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(-) Description

Title :  CRYSTAL STRUCTURE OF INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE FROM BACILLUS ANTHRACIS STR. AMES COMPLEXED WITH XMP
 
Authors :  Y. Kim, M. Makowska-Grzyska, J. Hasseman, W. F. Anderson, A. Joachimia
Date :  13 Sep 11  (Deposition) - 05 Oct 11  (Release) - 10 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  B  (4x)
Keywords :  Tim Barrel, Cbs Domain, Cytosol, Oxidoreductase, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Makowska-Grzyska, Y. Kim, R. Wu, R. Wilton, D. R. Gollapalli, X. K. Wang, R. Zhang, R. Jedrzejczak, J. C. Mack, N. Maltseva, R. Mulligan, T. A. Binkowski, P. Gornicki, M. L. Kuhn, W. F. Anderson, L. Hedstrom, A. Joachimiak
Bacillus Anthracis Inosine 5'-Monophosphate Dehydrogenase I Action: The First Bacterial Series Of Structures Of Phosphate Ion-, Substrate-, And Product-Bound Complexes.
Biochemistry V. 51 6148 2012
PubMed-ID: 22788966  |  Reference-DOI: 10.1021/BI300511W

(-) Compounds

Molecule 1 - INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
    Chains: A, B
    EC Number: 1.1.1.205
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCG7
    Expression System Strain: BL21 MAGIC
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: IMPDH
    Gene: GUAB, BAS0011, BA_0008, GBAA_0008
    Mutation: YES
    Organism Common: ANTHRAX,ANTHRAX BACTERIUM
    Organism Scientific: BACILLUS ANTHRACIS
    Organism Taxid: 198094
    Strain: AMES

 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, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1SO41Ligand/IonSULFATE ION
2TAR1Ligand/IonD(-)-TARTARIC ACID
3XMP2Ligand/IonXANTHOSINE-5'-MONOPHOSPHATE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1SO4-1Ligand/IonSULFATE ION
2TAR-1Ligand/IonD(-)-TARTARIC ACID
3XMP4Ligand/IonXANTHOSINE-5'-MONOPHOSPHATE
Biological Unit 2 (3, 12)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
2TAR4Ligand/IonD(-)-TARTARIC ACID
3XMP4Ligand/IonXANTHOSINE-5'-MONOPHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:49 , MET A:51 , GLY A:305 , SER A:306 , ILE A:307 , CYS A:308 , THR A:310 , ASP A:341 , GLY A:342 , GLY A:343 , GLY A:364 , SER A:365 , TYR A:388 , GLY A:390 , HOH A:501BINDING SITE FOR RESIDUE XMP A 500
2AC2SOFTWAREALA B:49 , MET B:51 , GLY B:305 , SER B:306 , CYS B:308 , THR B:310 , ASP B:341 , GLY B:342 , GLY B:343 , GLY B:364 , SER B:365 , TYR B:388 , GLY B:390 , MET B:391 , HOH B:505 , HOH B:514 , HOH B:527 , HOH B:529BINDING SITE FOR RESIDUE XMP B 500
3AC3SOFTWAREILE B:137 , THR B:139 , ASP B:142 , THR B:158 , ILE B:183 , SO4 B:502BINDING SITE FOR RESIDUE TAR B 501
4AC4SOFTWARETHR B:139 , ARG B:141 , TAR B:501 , HOH B:536BINDING SITE FOR RESIDUE SO4 B 502

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TSD)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:279 -Asn A:280
2Gly B:279 -Asn B:280

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TSD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TSD)

(-) Exons   (0, 0)

(no "Exon" information available for 3TSD)

(-) 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:442
 aligned with Q81W29_BACAN | Q81W29 from UniProtKB/TrEMBL  Length:487

    Alignment length:477
                                1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                        
                                |    6        16        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       
         Q81W29_BACAN     - ----MWESKFVKEGLTFDDVLLVPAKSDVLPREVSVKTVLSESLQLNIPLISAGMDTVTEADMAIAMARQGGLGIIHKNMSIEQQAEQVDKVKRSESGVISDPFFLTPEHQVYDAEHLMGKYRISGVPVVNNLDERKLVGIITNRDMRFIQDYSIKISDVMTKEQLITAPVGTTLSEAEKILQKYKIEKLPLVDNNGVLQGLITIKDIEKVIEFPNSAKDKQGRLLVGAAVGVTADAMTRIDALVKASVDAIVLDTAHGHSQGVIDKVKEVRAKYPSLNIIAGNVATAEATKALIEAGANVVKVGIGPGSICTTRVVAGVGVPQLTAVYDCATEARKHGIPVIADGGIKYSGDMVKALAAGAHVVMLGSMFAGVAESPGETEIYQGRQFKVYRGMGSVGAMEKGSKDRYFQEGNKKLVPEGIEGRVPYKGPLADTVHQLVGGLRAGMGYCGAQDLEFLRENAQFIRMSGAGLLESHP 473
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhh.......hhh.eee...............eeee..eee...eee.......hhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh...............hhhhhhhhhhhhh..eeeee.......eeeeeehhhhh.............-......ee...hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhh.............eeee....hhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhh...eeee........hhhhhhh...hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh...eeeehhhhh........------........----------------------------........hhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.eee.hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tsd A  -3 QSNAMWESKFVKEGLTFDDVLLVPAKSDVLPREVSVKTVLSESLQLNIPLISAGMDTVTEADMAIAMARQGGLGIIHKNMSIEQQAEQVDKVKRSESGVISDPFFLTPEHQVYDAEHLMGKYRISGVPVVNNLDERKLVGIITNRDMRFIQDYSIKISDVM-KEQLITAPVGTTLSEAEKILQKYKIEKLPLVDNNGVLQGLITIKDIEKVIEFPNSAKDKQGRLLVGAAVGVTADAMTRIDALVKASVDAIVLDTAHGHSQGVIDKVKEVRAKYPSLNIIAGNVATAEATKALIEAGANVVKVGIGPGSICTTRVVAGVGVPQLTAVYDCATEARKHGIPVIADGGIKYSGDMVKALAAGAHVVMLGSMFAGVAESPGE------RQFKVYRG----------------------------EGRVPYKGPLADTVHQLVGGLRAGMGYCGAQDLEFLRENAQFIRMSGAGLLESHP 473
                                     6        16        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   |     -         -         -  |    426       436       446       456       466       
                                                                                                                                                                                          157 |                                                                                                                                                                                                                      376    383    390                          419                                                      
                                                                                                                                                                                            159                                                                                                                                                                                                                                                                                                                          


Chain B from PDB  Type:PROTEIN  Length:426
 aligned with Q81W29_BACAN | Q81W29 from UniProtKB/TrEMBL  Length:487

    Alignment length:482
                                      1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
                                     -|       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       420       430       440       450       460       470  
         Q81W29_BACAN     - ----------MWESKFVKEGLTFDDVLLVPAKSDVLPREVSVKTVLSESLQLNIPLISAGMDTVTEADMAIAMARQGGLGIIHKNMSIEQQAEQVDKVKRSESGVISDPFFLTPEHQVYDAEHLMGKYRISGVPVVNNLDERKLVGIITNRDMRFIQDYSIKISDVMTKEQLITAPVGTTLSEAEKILQKYKIEKLPLVDNNGVLQGLITIKDIEKVIEFPNSAKDKQGRLLVGAAVGVTADAMTRIDALVKASVDAIVLDTAHGHSQGVIDKVKEVRAKYPSLNIIAGNVATAEATKALIEAGANVVKVGIGPGSICTTRVVAGVGVPQLTAVYDCATEARKHGIPVIADGGIKYSGDMVKALAAGAHVVMLGSMFAGVAESPGETEIYQGRQFKVYRGMGSVGAMEKGSKDRYFQEGNKKLVPEGIEGRVPYKGPLADTVHQLVGGLRAGMGYCGAQDLEFLRENAQFIRMSGAGLLESH 472
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh..hhhhhh.......hhh.eee...............eeee..eee...eee.......hhhhhhhhhhh..eeee....hhhhhhhhhhhhhh...---------.....-----.hhhhhh..ee...-----....-.ee.hhhh..---..hhhhhh...--..ee...hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhh.............eeee....hhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhh..eeee........hhhhhh....hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh...eeee.............-----...eeeee..--------------------------.eeeee...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.eee.hhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tsd B  -9 TENLYFQSNAMWESKFVKEGLTFDDVLLVPAKSDVLPREVSVKTVLSESLQLNIPLISAGMDTVTEADMAIAMARQGGLGIIHKNMSIEQQAEQVDKVKRSES---------TPEHQ-----HLMGKYRISGVPVV-----RKLV-IITNRDMRFI---SIKISDVMTKE--ITAPVGTTLSEAEKILQKYKIEKLPLVDNNGVLQGLITIKDIEKVIEFPNSAKDKQGRLLVGAAVGVTADAMTRIDALVKASVDAIVLDTAHGHSQGVIDKVKEVRAKYPSLNIIAGNVATAEATKALIEAGANVVKVGIGPGSICTTRVVAGVGVPQLTAVYDCATEARKHGIPVIADGGIKYSGDMVKALAAGAHVVMLGSMFAGVAESPGE-----GRQFKVYRGM--------------------------IEGRVPYKGPLADTVHQLVGGLRAGMGYCGAQDLEFLRENAQFIRMSGAGLLESH 472
                                     0        10        20        30        40        50        60        70        80        90  |      -  |   |  -  |    120     |   - |  | |140     | 150       160  |    170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370     |   - |     390|        -         -       420       430       440       450       460       470  
                                                                                                                                 93       103 107   113          126   132  | |      146 150       160  |                                                                                                                                                                                                                  376   382      391                        418                                                      
                                                                                                                                                                          135 |                       163                                                                                                                                                                                                                                                                                                                     
                                                                                                                                                                            137
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3TSD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TSD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TSD)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q81W29_BACAN | Q81W29)
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.

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  3tsd
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 Related Entries

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

UniProtKB/TrEMBL
        Q81W29_BACAN | Q81W29: 3tsb 3usb 4mjm 4my1 4my8 4my9 4mya 4myx 4qm1 5urr 5urs 5uuv 5uuw 5uuz

(-) Related Entries Specified in the PDB File

3tsb THE SAME PROTEIN APO-FORM RELATED ID: IDP01178 RELATED DB: TARGETDB