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(-) Description

Title :  CRYSTAL STRUCTURE OF THE INOSINE 5'-MONOPHOSPHATE DEHYDROGENASE WITH AN INTERNAL DELETION OF THE CBS DOMAIN FROM BACILLUS ANTHRACIS STR. AMES COMPLEXED WITH INHIBITOR D67
 
Authors :  Y. Kim, M. Makowska-Grzyska, M. Gu, K. Mandapati, D. Gollapalli, S. K. G M. Zhang, L. Hedstrom, W. F. Anderson, A. Joachimiak, Csgid, Center F Structural Genomics Of Infectious Diseases (Csgid)
Date :  14 Jun 14  (Deposition) - 23 Jul 14  (Release) - 08 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Niaid, National Institute Of Allergy And Infectious Diseases, Center For Structural Genomics Of Infectious Diseases, Csgid, Tim Barrel, Alpha-Beta Structure, Oxidoreductase- Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, M. Makowska-Grzyska, M. Gu, K. Mandapati, D. Gollapalli, S. K. Gorla, M. Zhang, L. Hedstrom, W. F. Anderson, A. Joachimiak, Csgi
Crystal Structure Of The Inosine 5'-Monophosphate Dehydrogenase With An Internal Deletion Of The Cbs Domain From Bacillus Anthracis Str. Ames Complexed With Inhibitor D67
To Be Published 2014
PubMed: search

(-) Compounds

Molecule 1 - INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.1.1.205
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21 DE3 GOLD
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: IMPDH-DELTA-L-CBS
    Gene: GUAB, BA_0008, BAS0011, GBAA_0008
    Mutation: YES
    Organism Common: ANTHRAX,ANTHRAX BACTERIUM
    Organism Scientific: BACILLUS ANTHRACIS
    Organism Taxid: 1392
    Strain: AMES
    Synonym: IMP DEHYDROGENASE, IMPD, IMPDH

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
139H4Ligand/Ion2-(3-METHYL-4-OXO-3,4-DIHYDROPHTHALAZIN-1-YL)-N-(6,7,8,9-TETRAHYDRODIBENZO[B,D]FURAN-2-YL)ACETAMIDE
2IMP4Ligand/IonINOSINIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:306 , ILE A:307 , CYS A:308 , ASP A:341 , GLY A:342 , GLY A:343 , GLY A:364 , SER A:365 , TYR A:388 , GLY A:390 , MET A:391 , GLY A:392 , GLU A:416 , GLY A:417 , 39H C:501BINDING SITE FOR RESIDUE IMP A 500
2AC2SOFTWARESER A:23 , PRO A:27 , ALA A:441 , GLY A:444 , TYR A:445 , MET B:391 , MET B:397 , GLU B:416 , IMP B:500BINDING SITE FOR RESIDUE 39H A 501
3AC3SOFTWARE39H A:501 , ALA B:49 , MET B:51 , GLY B:305 , SER B:306 , ILE B:307 , CYS B:308 , ASP B:341 , GLY B:342 , GLY B:343 , GLY B:364 , SER B:365 , TYR B:388 , GLY B:390 , MET B:391 , GLY B:392 , GLU B:416 , GLY B:417 , HOH B:603BINDING SITE FOR RESIDUE IMP B 500
4AC4SOFTWARESER B:23 , VAL B:25 , LEU B:26 , GLY B:444 , TYR B:445 , ALA D:253 , MET D:391 , GLU D:416 , IMP D:500BINDING SITE FOR RESIDUE 39H B 501
5AC5SOFTWAREALA A:253 , SER A:257 , MET A:397 , GLU A:416 , IMP A:500 , SER C:23 , VAL C:25 , LEU C:26 , ALA C:441 , GLY C:444BINDING SITE FOR RESIDUE 39H C 501
6AC6SOFTWAREALA C:49 , MET C:51 , SER C:306 , ILE C:307 , CYS C:308 , ASP C:341 , GLY C:342 , GLY C:343 , GLY C:364 , SER C:365 , TYR C:388 , GLY C:390 , MET C:391 , GLY C:392 , GLU C:416 , GLY C:417 , 39H C:503BINDING SITE FOR RESIDUE IMP C 502
7AC7SOFTWAREALA C:253 , HIS C:254 , MET C:391 , GLU C:416 , IMP C:502 , SER D:23 , ALA D:441 , GLY D:444 , TYR D:445BINDING SITE FOR RESIDUE 39H C 503
8AC8SOFTWARE39H B:501 , MET D:51 , GLY D:305 , SER D:306 , ILE D:307 , CYS D:308 , ASP D:341 , GLY D:342 , GLY D:343 , GLY D:364 , SER D:365 , TYR D:388 , GLY D:390 , MET D:391 , GLY D:392 , GLU D:416 , GLY D:417BINDING SITE FOR RESIDUE IMP D 500

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QM1)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:279 -Asn A:280
2Gly B:279 -Asn B:280
3Gly C:279 -Asn C:280
4Gly D:279 -Asn D:280

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QM1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QM1)

(-) Exons   (0, 0)

(no "Exon" information available for 4QM1)

(-) 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:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh......hhh.eee.......hhhhh...ee.....ee...eee.......hhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhh..eeee........hhhhhh....hhhhhhhhhhhhhhh....eeee....hhhhhhhhhh....eeeehhhhhh........eee..eeeeeee...hhhhhhh.....eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.eee.hhhhhh.ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qm1 A  -4 FQSNAMWESKFVKEGLTFDDVLLVPAKSDVLPREVSVKTVLSESLQLNIPLISAGMDTVTEADMAIAMARQGGLGIIHKNMSIEQQAEQVDKVKRSGGLLVGAAVGVTADAMTRIDALVKASVDAIVLDTAHGHSQGVIDKVKEVRAKYPSLNIIAGNVATAEATKALIEAGANVVKVGIGPGSICTTRVVAGVGVPQLTAVYDCATEARKHGIPVIADGGIKYSGDMVKALAAGAHVVMLGSMFAGVAESPGETEIYQGRQFKVYRGMGSVGAMEKVPEGIEGRVPYKGPLADTVHQLVGGLRAGMGYCGAQDLEFLRENAQFIRMSGAGLLVQIT 479
                                     5        15        25        35        45        55        65        75        85      |222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392      |416       426       436       446       456       466  ||   
                                                                                                                           92|                                                                                                                                                                                399|                                                    469|   
                                                                                                                           220                                                                                                                                                                                 414                                                     476   


Chain B from PDB  Type:PROTEIN  Length:345
                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.....ee..hhh.eee.......hhhhh...ee.....ee...eee.......hhhhhhhhhhh..eeee....hhhhhhhhhhhhhh.....eeeeee...hhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhh....eeee........hhhhhh....hhhhhhhhhhhhhhh....eeee.....hhhhhhhhh....eeee..............eee..eeeeeee...hhhhhh........eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.eee..hhhhh..ee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qm1 B  -2 SNAMWESKFVKEGLTFDDVLLVPAKSDVLPREVSVKTVLSESLQLNIPLISAGMDTVTEADMAIAMARQGGLGIIHKNMSIEQQAEQVDKVKRSGGLLVGAAVGVTADAMTRIDALVKASVDAIVLDTAHGHSQGVIDKVKEVRAKYPSLNIIAGNVATAEATKALIEAGANVVKVGIGPGSICTTRVVAGVGVPQLTAVYDCATEARKHGIPVIADGGIKYSGDMVKALAAGAHVVMLGSMFAGVAESPGETEIYQGRQFKVYRGMGSVGAMEKKLVPEGIEGRVPYKGPLADTVHQLVGGLRAGMGYCGAQDLEFLRENAQFIRMSGAGLLHVQITKEAPNYS 486
                                     7        17        27        37        47        57        67        77        87    || 224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394    || 416       426       436       446       456       466  ||   481     
                                                                                                                         92|                                                                                                                                                                                399|                                                      469|           
                                                                                                                         220                                                                                                                                                                                 412                                                       475           


Chain C from PDB  Type:PROTEIN  Length:332
                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...ee..hhh.eee.......hhhhh...ee.....ee...eee.......hhhhhhhhhhh..eeee....hhhhhhhhhhhhhh.....eeeee....hhhhhhhhhhhh...eeee......hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhh....eeee........hhhhhh....hhhhhhhhhhhhhh.....eeee....hhhhhhhhhhh...eeeehhhhhh........eee..eeeeeee.............eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.eee.hhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qm1 C  -2 SNAMWESKFVKEGLTFDDVLLVPAKSDVLPREVSVKTVLSESLQLNIPLISAGMDTVTEADMAIAMARQGGLGIIHKNMSIEQQAEQVDKVKRSGGLLVGAAVGVTADAMTRIDALVKASVDAIVLDTAHGHSQGVIDKVKEVRAKYPSLNIIAGNVATAEATKALIEAGANVVKVGIGPGSICTTRVVAGVGVPQLTAVYDCATEARKHGIPVIADGGIKYSGDMVKALAAGAHVVMLGSMFAGVAESPGETEIYQGRQFKVYRGMGSVGAMVPEGIEGRVPYKGPLADTVHQLVGGLRAGMGYCGAQDLEFLRENAQFIRMSGAGLLVQI 478
                                     7        17        27        37        47        57        67        77        87    || 224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394  ||   420       430       440       450       460       476  
                                                                                                                         92|                                                                                                                                                                              397|                                                    469|  
                                                                                                                         220                                                                                                                                                                               414                                                     476  


Chain D from PDB  Type:PROTEIN  Length:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhh......hhh.eee.......hhhhh...ee.....ee...eee.......hhhhhhhhhh...eeee....hhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhh....eeee........hhhhhh....hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh...eeeehhhhhh........eee..eeeeeee...hhhhhh......eeeee...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.eee.hhhhhh...ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qm1 D  -1 NAMWESKFVKEGLTFDDVLLVPAKSDVLPREVSVKTVLSESLQLNIPLISAGMDTVTEADMAIAMARQGGLGIIHKNMSIEQQAEQVDKVKRSGGLLVGAAVGVTADAMTRIDALVKASVDAIVLDTAHGHSQGVIDKVKEVRAKYPSLNIIAGNVATAEATKALIEAGANVVKVGIGPGSICTTRVVAGVGVPQLTAVYDCATEARKHGIPVIADGGIKYSGDMVKALAAGAHVVMLGSMFAGVAESPGETEIYQGRQFKVYRGMGSVGAMELVPEGIEGRVPYKGPLADTVHQLVGGLRAGMGYCGAQDLEFLRENAQFIRMSGAGLLESVQIT 479
                                     8        18        28        38        48        58        68        78        88   ||  225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395  ||   419       429       439       449       459       469 ||   
                                                                                                                        92|                                                                                                                                                                               398|                                                       471|   
                                                                                                                        220                                                                                                                                                                                413                                                        476
   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 4QM1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QM1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QM1)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:279 - Asn A:280   [ RasMol ]  
    Gly B:279 - Asn B:280   [ RasMol ]  
    Gly C:279 - Asn C:280   [ RasMol ]  
    Gly D:279 - Asn D:280   [ RasMol ]  
 

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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

3tsb WILD-TYPE, PHOSPHATE BOUND FORM
3tsd WILD-TYPE, COMPLEXED WITH PRODUCT, XMP
3usb WILD-TYPE, SUBSTRATE IMP BOUND-FORM
4mjm SHORT INTERNAL DELETION OF CBS DOMAIN (95-200) AND GLY IS INSERTED AT 95. RELATED ID: CSGID-IDP01178 RELATED DB: TARGETTRACK