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(-) Description

Title :  CRYSTAL STRUCTURE OF THE INOSINE 5'-MONOPHOSPHATE DEHYDROGENASE, WITH A INTERNAL DELETION OF CBS DOMAIN FROM CAMPYLOBACTER JEJUNI COMPLEXED WITH INHIBITOR COMPOUND P12
 
Authors :  Y. Kim, M. Makowska-Grzyska, M. Gu, W. F. Anderson, A. Joachimiak, Csgi For Structural Genomics Of Infectious Diseases (Csgid)
Date :  28 Sep 13  (Deposition) - 01 Jan 14  (Release) - 01 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (4x)
Biol. Unit 2:  B  (4x)
Biol. Unit 3:  C  (4x)
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, W. F. Anderson, A. Joachimiak
Crystal Structure Of The Inosine 5'-Monophosphate Dehydrogenase, With A Internal Deletion Of Cbs Domain From Campylobacter Jejuni Complexed With Inhibitor Compound P12
To Be Published 2013
PubMed: search

(-) Compounds

Molecule 1 - INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
    Chains: A, B, C
    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-S-CBS
    Gene: GUAB, CJ1058C
    Mutation: YES
    Organism Scientific: CAMPYLOBACTER JEJUNI SUBSP. JEJUNI
    Organism Taxid: 192222
    Strain: NCTC 11168
    Synonym: IMP DEHYDROGENASE, IMPD, IMPDH

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (4x): A  
Biological Unit 2 (4x):  B 
Biological Unit 3 (4x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 21)

Asymmetric Unit (6, 21)
No.NameCountTypeFull Name
12F13Ligand/Ion1-(4-BROMOPHENYL)-3-{2-[3-(PROP-1-EN-2-YL)PHENYL]PROPAN-2-YL}UREA
2ACY2Ligand/IonACETIC ACID
3IMP3Ligand/IonINOSINIC ACID
4K3Ligand/IonPOTASSIUM ION
5PO46Ligand/IonPHOSPHATE ION
6SO44Ligand/IonSULFATE ION
Biological Unit 1 (4, 24)
No.NameCountTypeFull Name
12F14Ligand/Ion1-(4-BROMOPHENYL)-3-{2-[3-(PROP-1-EN-2-YL)PHENYL]PROPAN-2-YL}UREA
2ACY-1Ligand/IonACETIC ACID
3IMP4Ligand/IonINOSINIC ACID
4K-1Ligand/IonPOTASSIUM ION
5PO412Ligand/IonPHOSPHATE ION
6SO44Ligand/IonSULFATE ION
Biological Unit 2 (4, 24)
No.NameCountTypeFull Name
12F14Ligand/Ion1-(4-BROMOPHENYL)-3-{2-[3-(PROP-1-EN-2-YL)PHENYL]PROPAN-2-YL}UREA
2ACY-1Ligand/IonACETIC ACID
3IMP4Ligand/IonINOSINIC ACID
4K-1Ligand/IonPOTASSIUM ION
5PO48Ligand/IonPHOSPHATE ION
6SO48Ligand/IonSULFATE ION
Biological Unit 3 (5, 24)
No.NameCountTypeFull Name
12F14Ligand/Ion1-(4-BROMOPHENYL)-3-{2-[3-(PROP-1-EN-2-YL)PHENYL]PROPAN-2-YL}UREA
2ACY8Ligand/IonACETIC ACID
3IMP4Ligand/IonINOSINIC ACID
4K-1Ligand/IonPOTASSIUM ION
5PO44Ligand/IonPHOSPHATE ION
6SO44Ligand/IonSULFATE ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:46 , MET A:48 , GLY A:298 , SER A:299 , ILE A:300 , CYS A:301 , ASP A:334 , GLY A:335 , GLY A:336 , MET A:355 , GLY A:357 , SER A:358 , TYR A:381 , GLY A:383 , MET A:384 , GLY A:385 , GLU A:411 , GLY A:412 , 2F1 A:501 , HOH A:601 , HOH A:606 , HOH A:610 , HOH A:615 , HOH A:628BINDING SITE FOR RESIDUE IMP A 500
02AC2SOFTWAREVAL A:22 , ALA A:246 , THR A:303 , GLY A:385 , GLU A:411 , GLY A:439 , TYR A:440 , IMP A:500BINDING SITE FOR RESIDUE 2F1 A 501
03AC3SOFTWAREGLY A:296 , GLY A:298 , CYS A:301 , GLU A:465 , SER A:466 , HIS A:467BINDING SITE FOR RESIDUE K A 502
04AC4SOFTWAREHIS A:54 , ARG A:55BINDING SITE FOR RESIDUE SO4 A 503
05AC5SOFTWAREARG A:62BINDING SITE FOR RESIDUE PO4 A 504
06AC6SOFTWARETYR A:378 , ARG A:416 , THR A:472BINDING SITE FOR RESIDUE PO4 A 505
07AC7SOFTWARETYR A:373 , GLN A:374BINDING SITE FOR RESIDUE PO4 A 506
08AC8SOFTWAREALA B:46 , MET B:48 , ASN B:273 , GLY B:298 , SER B:299 , ILE B:300 , CYS B:301 , ASP B:334 , GLY B:335 , GLY B:336 , MET B:355 , GLY B:357 , SER B:358 , TYR B:381 , GLY B:383 , MET B:384 , GLY B:385 , GLU B:411 , GLY B:412 , 2F1 B:501 , HOH B:604 , HOH B:636 , HOH B:637 , HOH B:654BINDING SITE FOR RESIDUE IMP B 500
09AC9SOFTWAREALA B:246 , THR B:303 , MET B:384 , GLY B:385 , MET B:390 , GLU B:411 , GLY B:439 , TYR B:440 , IMP B:500BINDING SITE FOR RESIDUE 2F1 B 501
10BC1SOFTWAREGLY B:296 , GLY B:298 , CYS B:301 , GLU B:465 , SER B:466 , HIS B:467BINDING SITE FOR RESIDUE K B 502
11BC2SOFTWARETYR B:378 , ARG B:416 , THR B:472BINDING SITE FOR RESIDUE PO4 B 503
12BC3SOFTWAREARG B:62BINDING SITE FOR RESIDUE SO4 B 504
13BC4SOFTWAREHIS B:54BINDING SITE FOR RESIDUE SO4 B 505
14BC5SOFTWAREGLN B:226 , ARG B:229BINDING SITE FOR RESIDUE PO4 B 506
15BC6SOFTWARETYR B:373 , GLN B:374 , TYR C:373BINDING SITE FOR RESIDUE ACY C 501
16BC7SOFTWAREALA C:46 , MET C:48 , GLY C:298 , SER C:299 , ILE C:300 , CYS C:301 , ASP C:334 , GLY C:335 , GLY C:336 , MET C:355 , GLY C:357 , SER C:358 , TYR C:381 , GLY C:383 , MET C:384 , GLY C:385 , GLU C:411 , GLY C:412 , 2F1 C:503 , HOH C:615 , HOH C:625 , HOH C:655 , HOH C:656BINDING SITE FOR RESIDUE IMP C 502
17BC8SOFTWAREALA C:246 , HIS C:247 , THR C:303 , MET C:384 , GLY C:385 , MET C:390 , GLU C:411 , GLY C:439 , TYR C:440 , IMP C:502BINDING SITE FOR RESIDUE 2F1 C 503
18BC9SOFTWAREGLY C:296 , GLY C:298 , CYS C:301 , GLU C:465 , SER C:466 , HIS C:467BINDING SITE FOR RESIDUE K C 504
19CC1SOFTWAREHIS C:54BINDING SITE FOR RESIDUE SO4 C 505
20CC2SOFTWAREARG C:376 , TYR C:378 , ARG C:416 , THR C:472BINDING SITE FOR RESIDUE PO4 C 506
21CC3SOFTWAREILE C:75 , GLN C:226 , MET C:227 , ASP C:228 , ARG C:229BINDING SITE FOR RESIDUE ACY C 507

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4MZ1)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Gly A:272 -Asn A:273
2Gly B:272 -Asn B:273
3Gly C:272 -Asn C:273

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MZ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MZ1)

(-) Exons   (0, 0)

(no "Exon" information available for 4MZ1)

(-) 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:354
                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4mz1a_ A: automated matches                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhh.eee.......hhhhh...ee.....ee...eee.......hhhhhhhhhhh..eeee....hhhhhhhhhhhhhh.................eeee...hhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhh..eeee........hhhhhhh...hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhh...eeeehhhhhh........eee..eeeeeee...hhhhhh.......eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.eee.hhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mz1 A   0 AMKIVKRALTFEDVLLRPGYSEVLPKEVKIHTKLTKNITLNMPLISAAMDTVTEHRAAIMMARLGGLGVIHKNMDIASQVREVKRVKKSKEYPDANKDNFGRLRVGAAIGVGQMDRVDALVEAGVDVVVLDSAHGHSKGIIDTVKAIKAKYPNLDLIAGNIATAAAAKALCEAGVDAVKVGIGPGSICTTRIVSGVGVPQISAIDECVEEANKFGVPVIADGGIKYSGDIAKALAVGASSVMIGSLLAGTDESPGELFTYQGRQYKSYRGMGSLGAMQKLVPEGIEGRVPYVGSIRSVVHQLLGGLRSSMGYVGAKDIEDFQKRAEFVEITTAGLKESHVHDVTITHEAPNYKV 482
                                     9        19        29        39        49        59        69        79       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       408       418       428       438       448       458       468       478    
                                                                                                                   88|                                                                                                                                                                                         391|                                                                           
                                                                                                                   203                                                                                                                                                                                          407                                                                           


Chain B from PDB  Type:PROTEIN  Length:354
                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains d4mz1b_ B: automated matches                                                                                                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhh.eee.......hhhhh...ee.....ee...eee.......hhhhhhhhhhhh.eeee....hhhhhhhhhhhhhh.................eeee...hhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhh..eeee........hhhhhh....hhhhhhhhhhhhhhh....eeee....hhhhhhhhhhh...eeeehhhhhh........eee..eeeeeee................eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.eee.hhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4mz1 B   0 AMKIVKRALTFEDVLLRPGYSEVLPKEVKIHTKLTKNITLNMPLISAAMDTVTEHRAAIMMARLGGLGVIHKNMDIASQVREVKRVKKSKEYPDANKDNFGRLRVGAAIGVGQMDRVDALVEAGVDVVVLDSAHGHSKGIIDTVKAIKAKYPNLDLIAGNIATAAAAKALCEAGVDAVKVGIGPGSICTTRIVSGVGVPQISAIDECVEEANKFGVPVIADGGIKYSGDIAKALAVGASSVMIGSLLAGTDESPGELFTYQGRQYKSYRGMGSLGAMQKLVPEGIEGRVPYVGSIRSVVHQLLGGLRSSMGYVGAKDIEDFQKRAEFVEITTAGLKESHVHDVTITHEAPNYKV 482
                                     9        19        29        39        49        59        69        79       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       408       418       428       438       448       458       468       478    
                                                                                                                   88|                                                                                                                                                                                         391|                                                                           
                                                                                                                   203                                                                                                                                                                                          407                                                                           


Chain C from PDB  Type:PROTEIN  Length:361
                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4mz1c_ C: automated matches                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhh.eee...............ee.....ee...eee.......hhhhhhhhhhh..eeee....hhhhhhhhhhhhhh.........................eeee...hhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhh..eeee........hhhhhhh...hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh...eeeehhhhhh........eee..eeeeeee....hhhhh.......eeeee...hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.eee.hhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mz1 C   1 MKIVKRALTFEDVLLRPGYSEVLPKEVKIHTKLTKNITLNMPLISAAMDTVTEHRAAIMMARLGGLGVIHKNMDIASQVREVKRVKKSESGGIKKRKEYPDANKDNFGRLRVGAAIGVGQMDRVDALVEAGVDVVVLDSAHGHSKGIIDTVKAIKAKYPNLDLIAGNIATAAAAKALCEAGVDAVKVGIGPGSICTTRIVSGVGVPQISAIDECVEEANKFGVPVIADGGIKYSGDIAKALAVGASSVMIGSLLAGTDESPGELFTYQGRQYKSYRGMGSLGAMQKLVPEGIEGRVPYVGSIRSVVHQLLGGLRSSMGYVGAKDIEDFQKRAEFVEITTAGLKESHVHDVTITHEAPNYKV 482
                                    10        20        30        40        50        60        70        80        90 |||   206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386    || 411       421       431       441       451       461       471       481 
                                                                                                                      92||                                                                                                                                                                                            391|                                                                           
                                                                                                                      196|                                                                                                                                                                                             407                                                                           
                                                                                                                       200
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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, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MZ1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MZ1)

(-) Gene Ontology  (8, 8)

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