKVYDYKGSGVAMAMYNTDESIEGFAHSSFKLAIDKKLNLFLSTKNTILKKYDGRFKDIFQEVYEAQYKSKFEQLGIHYEHRLIDDMVAQMIKSKGGFIMALKNYDGDVQSDIVAQGFGSLGLMTSILVTPDGKTFESEAAHGTVTRHYRKYQKGEETSTNSIASIFAWSRGLLKRGELDNTPALCKFANILESATLNTVQQDGIMTKDLALACGNNERSAYVTTEEFLDAVEKRLQKEIKSI 412
                                    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       350       360       370       380       390       400       410  

Chain E from PDB  Type:PROTEIN  Length:409
 aligned with IDHP_YEAST | P21954 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:409
                                    27        37        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       407       417         
           IDHP_YEAST    18 SKIKVKQPVVELDGDEMTRIIWDKIKKKLILPYLDVDLKYYDLSVESRDATSDKITQDAAEAIKKYGVGIKCATITPDEARVKEFNLHKMWKSPNGTIRNILGGTVFREPIVIPRIPRLVPRWEKPIIIGRHAHGDQYKATDTLIPGPGSLELVYKPSDPTTAQPQTLKVYDYKGSGVAMAMYNTDESIEGFAHSSFKLAIDKKLNLFLSTKNTILKKYDGRFKDIFQEVYEAQYKSKFEQLGIHYEHRLIDDMVAQMIKSKGGFIMALKNYDGDVQSDIVAQGFGSLGLMTSILVTPDGKTFESEAAHGTVTRHYRKYQKGEETSTNSIASIFAWSRGLLKRGELDNTPALCKFANILESATLNTVQQDGIMTKDLALACGNNERSAYVTTEEFLDAVEKRLQKEIKS 426
               SCOP domains d2qfwe_ E: automated matches                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2qfwE00 E:3-411 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee....eeeee.hhhhhhhhhhhhhhhh...ee..eeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhh.......hhhhhhhhhhh.eeeeee..............eeeeeeee..hhhhhheeeee...eeeeeeeee........eeeeeeee...eeeeeeeeehhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhh....eeeeee......eeee.....hhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhh........hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ----------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qfw E   3 SKIKVKQPVVELDGDEMTRIIWDKIKKKLILPYLDVDLKYYDLSVESRDATSDKITQDAAEAIKKYGVGIKCATITPDEARVKEFNLHKMWKSPNGTIRNILGGTVFREPIVIPRIPRLVPRWEKPIIIGRHAHGDQYKATDTLIPGPGSLELVYKPSDPTTAQPQTLKVYDYKGSGVAMAMYNTDESIEGFAHSSFKLAIDKKLNLFLSTKNTILKKYDGRFKDIFQEVYEAQYKSKFEQLGIHYEHRLIDDMVAQMIKSKGGFIMALKNYDGDVQSDIVAQGFGSLGLMTSILVTPDGKTFESEAAHGTVTRHYRKYQKGEETSTNSIASIFAWSRGLLKRGELDNTPALCKFANILESATLNTVQQDGIMTKDLALACGNNERSAYVTTEEFLDAVEKRLQKEIKS 411
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402         

Chain F from PDB  Type:PROTEIN  Length:411
 aligned with IDHP_YEAST | P21954 from UniProtKB/Swiss-Prot  Length:428

    Alignment length:411
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426 
           IDHP_YEAST    17 FSKIKVKQPVVELDGDEMTRIIWDKIKKKLILPYLDVDLKYYDLSVESRDATSDKITQDAAEAIKKYGVGIKCATITPDEARVKEFNLHKMWKSPNGTIRNILGGTVFREPIVIPRIPRLVPRWEKPIIIGRHAHGDQYKATDTLIPGPGSLELVYKPSDPTTAQPQTLKVYDYKGSGVAMAMYNTDESIEGFAHSSFKLAIDKKLNLFLSTKNTILKKYDGRFKDIFQEVYEAQYKSKFEQLGIHYEHRLIDDMVAQMIKSKGGFIMALKNYDGDVQSDIVAQGFGSLGLMTSILVTPDGKTFESEAAHGTVTRHYRKYQKGEETSTNSIASIFAWSRGLLKRGELDNTPALCKFANILESATLNTVQQDGIMTKDLALACGNNERSAYVTTEEFLDAVEKRLQKEIKSI 427
               SCOP domains d2qfwf_ F: automated matches                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2qfwF00 F:2-412 Isopropylmalate Dehydrogenase                                                                                                                                                                                                                                                                                                                                                                               CATH domains
           Pfam domains (1) ----Iso_dh-2qfwF01 F:6-401                                                                                                                                                                                                                                                                                                                                                                                      ----------- Pfam domains (1)
           Pfam domains (2) ----Iso_dh-2qfwF02 F:6-401                                                                                                                                                                                                                                                                                                                                                                                      ----------- Pfam domains (2)
           Pfam domains (3) ----Iso_dh-2qfwF03 F:6-401                                                                                                                                                                                                                                                                                                                                                                                      ----------- Pfam domains (3)
           Pfam domains (4) ----Iso_dh-2qfwF04 F:6-401                                                                                                                                                                                                                                                                                                                                                                                      ----------- Pfam domains (4)
           Pfam domains (5) ----Iso_dh-2qfwF05 F:6-401                                                                                                                                                                                                                                                                                                                                                                                      ----------- Pfam domains (5)
           Pfam domains (6) ----Iso_dh-2qfwF06 F:6-401                                                                                                                                                                                                                                                                                                                                                                                      ----------- Pfam domains (6)
         Sec.struct. author ...ee....eeeee.hhhhhhhhhhhhhhhh...ee..eeeee.hhhhhhhh.hhhhhhhhhhhhhhheeee......hhhhhhhh.......hhhhhhhhhhh.eeeeee................eeeeee..hhhhh.eeeee...eeeeeeeee........eeeeeeee...eeeeeeeeehhhhhhhhhhhhhhhhhhh.eeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhh....eeeeee......eeeee....hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------IDH_IMDH            ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2qfw F   2 FSKIKVKQPVVELDGDEMTRIIWDKIKKKLILPYLDVDLKYYDLSVESRDATSDKITQDAAEAIKKYGVGIKCATITPDEARVKEFNLHKMWKSPNGTIRNILGGTVFREPIVIPRIPRLVPRWEKPIIIGRHAHGDQYKATDTLIPGPGSLELVYKPSDPTTAQPQTLKVYDYKGSGVAMAMYNTDESIEGFAHSSFKLAIDKKLNLFLSTKNTILKKYDGRFKDIFQEVYEAQYKSKFEQLGIHYEHRLIDDMVAQMIKSKGGFIMALKNYDGDVQSDIVAQGFGSLGLMTSILVTPDGKTFESEAAHGTVTRHYRKYQKGEETSTNSIASIFAWSRGLLKRGELDNTPALCKFANILESATLNTVQQDGIMTKDLALACGNNERSAYVTTEEFLDAVEKRLQKEIKSI 412
                                    11        21        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 

   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)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 6)

Asymmetric Unit

(-) CATH Domains  (1, 6)

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

(-) Pfam Domains  (1, 6)

Asymmetric Unit
(-)
Clan: Iso_DH (49)

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (IDHP_YEAST | P21954)
molecular function
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0004450    isocitrate dehydrogenase (NADP+) activity    Catalysis of the reaction: isocitrate + NADP+ = 2-oxoglutarate + CO2 + NADPH + H+.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
    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:0006537    glutamate biosynthetic process    The chemical reactions and pathways resulting in the formation of glutamate, the anion of 2-aminopentanedioic acid.
    GO:0006097    glyoxylate cycle    A modification of the TCA cycle occurring in some plants and microorganisms, in which isocitrate is cleaved to glyoxylate and succinate. Glyoxylate can then react with acetyl-CoA to form malate.
    GO:0006102    isocitrate metabolic process    The chemical reactions and pathways involving isocitrate, the anion of isocitric acid, 1-hydroxy-1,2,3-propanetricarboxylic acid. Isocitrate is an important intermediate in the TCA cycle and the glycoxylate 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:0006099    tricarboxylic acid cycle    A nearly universal metabolic pathway in which the acetyl group of acetyl coenzyme A is effectively oxidized to two CO2 and four pairs of electrons are transferred to coenzymes. The acetyl group combines with oxaloacetate to form citrate, which undergoes successive transformations to isocitrate, 2-oxoglutarate, succinyl-CoA, succinate, fumarate, malate, and oxaloacetate again, thus completing the cycle. In eukaryotes the tricarboxylic acid is confined to the mitochondria. See also glyoxylate cycle.
cellular component
    GO:0042645    mitochondrial nucleoid    The region of a mitochondrion to which the DNA is confined.
    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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 Related Entries

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

UniProtKB/Swiss-Prot
        IDHP_YEAST | P219542qfv 2qfx 2qfy

(-) Related Entries Specified in the PDB File

2qfv THE SAME PROTEIN COMPLEXED WITH NADP(+)
2qfx
2qfy