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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 Q21
 
Authors :  Y. Kim, M. Makowska-Grzyska, M. Gu, S. K. Gorla, M. Kavitha, G. Cuny, L. H W. F. Anderson, A. Joachimiak, Csgid, Center For Structural Genom Infectious Diseases (Csgid)
Date :  27 Sep 13  (Deposition) - 13 Nov 13  (Release) - 13 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.29
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (2x)
Biol. Unit 2:  B,C  (2x)
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, S. K. Gorla, M. Kavitha, G. Cuny, L. Hedstrom, W. F. Anderson, A. Joachimiak
Crystal Structure Of The Inosine 5'-Monophosphate Dehydrogenase With An Internal Deletion Of The Cbs Domain From Bacillus Anthracis Str. Ames Complexed With Inhibitor Q21
To Be Published 2013
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 MAGIC
    Expression System Taxid: 511693
    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: 198094
    Strain: AMES
    Synonym: IMP DEHYDROGENASE, IMPD, IMPDH

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (2x): A  D
Biological Unit 2 (2x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 24)

Asymmetric Unit (5, 24)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2EDO6Ligand/Ion1,2-ETHANEDIOL
3FMT8Ligand/IonFORMIC ACID
4IMP4Ligand/IonINOSINIC ACID
5Q214Ligand/Ion(2S)-2-(NAPHTHALEN-1-YLOXY)-N-[2-(PYRIDIN-4-YL)-1,3-BENZOXAZOL-5-YL]PROPANAMIDE
Biological Unit 1 (5, 26)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2EDO8Ligand/Ion1,2-ETHANEDIOL
3FMT8Ligand/IonFORMIC ACID
4IMP4Ligand/IonINOSINIC ACID
5Q214Ligand/Ion(2S)-2-(NAPHTHALEN-1-YLOXY)-N-[2-(PYRIDIN-4-YL)-1,3-BENZOXAZOL-5-YL]PROPANAMIDE
Biological Unit 2 (5, 22)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2EDO4Ligand/Ion1,2-ETHANEDIOL
3FMT8Ligand/IonFORMIC ACID
4IMP4Ligand/IonINOSINIC ACID
5Q214Ligand/Ion(2S)-2-(NAPHTHALEN-1-YLOXY)-N-[2-(PYRIDIN-4-YL)-1,3-BENZOXAZOL-5-YL]PROPANAMIDE

(-) Sites  (22, 22)

Asymmetric Unit (22, 22)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:49 , MET A:51 , ASN A:280 , GLY A:305 , SER A:306 , ILE A:307 , CYS A:308 , ASP A:341 , GLY A:342 , GLY A:343 , MET A:362 , GLY A:364 , SER A:365 , TYR A:388 , GLY A:390 , MET A:391 , GLY A:392 , GLU A:416 , GLY A:417 , Q21 A:502 , HOH A:606 , HOH A:638 , HOH A:653 , HOH A:654BINDING SITE FOR RESIDUE IMP A 501
02AC2SOFTWAREALA A:253 , SER A:257 , MET A:391 , GLY A:392 , GLU A:416 , IMP A:501 , HOH A:609BINDING SITE FOR RESIDUE Q21 A 502
03AC3SOFTWAREVAL A:30 , SER A:31 , VAL A:32 , LYS A:33 , ARG A:440BINDING SITE FOR RESIDUE EDO A 503
04AC4SOFTWAREALA A:62 , ARG A:65 , GLU A:372BINDING SITE FOR RESIDUE EDO A 504
05AC5SOFTWAREALA A:64 , GLY A:67 , GLY A:68 , LEU A:222BINDING SITE FOR RESIDUE FMT A 505
06AC6SOFTWARESER A:273 , ASN A:275BINDING SITE FOR RESIDUE FMT A 506
07AC7SOFTWARETYR A:346 , SER A:347 , VAL D:312BINDING SITE FOR RESIDUE ACY A 507
08AC8SOFTWAREALA B:49 , MET B:51 , ASN B:280 , GLY B:305 , SER B:306 , ILE B:307 , CYS B:308 , ASP B:341 , GLY B:343 , LEU B:363 , GLY B:364 , SER B:365 , TYR B:388 , GLY B:390 , MET B:391 , GLY B:392 , GLU B:416 , GLY B:417 , Q21 B:502 , HOH B:609 , HOH B:613 , HOH B:619 , HOH B:637BINDING SITE FOR RESIDUE IMP B 501
09AC9SOFTWAREALA B:253 , SER B:257 , MET B:391 , GLY B:392 , MET B:397 , LEU B:413 , GLU B:416 , IMP B:501BINDING SITE FOR RESIDUE Q21 B 502
10BC1SOFTWAREARG B:268BINDING SITE FOR RESIDUE EDO B 503
11BC2SOFTWAREASN B:275 , ASN B:296BINDING SITE FOR RESIDUE FMT B 504
12BC3SOFTWAREGLU B:9 , THR B:322BINDING SITE FOR RESIDUE EDO B 505
13BC4SOFTWARETYR B:424 , LYS B:425 , GLY B:426 , HOH B:656 , HOH B:676BINDING SITE FOR RESIDUE FMT B 506
14BC5SOFTWARESER B:23 , VAL B:25 , PRO B:27 , ALA B:441 , GLY B:444 , TYR B:445 , ALA C:253 , SER C:257 , MET C:391 , GLY C:392 , LEU C:413 , GLU C:416 , IMP C:501BINDING SITE FOR RESIDUE Q21 B 507
15BC6SOFTWAREQ21 B:507 , ALA C:49 , MET C:51 , ASN C:280 , GLY C:305 , SER C:306 , CYS C:308 , ASP C:341 , 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 , HOH C:601 , HOH C:608 , HOH C:621 , HOH C:660BINDING SITE FOR RESIDUE IMP C 501
16BC7SOFTWAREGLN C:41 , LEU C:42 , ASN C:43 , HOH C:646 , HOH C:649BINDING SITE FOR RESIDUE FMT C 502
17BC8SOFTWARELEU C:11 , THR C:322 , TYR C:325BINDING SITE FOR RESIDUE ACY C 503
18BC9SOFTWAREGLY A:437 , LYS D:412 , LEU D:413 , VAL D:414 , HOH D:644BINDING SITE FOR RESIDUE EDO D 501
19CC1SOFTWAREALA D:49 , MET D:51 , ASN D:280 , SER D:306 , ILE D:307 , CYS D:308 , ASP D:341 , GLY D:342 , GLY D:343 , LEU D:363 , GLY D:364 , SER D:365 , TYR D:388 , GLY D:390 , MET D:391 , GLY D:392 , GLU D:416 , GLY D:417 , Q21 D:503 , HOH D:601 , HOH D:606 , HOH D:609 , HOH D:635BINDING SITE FOR RESIDUE IMP D 502
20CC2SOFTWARESER A:23 , LEU A:26 , ALA A:441 , TYR A:445 , ALA D:253 , SER D:257 , MET D:391 , GLY D:392 , LEU D:413 , VAL D:414 , GLU D:416 , IMP D:502 , HOH D:621BINDING SITE FOR RESIDUE Q21 D 503
21CC3SOFTWARETHR D:322BINDING SITE FOR RESIDUE FMT D 504
22CC4SOFTWAREARG D:268 , SER D:273 , ASN D:275 , ASN D:296BINDING SITE FOR RESIDUE FMT D 506

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4MY8)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric 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 4MY8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MY8)

(-) Exons   (0, 0)

(no "Exon" information available for 4MY8)

(-) 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:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains d4my8a_ A: automated matches                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh.......hhh.eee.......hhhhh...eeee..eee...eee.......hhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhh.....eeee....hhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhh..eeee........hhhhhh....hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhh...eeeehhhhhh........eee..eeeeeee...hhhhhhhh........eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.eeee.hhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4my8 A  -1 NAMWESKFVKEGLTFDDVLLVPAKSDVLPREVSVKTVLSESLQLNIPLISAGMDTVTEADMAIAMARQGGLGIIHKNMSIEQQAEQVDKVKRSGGLLVGAAVGVTADAMTRIDALVKASVDAIVLDTAHGHSQGVIDKVKEVRAKYPSLNIIAGNVATAEATKALIEAGANVVKVGIGPGSICTTRVVAGVGVPQLTAVYDCATEARKHGIPVIADGGIKYSGDMVKALAAGAHVVMLGSMFAGVAESPGETEIYQGRQFKVYRGMGSVGAMEKGSKLVPEGIEGRVPYKGPLADTVHQLVGGLRAGMGYCGAQDLEFLRENAQFIRMSGAGLLE 470
                                     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     ||415       425       435       445       455       465     
                                                                                                                        92|                                                                                                                                                                                  401|                                                          
                                                                                                                        220                                                                                                                                                                                   412                                                          


Chain B from PDB  Type:PROTEIN  Length:331
                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains d4my8b_ B: automated matches                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.......hhh.eee.......hhhhh...eeee..eee...eee.......hhhhhhhhhhh..eeee....hhhhhhhhhhhhhh......eeee....hhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhh..eeee........hhhhhh....hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhh...eeeehhhhhh........eee..eeeeeee...hhhhhhh......eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.eee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4my8 B  -1 NAMWESKFVKEGLTFDDVLLVPAKSDVLPREVSVKTVLSESLQLNIPLISAGMDTVTEADMAIAMARQGGLGIIHKNMSIEQQAEQVDKVKRSGGLLVGAAVGVTADAMTRIDALVKASVDAIVLDTAHGHSQGVIDKVKEVRAKYPSLNIIAGNVATAEATKALIEAGANVVKVGIGPGSICTTRVVAGVGVPQLTAVYDCATEARKHGIPVIADGGIKYSGDMVKALAAGAHVVMLGSMFAGVAESPGETEIYQGRQFKVYRGMGSVGAMEKLVPEGIEGRVPYKGPLADTVHQLVGGLRAGMGYCGAQDLEFLRENAQFIRMSGAGLL 469
                                     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   ||  418       428       438       448       458       468 
                                                                                                                        92|                                                                                                                                                                                399|                                                        
                                                                                                                        220                                                                                                                                                                                 413                                                        


Chain C from PDB  Type:PROTEIN  Length:332
                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4my8c_ C: automated matches                                                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh...ee..hhh.eee.......hhhhh...eeee..eee...eee.......hhhhhhhhhhh..eeee....hhhhhhhhhhhhhh......eeee....hhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhh..eeee........hhhhhhh...hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh...eeeehhhhhh........eee..eeeeeee...hhhhhhh.......eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.eee.hhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4my8 C  -1 NAMWESKFVKEGLTFDDVLLVPAKSDVLPREVSVKTVLSESLQLNIPLISAGMDTVTEADMAIAMARQGGLGIIHKNMSIEQQAEQVDKVKRSGGLLVGAAVGVTADAMTRIDALVKASVDAIVLDTAHGHSQGVIDKVKEVRAKYPSLNIIAGNVATAEATKALIEAGANVVKVGIGPGSICTTRVVAGVGVPQLTAVYDCATEARKHGIPVIADGGIKYSGDMVKALAAGAHVVMLGSMFAGVAESPGETEIYQGRQFKVYRGMGSVGAMEKKLVPEGIEGRVPYKGPLADTVHQLVGGLRAGMGYCGAQDLEFLRENAQFIRMSGAGLL 469
                                     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   ||  417       427       437       447       457       467  
                                                                                                                        92|                                                                                                                                                                                399|                                                         
                                                                                                                        220                                                                                                                                                                                 412                                                         


Chain D from PDB  Type:PROTEIN  Length:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4my8d_ D: automated matches                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhh...eee.hhh.eee.......hhhhh...eeee..eee...eee.......hhhhhhhhhhhh.eeee....hhhhhhhhhhhhhh......eeee....hhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhh..eeee........hhhhhh....hhhhhhhhhhhhhhhh...eeee....hhhhhhhhhhh...eeeehhhhhh........eee..eeeeeee...hhhhhhhh........eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.eee..hhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4my8 D  -1 NAMWESKFVKEGLTFDDVLLVPAKSDVLPREVSVKTVLSESLQLNIPLISAGMDTVTEADMAIAMARQGGLGIIHKNMSIEQQAEQVDKVKRSGGLLVGAAVGVTADAMTRIDALVKASVDAIVLDTAHGHSQGVIDKVKEVRAKYPSLNIIAGNVATAEATKALIEAGANVVKVGIGPGSICTTRVVAGVGVPQLTAVYDCATEARKHGIPVIADGGIKYSGDMVKALAAGAHVVMLGSMFAGVAESPGETEIYQGRQFKVYRGMGSVGAMEKGSKLVPEGIEGRVPYKGPLADTVHQLVGGLRAGMGYCGAQDLEFLRENAQFIRMSGAGLLES 471
                                     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     ||415       425       435       445       455       465      
                                                                                                                        92|                                                                                                                                                                                  401|                                                           
                                                                                                                        220                                                                                                                                                                                   412
   Legend:   → Mismatch (orange background)
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  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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MY8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MY8)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)

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  4my8
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  Q81W29_BACAN | Q81W29
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  1.1.1.205
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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 4my9 4mya 4myx 4qm1 5urr 5urs 5uuv 5uuw 5uuz

(-) Related Entries Specified in the PDB File

3mjm SHORT INTERNAL DELETION OF CBS DOMAIN (95-200) AND GLY IS INSERTED AT 95.
3mxs AN INTERNAL DELETION OF THE CBS DOMAIN COMPLEXED WITH INHIBITOR D67
3my1 AN INTERNAL DELETION OF THE CBS DOMAIN COMPLEXED WITH INHIBITOR P68 RELATED ID: IDP01178 RELATED DB: TARGETTRACK
3tsb WILD-TYPE, PHOSPHATE BOUND FORM
3tsd WILD-TYPE, COMPLEXED WITH PRODUCT, XMP
3usb WILD-TYPE, SUBSTRATE IMP BOUND-FORM