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(-) Description

Title :  CRYSTAL STRUCTURE OF THE COVALENT COMPLEX BETWEEN THE BACILLUS SUBTILIS GLUTAMINASE YBGJ AND 5-OXO-L-NORLEUCINE FORMED BY REACTION OF THE PROTEIN WITH 6-DIAZO-5-OXO-L-NORLEUCINE
 
Authors :  A. U. Singer, Y. Kim, I. Dementieva, E. Vinokour, A. Joachimiak, A. Savchenko, A. Yakunin
Date :  21 Dec 07  (Deposition) - 20 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.29
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Covalent Complex, Ybas Glutaminase, Don, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Brown, A. Singer, M. Proudfoot, T. Skarina, Y. Kim, C. Chang, I. Dementieva, E. Kuznetsova, C. F. Gonzalez, A. Joachimiak, A. Savchenko, A. F. Yakunin
Functional And Structural Characterization Of Four Glutaminases From Escherichia Coli And Bacillus Subtilis.
Biochemistry V. 47 5724 2008
PubMed-ID: 18459799  |  Reference-DOI: 10.1021/BI800097H
(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
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Vector Type: PLASMID
    Gene: GLSA1, GLSA, YBGJ, BSU02430
    Organism Scientific: BACILLUS SUBTILIS
    Strain: 168

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 24)

Asymmetric Unit (2, 24)
No.NameCountTypeFull Name
1MSE22Mod. Amino AcidSELENOMETHIONINE
2ONL2Ligand/Ion5-OXO-L-NORLEUCINE
Biological Unit 1 (2, 24)
No.NameCountTypeFull Name
1MSE22Mod. Amino AcidSELENOMETHIONINE
2ONL2Ligand/Ion5-OXO-L-NORLEUCINE
Biological Unit 2 (2, 48)
No.NameCountTypeFull Name
1MSE44Mod. Amino AcidSELENOMETHIONINE
2ONL4Ligand/Ion5-OXO-L-NORLEUCINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:73 , SER A:74 , LYS A:77 , ASN A:126 , GLU A:170 , ASN A:177 , TYR A:201 , TYR A:253 , GLY A:270BINDING SITE FOR RESIDUE ONL A 401
2AC2SOFTWARETYR B:37 , GLN B:73 , SER B:74 , LYS B:77 , ASN B:126 , GLU B:170 , ASN B:177 , TYR B:201 , CYS B:205 , TYR B:253 , GLY B:270 , HOH B:536BINDING SITE FOR RESIDUE ONL B 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BRM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BRM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BRM)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BRM)

(-) Exons   (0, 0)

(no "Exon" information available for 3BRM)

(-) 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:290
 aligned with GLSA1_BACSU | O31465 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:315
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322     
          GLSA1_BACSU    13 NPALQLHDWVEYYRPFAANGQSANYIPALGKVNDSQLGICVLEPDGTMIHAGDWNVSFTMQSISKVISFIAACMSRGIPYVLDRVDVEPTGDAFNSIIRLEINKPGKPFNPMINAGALTIASILPGESAYEKLEFLYSVMETLIGKRPRIHEEVFRSEWETAHRNRALAYYLKETNFLEAEVEETLEVYLKQCAMESTTEDIALIGLILAHDGYHPIRHEQVIPKDVAKLAKALMLTCGMYNASGKYAAFVGVPAKSGVSGGIMALVPPSARREQPFQSGCGIGIYGPAIDEYGNSLTGGMLLKHMAQEWELSIF 327
               SCOP domains d3brma_ A: Probable glu   tamin ase YbgJ                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 3brmA01 A:13-70,A:209-3   21                              3brmA02 A:71-208  [code=1.10.15                 00.10, no name defined]                                                                   3brmA01 A:13-70,A:209-321 Probable glutaminase ybgj; domain 1                                                    ------ CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh...---hhhhh-.....eeeee.....eeeee.....ee...hhhhhhhhhhhhhhhhhhhhh......-----------------......hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.eehhhhhhhhhhhhhh..ee....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eeeeee...----......eeeeee.........hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3brm A  13 NPALQLHDWVEYYRPFAANGQSA---PALGK-NDSQLGICVLEPDGTmIHAGDWNVSFTmQSISKVISFIAACmSRGIPYVLDRVDVEP-----------------KPFNPmINAGALTIASILPGESAYEKLEFLYSVmETLIGKRPRIHEEVFRSEWETAHRNRALAYYLKETNFLEAEVEETLEVYLKQCAmESTTEDIALIGLILAHDGYHPIRHEQVIPKDVAKLAKALmLTCGmYNASGKYAAFVGVPAKSGVSGGImALVPPS----QPFQSGCGIGIYGPAIDEYGNSLTGGmLLKHmAQEWELSIF 327
                                    22        32  |   | 42| |     52       |62        72        82   |    92        |-         -      |122 |     132       142       152       162       172       182       192       202    |  212       222       232       242    |  252       262       272   |   282    |  292       302       312|    | 322     
                                                 35  39  43 |             60-MSE      72-MSE        86-MSE        101               119    |                         152-MSE                                                207-MSE                                 247-MSE|                     276-MSE82  287                       313-MSE|         
                                                           45                                                                            124-MSE                                                                                                                         252-MSE                                                           318-MSE     


Chain B from PDB  Type:PROTEIN  Length:292
 aligned with GLSA1_BACSU | O31465 from UniProtKB/Swiss-Prot  Length:327

    Alignment length:315
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322     
          GLSA1_BACSU    13 NPALQLHDWVEYYRPFAANGQSANYIPALGKVNDSQLGICVLEPDGTMIHAGDWNVSFTMQSISKVISFIAACMSRGIPYVLDRVDVEPTGDAFNSIIRLEINKPGKPFNPMINAGALTIASILPGESAYEKLEFLYSVMETLIGKRPRIHEEVFRSEWETAHRNRALAYYLKETNFLEAEVEETLEVYLKQCAMESTTEDIALIGLILAHDGYHPIRHEQVIPKDVAKLAKALMLTCGMYNASGKYAAFVGVPAKSGVSGGIMALVPPSARREQPFQSGCGIGIYGPAIDEYGNSLTGGMLLKHMAQEWELSIF 327
               SCOP domains d3brmb_ B: Probable glutaminase YbgJ                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 3brmB01 B:13-70,B:209-321                                 3brmB02 B:71-208  [code=1.10.15                  00.10, no name defined]                                                                  3brmB01 B:13-70,B:209-321 Probable glutaminase ybgj; domain 1                                                    ------ CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhh.....hhhhh.......eeeee.....eeeee.....ee...hhhhhhhhhhhhhhhhhhhhh......------------------.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.eehhhhhhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eeeeee..-----......eeeeee.........hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3brm B  13 NPALQLHDWVEYYRPFAANGQSANYIPALGKVNDSQLGICVLEPDGTmIHAGDWNVSFTmQSISKVISFIAACmSRGIPYVLDRVDVEP------------------PFNPmINAGALTIASILPGESAYEKLEFLYSVmETLIGKRPRIHEEVFRSEWETAHRNRALAYYLKETNFLEAEVEETLEVYLKQCAmESTTEDIALIGLILAHDGYHPIRHEQVIPKDVAKLAKALmLTCGmYNASGKYAAFVGVPAKSGVSGGImALVPP-----QPFQSGCGIGIYGPAIDEYGNSLTGGmLLKHmAQEWELSIF 327
                                    22        32        42        52       |62        72        82   |    92        |-         -       122 |     132       142       152       162       172       182       192       202    |  212       222       232       242    |  252       262       272   |    |-    |  292       302       312|    | 322     
                                                                          60-MSE      72-MSE        86-MSE        101                120   |                         152-MSE                                                207-MSE                                 247-MSE|                     276-MSE1   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 Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3BRM)

(-) Gene Ontology  (5, 5)

Asymmetric 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 2osu 3agf

(-) Related Entries Specified in the PDB File

1mki CRYSTAL STRUCTURE OF BACILLUS SUBTILIS PROBABLE GLUTAMINASE, MCSG TARGET APC1040
2osu PROBABLE GLUTAMINASE FROM BACILLUS SUBTILIS COMPLEXED WITH 6-DIAZO-5-OXO-L-NORLEUCINE