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(-) Description

Title :  CRYSTAL STRUCTURE OF BACILLUS SUBTILIS PROBABLE GLUTAMINASE, APC1040
 
Authors :  Y. Kim, I. Dementieva, E. Vinokour, A. Joachimiak, Midwest Center For Structural Genomics (Mcsg)
Date :  29 Aug 02  (Deposition) - 03 Jun 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Structural Genomics, Probable Glutaminase, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, 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 - PROBABLE GLUTAMINASE YBGJ
    Chains: A, B
    EC Number: 3.5.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: YBGJ
    Mutation: YES
    Organism Scientific: BACILLUS SUBTILIS
    Organism Taxid: 1423

 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  (4, 31)

Asymmetric Unit (4, 31)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2FMT1Ligand/IonFORMIC ACID
3MSE24Mod. Amino AcidSELENOMETHIONINE
4SEP2Mod. Amino AcidPHOSPHOSERINE
Biological Unit 1 (4, 31)
No.NameCountTypeFull Name
1EDO4Ligand/Ion1,2-ETHANEDIOL
2FMT1Ligand/IonFORMIC ACID
3MSE24Mod. Amino AcidSELENOMETHIONINE
4SEP2Mod. Amino AcidPHOSPHOSERINE
Biological Unit 2 (4, 62)
No.NameCountTypeFull Name
1EDO8Ligand/Ion1,2-ETHANEDIOL
2FMT2Ligand/IonFORMIC ACID
3MSE48Mod. Amino AcidSELENOMETHIONINE
4SEP4Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:262 , LYS A:316 , EDO A:1303BINDING SITE FOR RESIDUE EDO A 1302
2AC2SOFTWARETYR A:259 , GLY A:312 , EDO A:1302 , HOH A:1386BINDING SITE FOR RESIDUE EDO A 1303
3AC3SOFTWAREASN A:188 , PHE A:189BINDING SITE FOR RESIDUE EDO A 1305
4AC4SOFTWAREGLY B:312 , HOH B:1445BINDING SITE FOR RESIDUE EDO B 1304
5AC5SOFTWAREASP A:98 , PHE A:121BINDING SITE FOR RESIDUE FMT A 1301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1MKI)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Lys A:116 -Pro A:117
2Lys B:116 -Pro B:117
3Gln B:287 -Pro B:288

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1MKI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1MKI)

(-) Exons   (0, 0)

(no "Exon" information available for 1MKI)

(-) 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:312
 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 d1mkia       _ A: Probable glutamina         se YbgJ                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains --1mki       A01 A:2-70,A:209-327 Pr         obable glutaminase ybgj; d1mkiA02 A:71-208  [code=1.10.1500.10, no name defined]                                                                                    1mkiA01 A:2-70,A:209-327 Probable glutaminase ybgj; domain 1                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee..-------hhhhhhhhhhhhhhhhhhhh...---------.....eeeee.....eeeee.....ee...hhhhhhhhhhhhhhhhhhhhh.............hhhhhhh.........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.eehhhhhhhhhhhhhh..ee....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eeeeee.............eeeeee.........hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mki A   0 AmKELI-------NPALQLHDWVEYYRPFAANGQSA---------NDSQLGICVLEPDGTmIHAGDWNVSFTmQsISKVISFIAACmSRGIPYVLDRVDVEPTGDAFNSIIRLEINKPGKPFNPmINAGALTIASILPGESAYEKLEFLYSVmETLIGKRPRIHEEVFRSEWETAHRNRALAYYLKETNFLEAEVEETLEVYLKQCAmESTTEDIALIGLILAHDGYHPIRHEQVIPKDVAKLAKALmLTCGmYNASGKYAAFVGVPAKSGVSGGImALVPPSARREQPFQSGCGIGIYGPAIDEYGNSLTGGmLLKHmAQEWELSIF 327
                             |   |   -   |    19        29     |   -     |  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        
                             |   5      13                    35        45             60-MSE      72-MSE        86-MSE                               124-MSE                     152-MSE                                                207-MSE                                 247-MSE|                     276-MSE                              313-MSE|         
                             1-MSE                                                                   74-SEP                                                                                                                                                                           252-MSE                                                           318-MSE     


Chain B from PDB  Type:PROTEIN  Length:312
 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 d1mkib       _ B: Probable glutamina         se YbgJ                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains --1mki       B01 B:2-70,B:209-327 Pr         obable glutaminase ybgj; d1mkiB02 B:71-208  [code=1.10.1500.10, no name defined]                                                                                    1mkiB01 B:2-70,B:209-327 Probable glutaminase ybgj; domain 1                                                            CATH domains
           Pfam domains (1) ------       -------------------Glut         aminase-1mkiB01 B:32-327                                                                                                                                                                                                                                                                    Pfam domains (1)
           Pfam domains (2) ------       -------------------Glut         aminase-1mkiB02 B:32-327                                                                                                                                                                                                                                                                    Pfam domains (2)
         Sec.struct. author ..eee.-------hhhhhhhhhhhhhhhhhhhh...---------.....eeeee....eeeeee.....ee...hhhhhhhhhhhhhhhhhhhhh.............hhhhhhh.........hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.eehhhhhhhhhhhhhh..ee....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...eee....eeeeee.............eeeeee.........hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1mki B   0 AmKELI-------NPALQLHDWVEYYRPFAANGQSA---------NDSQLGICVLEPDGTmIHAGDWNVSFTmQsISKVISFIAACmSRGIPYVLDRVDVEPTGDAFNSIIRLEINKPGKPFNPmINAGALTIASILPGESAYEKLEFLYSVmETLIGKRPRIHEEVFRSEWETAHRNRALAYYLKETNFLEAEVEETLEVYLKQCAmESTTEDIALIGLILAHDGYHPIRHEQVIPKDVAKLAKALmLTCGmYNASGKYAAFVGVPAKSGVSGGImALVPPSARREQPFQSGCGIGIYGPAIDEYGNSLTGGmLLKHmAQEWELSIF 327
                             |   |   -   |    19        29     |   -     |  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        
                             1-MSE      13                    35        45             60-MSE      72-MSE        86-MSE                               124-MSE                     152-MSE                                                207-MSE                                 247-MSE|                     276-MSE                              313-MSE|         
                                                                                                     74-SEP                                                                                                                                                                           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  (1, 2)

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

(-) 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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  3.5.1.2
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 Related Entries

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

UniProtKB/Swiss-Prot
        GLSA1_BACSU | O31465: 2osu 3agf 3brm

(-) Related Entries Specified in the PDB File

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