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(-) Description

Title :  PROBABLE GLUTAMINASE FROM BACILLUS SUBTILIS COMPLEXED WITH 6-DIAZO-5-OXO-L-NORLEUCINE
 
Authors :  Y. Kim, I. Dementieva, E. Vinokour, F. Collart, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  06 Feb 07  (Deposition) - 06 Mar 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.29
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha-Beta Structure, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kim, I. Dementieva, E. Vinokour, F. Collart, A. Joachimiak
The Structure Of Probable Glutaminase From B. Subtilis Complexed With Its Inhibitor 6-Diazo-5-Oxo-L-Norleucine
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUTAMINASE 1
    Chains: A, B
    EC Number: 3.5.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: GLSA1, GLSA, BSU02430
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423
    Strain: 168

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 26)

Asymmetric/Biological Unit (2, 26)
No.NameCountTypeFull Name
1DON2Ligand/Ion6-DIAZENYL-5-OXO-L-NORLEUCINE
2MSE24Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR B:37 , ILE B:38 , GLN B:73 , SER B:74 , ASN B:126 , GLU B:170 , ALA B:174 , ASN B:177 , TYR B:201 , TYR B:253 , VAL B:271 , HOH B:441BINDING SITE FOR RESIDUE DON B 401
2AC2SOFTWARETYR A:37 , ILE A:38 , GLN A:73 , SER A:74 , ASN A:126 , GLU A:170 , THR A:173 , ALA A:174 , ASN A:177 , TYR A:201 , LEU A:202 , TYR A:253 , VAL A:271 , HOH A:403BINDING SITE FOR RESIDUE DON A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2OSU)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gln A:287 -Pro A:288
2Gln B:287 -Pro B:288

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OSU)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2OSU)

(-) Exons   (0, 0)

(no "Exon" information available for 2OSU)

(-) 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:306
 aligned with GLSA1_BACSU | O31465 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:328
                             1                                                                                                                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319        
          GLSA1_BACSU     - -MKELIKEHQKDINPALQLHDWVEYYRPFAANGQSANYIPALGKVNDSQLGICVLEPDGTMIHAGDWNVSFTMQSISKVISFIAACMSRGIPYVLDRVDVEPTGDAFNSIIRLEINKPGKPFNPMINAGALTIASILPGESAYEKLEFLYSVMETLIGKRPRIHEEVFRSEWETAHRNRALAYYLKETNFLEAEVEETLEVYLKQCAMESTTEDIALIGLILAHDGYHPIRHEQVIPKDVAKLAKALMLTCGMYNASGKYAAFVGVPAKSGVSGGIMALVPPSARREQPFQSGCGIGIYGPAIDEYGNSLTGGMLLKHMAQEWELSIF 327
               SCOP domains d2osua_ A   : Probable glutaminase YbgJ                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -------2o   suA01 A:7-70,A:209-321 Probable glutaminase ybgj; domain 1 2osuA02 A:71-208  [code=1.10.15                00.10, no name defined]                                                                    2osuA01 A:7-70,A:209-321 Probable glutaminase ybgj; domain 1                                                     ------ CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........---.hhhhhhhhhhhhhhhhhhhh.....hhhhhh......eeeee.....eeeee.....ee...hhhhhhhhhhhhhhhhhhhhh......----------------.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.eehhhhhhhhhhhhhh..ee....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eeeeee....---......eeeeee.........hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2osu A   0 AmKELIKEH---INPALQLHDWVEYYRPFAANGQSANYIPALGKVNDSQLGICVLEPDGTmIHAGDWNVSFTmQSISKVISFIAACmSRGIPYVLDRVDVEP----------------GKPFNPmINAGALTIASILPGESAYEKLEFLYSVmETLIGKRPRIHEEVFRSEWETAHRNRALAYYLKETNFLEAEVEETLEVYLKQCAmESTTEDIALIGLILAHDGYHPIRHEQVIPKDVAKLAKALmLTCGmYNASGKYAAFVGVPAKSGVSGGImALVPPSA---QPFQSGCGIGIYGPAIDEYGNSLTGGmLLKHmAQEWELSIF 327
                             |      |-  |     19        29        39        49        59|       69  |     79      | 89        99 |       -       119    |  129       139       149  |    159       169       179       189       199       209       219       229       239       249  |    259       269      |279   |   289       299       309   |   319        
                             |      8  12                                              60-MSE      72-MSE        86-MSE        101              118     |                         152-MSE                                                207-MSE                                 247-MSE|                     276-MSE283 287                       313-MSE|         
                             1-MSE                                                                                                                    124-MSE                                                                                                                         252-MSE                                                           318-MSE     


Chain B from PDB  Type:PROTEIN  Length:303
 aligned with GLSA1_BACSU | O31465 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:328
                             1                                                                                                                                                                                                                                                                                                                                      
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319        
          GLSA1_BACSU     - -MKELIKEHQKDINPALQLHDWVEYYRPFAANGQSANYIPALGKVNDSQLGICVLEPDGTMIHAGDWNVSFTMQSISKVISFIAACMSRGIPYVLDRVDVEPTGDAFNSIIRLEINKPGKPFNPMINAGALTIASILPGESAYEKLEFLYSVMETLIGKRPRIHEEVFRSEWETAHRNRALAYYLKETNFLEAEVEETLEVYLKQCAMESTTEDIALIGLILAHDGYHPIRHEQVIPKDVAKLAKALMLTCGMYNASGKYAAFVGVPAKSGVSGGIMALVPPSARREQPFQSGCGIGIYGPAIDEYGNSLTGGMLLKHMAQEWELSIF 327
               SCOP domains d2osub_      B: Probable glutaminase YbgJ                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains -------2     osuB01 B:7-70,B:209-321 Probable glutaminase ybgj; domain 2osuB02 B:71-208  [code=1.10.15                00.10, no name defined]                                                                    2osuB01 B:7-70,B:209-321 Probable glutaminase ybgj; domain 1                                                     ------ CATH domains
           Pfam domains (1) --------     -------------------Glutaminase-2osuB01 B:32-327                                                                                                                                                                                                                                                                             Pfam domains (1)
           Pfam domains (2) --------     -------------------Glutaminase-2osuB02 B:32-327                                                                                                                                                                                                                                                                             Pfam domains (2)
         Sec.struct. author ........-----hhhhhhhhhhhhhhhhhhhh.................eeeee.....eeeee.....ee...hhhhhhhhhhhhhhhhhhhhhhh....----------------.......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhheehhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eeeeee...----......eeeeee.........hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2osu B   0 AmKELIKE-----NPALQLHDWVEYYRPFAANGQSANYIPALGKVNDSQLGICVLEPDGTmIHAGDWNVSFTmQSISKVISFIAACmSRGIPYVLDRVDVEP----------------GKPFNPmINAGALTIASILPGESAYEKLEFLYSVmETLIGKRPRIHEEVFRSEWETAHRNRALAYYLKETNFLEAEVEETLEVYLKQCAmESTTEDIALIGLILAHDGYHPIRHEQVIPKDVAKLAKALmLTCGmYNASGKYAAFVGVPAKSGVSGGImALVPPS----QPFQSGCGIGIYGPAIDEYGNSLTGGmLLKHmAQEWELSIF 327
                             |     | -   |    19        29        39        49        59|       69  |     79      | 89        99 |       -       119    |  129       139       149  |    159       169       179       189       199       209       219       229       239       249  |    259       269      |279  |    289       299       309   |   319        
                             1-MSE 7    13                                             60-MSE      72-MSE        86-MSE        101              118     |                         152-MSE                                                207-MSE                                 247-MSE|                     276-MSE82  287                       313-MSE|         
                                                                                                                                                      124-MSE                                                                                                                         252-MSE                                                           318-MSE
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: Beta-lactamase (210)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (GLSA1_BACSU | O31465)
molecular function
    GO:0004359    glutaminase activity    Catalysis of the reaction: L-glutamine + H2O = L-glutamate + NH3.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
    GO:0006537    glutamate biosynthetic process    The chemical reactions and pathways resulting in the formation of glutamate, the anion of 2-aminopentanedioic acid.
    GO:0006543    glutamine catabolic process    The chemical reactions and pathways resulting in the breakdown of glutamine, 2-amino-4-carbamoylbutanoic acid.
    GO:0006541    glutamine metabolic process    The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        GLSA1_BACSU | O31465: 1mki 3agf 3brm

(-) Related Entries Specified in the PDB File

1mki PROBABLE GLUTAMINASE FROM BACILLUS SUBTILIS