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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF THE INOSINE MONOPHOSPHATE DEHYDROGENASE FROM MYCOBACTERIUM TUBERCULOSIS
 
Authors :  Y. Kim, M. Makowska-Grzyska, M. Gu, M. Kavitha, L. Hedstrom, W. F. Ander A. Joachimiak, Center For Structural Genomics Of Infectious D (Csgid)
Date :  11 May 15  (Deposition) - 17 Jun 15  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.69
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Impdh, Delta Cbs, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Makowska-Grzyska, Y. Kim, S. K. Gorla, Y. Wei, K. Mandapati, M. Zhang, N. Maltseva, G. Modi, H. I. Boshoff, M. Gu, C. Aldrich, G. D. Cuny, L. Hedstrom, A. Joachimiak
Mycobacterium Tuberculosis Impdh In Complexes With Substrates, Products And Antitubercular Compounds.
Plos One V. 10 38976 2015
PubMed-ID: 26440283  |  Reference-DOI: 10.1371/JOURNAL.PONE.0138976

(-) Compounds

Molecule 1 - INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE,INOSINE-5'- MONOPHOSPHATE DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.1.1.205, 1.1.1.205
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3) GOLD
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-125 AND 253-529 LINKED BY LINKER (GLY GLY)
    Gene: GUAB, GUAB2, RV3411C, MTCY78.17
    Organism Scientific: MYCOBACTERIUM TUBERCULOSIS (STRAIN ATCC 25618 / H37RV)
    Organism Taxid: 83332
    Strain: ATCC 25618 / H37RV
    Synonym: IMPDH

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 34)

Asymmetric/Biological Unit (4, 34)
No.NameCountTypeFull Name
1GOL11Ligand/IonGLYCEROL
2K4Ligand/IonPOTASSIUM ION
3PGO15Ligand/IonS-1,2-PROPANEDIOL
4PO44Ligand/IonPHOSPHATE ION

(-) Sites  (34, 34)

Asymmetric Unit (34, 34)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:338 , SER A:339 , GLY A:376 , GLY A:397 , SER A:398 , TYR A:421 , HOH A:720 , HOH A:722 , HOH A:741 , HOH A:758binding site for residue PO4 A 601
02AC2SOFTWAREPRO A:61 , ALA A:483 , GLY A:486 , TYR A:487 , GLU D:458 , PGO D:604binding site for residue PGO A 602
03AC3SOFTWAREALA A:285 , HIS A:286 , ASN A:289 , ASP A:453 , HOH A:753 , HOH A:827 , PGO C:603binding site for residue PGO A 603
04AC4SOFTWAREARG A:482 , PGO A:605 , MET C:271 , ASP C:274binding site for residue PGO A 604
05AC5SOFTWARETHR A:63 , ALA A:64 , ARG A:482 , PGO A:604 , HOH A:764 , TRP C:266binding site for residue PGO A 605
06AC6SOFTWAREGLN A:378 , LEU A:399 , GLN A:476 , TYR A:527 , HOH A:808binding site for residue GOL A 606
07AC7SOFTWAREASP A:48 , ASP A:49 , ILE A:504 , THR A:505 , PRO A:506 , LEU A:509 , THR C:505 , PRO C:506 , ALA C:507binding site for residue GOL A 607
08AC8SOFTWAREASP A:48 , GLN A:378 , TYR A:379 , ASP A:382 , HOH A:771 , LYS C:510 , HIS C:515 , ASP C:516binding site for residue GOL A 608
09AC9SOFTWAREGLU A:511 , SER A:512 , HIS A:513 , GLY D:336 , GLY D:338 , CYS D:341binding site for residue K A 609
10AD1SOFTWAREPRO A:506 , HOH A:703 , PRO B:506 , PRO C:506 , PRO D:506 , PGO D:601binding site for residue GOL A 610
11AD2SOFTWAREGLY A:336 , GLY A:338 , CYS A:341 , GLU C:511 , SER C:512 , HIS C:513binding site for residue K A 611
12AD3SOFTWAREGLY B:338 , SER B:339 , GLY B:375 , GLY B:376 , GLY B:397 , SER B:398 , TYR B:421 , HOH B:728 , HOH B:733 , HOH B:738 , HOH B:771binding site for residue PO4 B 601
13AD4SOFTWAREPRO B:61 , ALA B:483 , GLY B:486 , TYR B:487 , GLU C:458 , GOL C:604 , HOH C:739binding site for residue PGO B 602
14AD5SOFTWAREALA B:285 , HIS B:286 , ASN B:289 , HOH B:735binding site for residue PGO B 603
15AD6SOFTWAREGLN B:378 , TYR B:379 , LEU B:399 , TYR B:527 , HOH B:709 , HOH B:838binding site for residue GOL B 604
16AD7SOFTWAREGLU B:511 , SER B:512 , HIS B:513 , GLY C:336 , GLY C:338 , CYS C:341binding site for residue K B 605
17AD8SOFTWAREGLU B:458 , PRO D:61 , ALA D:483 , GLY D:486 , TYR D:487binding site for residue PGO B 606
18AD9SOFTWAREASP B:49 , THR B:505 , PRO B:506 , HOH B:874 , THR D:505 , PRO D:506 , ALA D:507binding site for residue PGO B 607
19AE1SOFTWAREASP B:48 , GLN B:378 , TYR B:379 , ASP B:382 , HOH B:820 , LYS D:510 , HIS D:515 , ASP D:516binding site for residue GOL B 608
20AE2SOFTWAREGLY B:336 , GLY B:338 , CYS B:341 , GLU D:511 , SER D:512 , HIS D:513binding site for residue K B 609
21AE3SOFTWARETHR B:505 , PRO B:506 , ALA B:507 , ASP C:48 , ASP C:49 , PRO C:506 , HOH C:822binding site for residue PGO C 601
22AE4SOFTWAREGLY C:338 , SER C:339 , GLY C:376 , GLY C:397 , SER C:398 , TYR C:421 , HOH C:735 , HOH C:737 , HOH C:738 , HOH C:764binding site for residue PO4 C 602
23AE5SOFTWAREGLU A:458 , PGO A:603 , HOH A:717 , ALA C:483 , GLY C:486 , TYR C:487binding site for residue PGO C 603
24AE6SOFTWAREPGO B:602 , ALA C:285 , HIS C:286 , ASN C:289 , HOH C:741 , HOH C:814binding site for residue GOL C 604
25AE7SOFTWAREASP C:65 , SER C:67 , ARG C:75 , HOH C:729binding site for residue GOL C 605
26AE8SOFTWARELYS B:510 , HIS B:515 , ASP B:516 , ASP C:48 , GLN C:378 , TYR C:379 , ASP C:382 , HOH C:794binding site for residue GOL C 606
27AE9SOFTWAREGLN C:378 , TYR C:379 , LEU C:399 , TYR C:527 , HOH C:702 , HOH C:833binding site for residue PGO C 607
28AF1SOFTWARETHR A:505 , PRO A:506 , ALA A:507 , GOL A:610 , ASP D:48 , ASP D:49 , THR D:505 , PRO D:506 , LEU D:509 , HOH D:710binding site for residue PGO D 601
29AF2SOFTWARELYS A:510 , HIS A:515 , ASP A:516 , ASP D:48 , GLN D:378 , TYR D:379 , ASP D:382 , HOH D:826binding site for residue GOL D 602
30AF3SOFTWAREGLY D:338 , SER D:339 , GLY D:375 , GLY D:376 , GLY D:397 , SER D:398 , TYR D:421 , HOH D:718 , HOH D:723 , HOH D:734 , HOH D:774binding site for residue PO4 D 603
31AF4SOFTWAREPGO A:602 , HOH A:802 , ALA D:285 , HIS D:286 , ASN D:289 , ASP D:453 , HOH D:827binding site for residue PGO D 604
32AF5SOFTWAREMET A:271 , ASP A:274 , PGO D:606binding site for residue PGO D 605
33AF6SOFTWARETRP A:266 , THR D:63 , ALA D:64 , ARG D:482 , PGO D:605 , HOH D:837binding site for residue PGO D 606
34AF7SOFTWAREGLN D:378 , TYR D:379 , LEU D:399 , TYR D:527 , HOH D:703 , HOH D:745binding site for residue GOL D 607

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ZQR)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:312 -Asn A:313
2Gly B:312 -Asn B:313
3Gly C:312 -Asn C:313
4Gly D:312 -Asn D:313

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ZQR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZQR)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZQR)

(-) Sequences/Alignments

Asymmetric/Biological 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:357
                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.hhh.eee.......hhhhh...ee.....ee...eee.......hhhhhhhhhhh..eeee....hhhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhh..eeee........hhhhhh....hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh...eeeehhhhhh.......eeee..eeeeeee...hhhhhh.........eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhh...eeeehhhhhhhhh....eeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zqr A  27 TDPVPTGGDDPHKVAMLGLTFDDVLLLPAASDVVPATADTSSQLTKKIRLKVPLVSSAMDTVTESRMAIAMARAGGMGVLHRNLPVAEQAGQVEMVKRSGGLLVGAAVGVGGDAWVRAMMLVDAGVDVLVVDTAHAHNRLVLDMVGKLKSEVGDRVEVVGGNVATRSAAAALVDAGADAVKVGVGPGSICTTRVVAGVGAPQITAILEAVAACRPAGVPVIADGGLQYSGDIAKALAAGASTAMLGSLLAGTAEAPGELIFVNGKQYKSYRGMGSLGAMREDKLVPEGIEGRVPFRGPLSSVIHQLTGGLRAAMGYTGSPTIEVLQQAQFVRITPAGLKESHPHDVAMTVEAPNYYA 528
                                    36        46        56        66        76        86        96       106       116       126||     261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431|      461       471       481       491       501       511       521       
                                                                                                                              127|                                                                                                                                                                               431|                                                                            
                                                                                                                               253                                                                                                                                                                                452                                                                            


Chain B from PDB  Type:PROTEIN  Length:357
                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.hhh.eee.......hhhhh...ee.....ee...eee.......hhhhhhhhhhh..eeee....hhhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhh..eeee........hhhhhh....hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh...eeeehhhhhh.......eeee..eeeeeee...hhhhhh.........eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhh...eeeehhhhhhhhh....eeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zqr B  27 TDPVPTGGDDPHKVAMLGLTFDDVLLLPAASDVVPATADTSSQLTKKIRLKVPLVSSAMDTVTESRMAIAMARAGGMGVLHRNLPVAEQAGQVEMVKRSGGLLVGAAVGVGGDAWVRAMMLVDAGVDVLVVDTAHAHNRLVLDMVGKLKSEVGDRVEVVGGNVATRSAAAALVDAGADAVKVGVGPGSICTTRVVAGVGAPQITAILEAVAACRPAGVPVIADGGLQYSGDIAKALAAGASTAMLGSLLAGTAEAPGELIFVNGKQYKSYRGMGSLGAMREDKLVPEGIEGRVPFRGPLSSVIHQLTGGLRAAMGYTGSPTIEVLQQAQFVRITPAGLKESHPHDVAMTVEAPNYYA 528
                                    36        46        56        66        76        86        96       106       116       126||     261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431|      461       471       481       491       501       511       521       
                                                                                                                              127|                                                                                                                                                                               431|                                                                            
                                                                                                                               253                                                                                                                                                                                452                                                                            


Chain C from PDB  Type:PROTEIN  Length:358
                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeee.hhh.eee...............ee.....ee...eee.......hhhhhhhhhhh..eeee....hhhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhh..eeee........hhhhhh....hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh...eeeehhhhhh........eee..eeeeeee...hhhhhh.........eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhh...eeeehhhhhhhhh....eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zqr C  26 TTDPVPTGGDDPHKVAMLGLTFDDVLLLPAASDVVPATADTSSQLTKKIRLKVPLVSSAMDTVTESRMAIAMARAGGMGVLHRNLPVAEQAGQVEMVKRSGGLLVGAAVGVGGDAWVRAMMLVDAGVDVLVVDTAHAHNRLVLDMVGKLKSEVGDRVEVVGGNVATRSAAAALVDAGADAVKVGVGPGSICTTRVVAGVGAPQITAILEAVAACRPAGVPVIADGGLQYSGDIAKALAAGASTAMLGSLLAGTAEAPGELIFVNGKQYKSYRGMGSLGAMREDKLVPEGIEGRVPFRGPLSSVIHQLTGGLRAAMGYTGSPTIEVLQQAQFVRITPAGLKESHPHDVAMTVEAPNYYA 528
                                    35        45        55        65        75        85        95       105       115       125 ||    260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430||     460       470       480       490       500       510       520        
                                                                                                                               127|                                                                                                                                                                               431|                                                                            
                                                                                                                                253                                                                                                                                                                                452                                                                            


Chain D from PDB  Type:PROTEIN  Length:357
                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeee.hhh.eee.......hhhhh...ee.....ee...eee.......hhhhhhhhhhh..eeee....hhhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhh..eeee........hhhhhh....hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh...eeeehhhhhh........eee..eeeeeee...hhhhhh.........eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhh...eeeehhhhhhhhh....eeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zqr D  27 TDPVPTGGDDPHKVAMLGLTFDDVLLLPAASDVVPATADTSSQLTKKIRLKVPLVSSAMDTVTESRMAIAMARAGGMGVLHRNLPVAEQAGQVEMVKRSGGLLVGAAVGVGGDAWVRAMMLVDAGVDVLVVDTAHAHNRLVLDMVGKLKSEVGDRVEVVGGNVATRSAAAALVDAGADAVKVGVGPGSICTTRVVAGVGAPQITAILEAVAACRPAGVPVIADGGLQYSGDIAKALAAGASTAMLGSLLAGTAEAPGELIFVNGKQYKSYRGMGSLGAMREDKLVPEGIEGRVPFRGPLSSVIHQLTGGLRAAMGYTGSPTIEVLQQAQFVRITPAGLKESHPHDVAMTVEAPNYYA 528
                                    36        46        56        66        76        86        96       106       116       126||     261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431|      461       471       481       491       501       511       521       
                                                                                                                              127|                                                                                                                                                                               431|                                                                            
                                                                                                                               253                                                                                                                                                                                452
   Legend:   → Mismatch (orange background)
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    → 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 4ZQR)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZQR)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZQR)

(-) Gene Ontology  (13, 13)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:312 - Asn A:313   [ RasMol ]  
    Gly B:312 - Asn B:313   [ RasMol ]  
    Gly C:312 - Asn C:313   [ RasMol ]  
    Gly D:312 - Asn D:313   [ RasMol ]  
 

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  4zqr
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 Related Entries

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

UniProtKB/Swiss-Prot
        IMDH_MYCTU | P9WKI7: 4zqm 4zqn 4zqo 4zqp 5upu 5upv

(-) Related Entries Specified in the PDB File

4zqm THE SAME PROTEIN IN THE COMPLEX WITH XMP AND NAD
4zqn THE SAME PROTEIN IN THE COMPLEX WITH IMP AND P41
4zqo THE SAME PROTEIN IN THE COMPLEX WITH IMP AND Q67
4zqp THE SAME PROTEIN IN THE COMPLEX WITH IMP AND MAD1 RELATED ID: CSGID-IDP91646 RELATED DB: TARGETTRACK