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(-) Description

Title :  CRYSTAL STRUCTURE OF INOSINE MONOPHOSPHATE DEHYDROGENASE IN COMPLEX WITH MYCOPHENOLIC ACID
 
Authors :  M. D. Sintchak, M. A. Fleming, O. Futer, S. A. Raybuck, S. P. Chambers, P. M. A. Murcko, K. P. Wilson
Date :  09 Aug 01  (Deposition) - 05 Sep 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  B  (4x)
Keywords :  Dehydrogenase, Impd, Impdh, Guanine Nucleotide Synthesis, Mycophenolic Acid, Mpa, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. D. Sintchak, M. A. Fleming, O. Futer, S. A. Raybuck, S. P. Chambers, P. R. Caron, M. A. Murcko, K. P. Wilson
Structure And Mechanism Of Inosine Monophosphate Dehydrogenase In Complex With The Immunosuppressant Mycophenolic Acid.
Cell(Cambridge, Mass. ) V. 85 921 1996
PubMed-ID: 8681386  |  Reference-DOI: 10.1016/S0092-8674(00)81275-1

(-) Compounds

Molecule 1 - INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE 2
    ChainsA, B
    EC Number1.1.1.205
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonCHINESE HAMSTER
    Organism ScientificCRICETULUS GRISEUS
    Organism Taxid10029
    SynonymIMP DEHYDROGENASE 2, IMPDH-II, IMPD 2

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (4x)A 
Biological Unit 2 (4x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1IMP2Ligand/IonINOSINIC ACID
2K2Ligand/IonPOTASSIUM ION
3MOA2Ligand/IonMYCOPHENOLIC ACID
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1IMP4Ligand/IonINOSINIC ACID
2K-1Ligand/IonPOTASSIUM ION
3MOA4Ligand/IonMYCOPHENOLIC ACID
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1IMP4Ligand/IonINOSINIC ACID
2K-1Ligand/IonPOTASSIUM ION
3MOA4Ligand/IonMYCOPHENOLIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:326 , CYS A:327 , GLY A:328 , CYS A:331 , GLU A:500 , GLY A:501 , GLY A:502BINDING SITE FOR RESIDUE K A 601
2AC2SOFTWAREGLY B:326 , GLY B:328 , CYS B:331 , GLU B:500 , GLY B:501 , GLY B:502BINDING SITE FOR RESIDUE K B 602
3AC3SOFTWARESER A:68 , MET A:70 , ARG A:322 , GLY A:328 , SER A:329 , CYS A:331 , ASP A:364 , GLY A:366 , MET A:386 , GLY A:387 , SER A:388 , TYR A:411 , GLY A:413 , MET A:414 , GLY A:415 , GLN A:441 , GLY A:442 , HOH A:617 , HOH A:653 , HOH A:664 , HOH A:738 , MOA A:1332BINDING SITE FOR RESIDUE IMP A 1331
4AC4SOFTWARESER B:68 , MET B:70 , ARG B:322 , GLY B:328 , SER B:329 , CYS B:331 , ASP B:364 , GLY B:366 , MET B:385 , GLY B:387 , SER B:388 , TYR B:411 , GLY B:413 , MET B:414 , GLY B:415 , GLN B:441 , GLY B:442 , HOH B:708 , HOH B:710 , HOH B:714 , HOH B:794 , MOA B:1333BINDING SITE FOR RESIDUE IMP B 1332
5AC5SOFTWAREASP A:274 , SER A:275 , SER A:276 , ASN A:303 , GLY A:324 , MET A:325 , GLY A:326 , CYS A:331 , THR A:333 , MET A:414 , GLY A:415 , GLN A:441 , HOH A:658 , HOH A:773 , IMP A:1331BINDING SITE FOR RESIDUE MOA A 1332
6AC6SOFTWAREASP B:274 , SER B:275 , SER B:276 , ASN B:303 , GLY B:324 , MET B:325 , GLY B:326 , THR B:333 , GLY B:415 , GLN B:441 , HOH B:725 , HOH B:770 , IMP B:1332BINDING SITE FOR RESIDUE MOA B 1333

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JR1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1JR1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1JR1)

(-) PROSITE Motifs  (2, 5)

Asymmetric Unit (2, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CBSPS51371 CBS domain profile.IMDH2_CRIGR114-173
179-237
 
  3A:114-155
A:179-237
B:233-237
2IMP_DH_GMP_REDPS00487 IMP dehydrogenase / GMP reductase signature.IMDH2_CRIGR321-333
 
  2A:321-333
B:321-333
Biological Unit 1 (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CBSPS51371 CBS domain profile.IMDH2_CRIGR114-173
179-237
 
  8A:114-155
A:179-237
-
2IMP_DH_GMP_REDPS00487 IMP dehydrogenase / GMP reductase signature.IMDH2_CRIGR321-333
 
  4A:321-333
-
Biological Unit 2 (2, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CBSPS51371 CBS domain profile.IMDH2_CRIGR114-173
179-237
 
  4-
-
B:233-237
2IMP_DH_GMP_REDPS00487 IMP dehydrogenase / GMP reductase signature.IMDH2_CRIGR321-333
 
  4-
B:321-333

(-) Exons   (0, 0)

(no "Exon" information available for 1JR1)

(-) 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:436
 aligned with IMDH2_CRIGR | P12269 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:498
                                    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       436       446       456       466       476       486       496       506        
          IMDH2_CRIGR    17 GLTAQQLFNCGDGLTYNDFLILPGYIDFTADQVDLTSALTKKITLKTPLVSSPMDTVTEAGMAIAMALTGGIGFIHHNCTPEFQANEVRKVKKYEQGFITDPVVLSPKDRVRDVFEAKARHGFCGIPITDTGRMGSRLVGIISSRDIDFLKEEEHDRFLEEIMTKREDLVVAPAGITLKEANEILQRSKKGKLPIVNENDELVAIIARTDLKKNRDYPLASKDAKKQLLCGAAIGTHEDDKYRLDLLALAGVDVVVLDSSQGNSIFQINMIKYMKEKYPNLQVIGGNVVTAAQAKNLIDAGVDALRVGMGCGSICITQEVLACGRPQATAVYKVSEYARRFGVPVIADGGIQNVGHIAKALALGASTVMMGSLLAATTEAPGEYFFSDGIRLKKYRGMGSLDAMDKHLSSQNRYFSEADKIKVAQGVSGAVQDKGSIHKFVPYLIAGIQHSCQDIGAKSLTQVRAMMYSGELKFEKRTSSAQVEGGVHSLHSYEKRLF 514
               SCOP domains d1jr1a1 A:17-112,A:233-514 Inosine monophosphate dehydrogenase (IMPDH)                          d1jr1a4     A:11  3-23               2 Type                       II inosine monophosphate de   hydrogenase CBS domains d1jr1a1 A:17-112,A:233-514 Inosine monophosphate dehydrogenase (IMPDH)                                                                                                                                                                                                                     SCOP domains
               CATH domains 1jr1A00 A:17-514 Aldolase class I                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  CATH domains
           Pfam domains (1) --------------------------------------------------------------------------------------------------------    ----  ----               ------                      CBS-1jr1A01 A:178-232                                  --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------                ------------------------------------------------------------------------------ Pfam domains (1)
           Pfam domains (2) --------------------------------------------------------------------------------------------------------    ----  ----               ------                      CBS-1jr1A02 A:178-232                                  --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------                ------------------------------------------------------------------------------ Pfam domains (2)
         Sec.struct. author ..hhhhhh......hhh.eee.......hhhhh...ee.....ee...eee.......hhhhhhhhhhhh.eeee....hhhhhhhhhhhhhh....ee.....----....--....---------------......----------------------..........ee...hhhhhhhhh....---.eeee...eeeeeehhhhhhhhhhh.............eeee...hhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhh..eeee........hhhhhhh...hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh...eeee..............ee....eeeeee........----------------.......eeeee...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh...eee.hhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------CBS  PDB: A:114-155 UniProt: 114-173                        -----CBS  PDB: A:179-237 UniProt: 179-237                       -----------------------------------------------------------------------------------IMP_DH_GMP_RE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jr1 A  17 GLTAQQLFNCGDGLTYNDFLILPGYIDFTADQVDLTSALTKKITLKTPLVSSPMDTVTEAGMAIAMALTGGIGFIHHNCTPEFQANEVRKVKKYEQGFITDPVV----DRVR--FEAK---------------MGSRLV----------------------IMTKREDLVVAPAGITLKEANEILQRSK---LPIVNENDELVAIIARTDLKKNRDYPLASKDAKKQLLCGAAIGTHEDDKYRLDLLALAGVDVVVLDSSQGNSIFQINMIKYMKEKYPNLQVIGGNVVTAAQAKNLIDAGVDALRVGMGCGSICITQEVLACGRPQATAVYKVSEYARRFGVPVIADGGIQNVGHIAKALALGASTVMMGSLLAATTEAPGEYFFSDGIRLKKYRGMGSLDAM----------------IKVAQGVSGAVQDKGSIHKFVPYLIAGIQHSCQDIGAKSLTQVRAMMYSGELKFEKRTSSAQVEGGVHSLHSYEKRLF 514
                                    26        36        46        56        66        76        86        96       106       116   |   126 |  |  | -         -   |    |-         -         - |     186       196        |-  |    216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416   |     -         -|      446       456       466       476       486       496       506        
                                                                                                                                 120  125  |  |  |             150  155                    178                        205 209                                                                                                                                                                                                                420              437                                                                             
                                                                                                                                         128  |  |                                                                                                                                                                                                                                                                                                                                                                                            
                                                                                                                                            131  |                                                                                                                                                                                                                                                                                                                                                                                            
                                                                                                                                               134                                                                                                                                                                                                                                                                                                                                                                                            

Chain B from PDB  Type:PROTEIN  Length:368
 aligned with IMDH2_CRIGR | P12269 from UniProtKB/Swiss-Prot  Length:514

    Alignment length:504
                                    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       420       430       440       450       460       470       480       490       500       510    
          IMDH2_CRIGR    11 SYVPDDGLTAQQLFNCGDGLTYNDFLILPGYIDFTADQVDLTSALTKKITLKTPLVSSPMDTVTEAGMAIAMALTGGIGFIHHNCTPEFQANEVRKVKKYEQGFITDPVVLSPKDRVRDVFEAKARHGFCGIPITDTGRMGSRLVGIISSRDIDFLKEEEHDRFLEEIMTKREDLVVAPAGITLKEANEILQRSKKGKLPIVNENDELVAIIARTDLKKNRDYPLASKDAKKQLLCGAAIGTHEDDKYRLDLLALAGVDVVVLDSSQGNSIFQINMIKYMKEKYPNLQVIGGNVVTAAQAKNLIDAGVDALRVGMGCGSICITQEVLACGRPQATAVYKVSEYARRFGVPVIADGGIQNVGHIAKALALGASTVMMGSLLAATTEAPGEYFFSDGIRLKKYRGMGSLDAMDKHLSSQNRYFSEADKIKVAQGVSGAVQDKGSIHKFVPYLIAGIQHSCQDIGAKSLTQVRAMMYSGELKFEKRTSSAQVEGGVHSLHSYEKRLF 514
               SCOP domains d1jr1b1 B:11-112,B:233-514 Inosine monophosphate dehydrogenase (IMPDH)                                                                                                                                                        d1jr1b1 B:11-112,B:233-514 Inosine monophosphate dehydrogenase (IMPDH)                                                                                                                                                                                                                     SCOP domains
               CATH domains 1jr1B00 B:11-514 Aldolase class I                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        CATH domains
           Pfam domains (1) -----------------IMPDH-1jr1B01 B:28-504                                                                                                                                                                                                                                                                                                                                                                                                                                                                       ---------- Pfam domains (1)
           Pfam domains (2) -----------------IMPDH-1jr1B02 B:28-504                                                                                                                                                                                                                                                                                                                                                                                                                                                                       ---------- Pfam domains (2)
         Sec.struct. author ........hhhhhhh.....hhh.eee.......hhhhh...ee.....ee...eee.......hhhhhhhhhhhh.eeee....hhhhhhhhhhhhhh...------------------------------------------------------------------------------------------------------------------------..............eeee...hhhhhhhhhhhhhh..eeee......hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhh..eeee........hhhhhh....hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh..eeeehhhhhh.......eee....eeeeee........----------------.......eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhh....eee.hhhhhhhhh............ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------CBS  PDB: - UniProt: 114-173                                -----CBS  PDB: B:233-237 UniProt: 179-237                       -----------------------------------------------------------------------------------IMP_DH_GMP_RE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jr1 B  11 SYVPDDGLTAQQLFNCGDGLTYNDFLILPGYIDFTADQVDLTSALTKKITLKTPLVSSPMDTVTEAGMAIAMALTGGIGFIHHNCTPEFQANEVRKVKKYEQ------------------------------------------------------------------------------------------------------------------------YPLASKDAKKQLLCGAAIGTHEDDKYRLDLLALAGVDVVVLDSSQGNSIFQINMIKYMKEKYPNLQVIGGNVVTAAQAKNLIDAGVDALRVGMGCGSICITQEVLACGRPQATAVYKVSEYARRFGVPVIADGGIQNVGHIAKALALGASTVMMGSLLAATTEAPGEYFFSDGIRLKKYRGMGSLDAM----------------IKVAQGVSGAVQDKGSIHKFVPYLIAGIQHSCQDIGAKSLTQVRAMMYSGELKFEKRTSSAQVEGGVHSLHSYEKRLF 514
                                    20        30        40        50        60        70        80        90       100       110 |       -         -         -         -         -         -         -         -         -         -         -         -  |    240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420         -      |440       450       460       470       480       490       500       510    
                                                                                                                               112                                                                                                                      233                                                                                                                                                                                        420              437                                                                             

   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  (2, 3)

Asymmetric Unit

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (2, 4)

Asymmetric Unit

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (IMDH2_CRIGR | P12269)
molecular function
    GO:0003938    IMP dehydrogenase activity    Catalysis of the reaction: inosine 5'-phosphate + NAD+ + H2O = xanthosine 5'-phosphate + NADH + H+.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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.
biological process
    GO:0006177    GMP biosynthetic process    The chemical reactions and pathways resulting in the formation of GMP, guanosine monophosphate.
    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:0006164    purine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a purine nucleotide, a compound consisting of nucleoside (a purine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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(-) Related Entries Specified in the PDB File

1ak5 INOSINE MONOPHOSPHATE DEHYDROGENASE (IMPDH) FROM TRITRICHOMONAS FOETUS
1b3o TERNARY COMPLEX OF HUMAN TYPE-II INOSINE MONOPHOSPHATE DEHYDROGENASE WITH 6-CL-IMP AND SELENAZOLE ADENINE DINUCLEOTIDE
1zfj INOSINE MONOPHOSPHATE DEHYDROGENASE (IMPDH; EC 1.1.1.205) FROM STREPTOCOCCUS PYOGENES