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(-) Description

Title :  PROBABLE GLUTAMINASE FROM GEOBACILLUS KAUSTOPHILUS HTA426
 
Authors :  B. D. Dillard, A. Ebihara, A. Shinkai, S. Kuramitsu, S. Yokoyama, J. P. R C. Wang, Riken Structural Genomics/Proteomics Initiative (Rsg Southeast Collaboratory For Structural Genomics (Secsg)
Date :  29 Mar 07  (Deposition) - 12 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.07
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Glutaminase, Secsg, Riken, Structural Genomics, Psi, Protein Structure Initiative, Riken Structural Genomics/Proteomics Initiative, Rsgi, Southeast Collaboratory For Structural Genomics, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. D. Dillard, A. Ebihara, A. Shinkai, S. Kuramitsu, S. Yokoyama, J. P. Rose, B-C. Wang
Glutaminase From Geobacillus Kaustophilus Hta426
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLUTAMINASE
    Chains: A, B, C, D
    EC Number: 3.5.1.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-15B
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GK2125
    Organism Scientific: GEOBACILLUS KAUSTOPHILUS
    Organism Taxid: 235909
    Strain: HTA426

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2PBY)

(-) Sites  (0, 0)

(no "Site" information available for 2PBY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2PBY)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PBY)

(-) 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:291
 aligned with GLSA_GEOKA | Q5KY26 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:307
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       
           GLSA_GEOKA     2 LVYNQEELVRFVEEAKQYARYGKVADYIPALGKANPNELSIAIYTPDDEVVSAGDVTVKVTLQSISKIIALALVLIDRGEDEVFHKVGMEPTDYPFHSIAKLEEKPAKPLNPMINAGALVVTSMIQGGSVSERLERLLAFVRRLAGNERISYSDEVARSEFETAFLNRSLCYFLKQHRIIDEDVEELMELYTKQCAIEMTCIDLARIGLVLALDGRDPHSSEPLMPLDVARICKTFMVTCGMYNSSGEFAIKVGIPAKSGVSGGILAAVPGRCGIGVFGPALDDKGNSLTGVKLLERLSKTYSLSIF 308
               SCOP domains d2pbya_ A: automated matches                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2pbyA01 A:2-61,A:200-302 Probable glutaminase ybgj; domain 12pbyA02 A:62-199  [code=1.10.15                00.10, no name defined]                                                                    2pbyA01 A:2-61,A:200-302 Probable glutaminase ybgj; domain 1                                           ------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhh.....hhhhhhh.....eeeeee...eeeeee.....ee..hhhhhhhhhhhhhhhhhhhhhhhh....----------------......hhhhhhhhhh.....hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.eehhhhhhhhhhhhhh............hhhhhhhhhhhhhhh....hhhhhhhhh...eee....eeeeee...eeeeee.........hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pby A   2 LVYNQEELVRFVEEAKQYARYGKVADYIPALGKANPNELSIAIYTPDDEVVSAGDVTVKVTLQSISKIIALALVLIDRGEDEVFHKVGMEP----------------KPLNPMINAGALVVTSMIQGGSVSERLERLLAFVRRLAGNERISYSDEVARSEFETAFLNRSLCYFLKQHRIIDEDVEELMELYTKQCAIEMTCIDLARIGLVLALDGRDPHSSEPLMPLDVARICKTFMVTCGMYNSSGEFAIKVGIPAKSGVSGGILAAVPGRCGIGVFGPALDDKGNSLTGVKLLERLSKTYSLSIF 308
                                    11        21        31        41        51        61        71        81        91|        -       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       
                                                                                                                     92              109                                                                                                                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:290
 aligned with GLSA_GEOKA | Q5KY26 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:305
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303     
           GLSA_GEOKA     4 YNQEELVRFVEEAKQYARYGKVADYIPALGKANPNELSIAIYTPDDEVVSAGDVTVKVTLQSISKIIALALVLIDRGEDEVFHKVGMEPTDYPFHSIAKLEEKPAKPLNPMINAGALVVTSMIQGGSVSERLERLLAFVRRLAGNERISYSDEVARSEFETAFLNRSLCYFLKQHRIIDEDVEELMELYTKQCAIEMTCIDLARIGLVLALDGRDPHSSEPLMPLDVARICKTFMVTCGMYNSSGEFAIKVGIPAKSGVSGGILAAVPGRCGIGVFGPALDDKGNSLTGVKLLERLSKTYSLSIF 308
               SCOP domains d2pbyb_ B: automated matches                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains 2pbyB01 B:4-60,B:200-302                                 2pbyB02 B:61-199  [code=1.10.150               0.10, no name defined]                                                                      2pbyB01 B:4-60,B:200-302 Probable glutaminase ybgj; domain 1                                           ------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.....hhhhhhh.....eeeee.....eeeee....ee...hhhhhhhhhhhhhhhhhhhhhhh.....---------------.......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.eehhhhhhhhhhhhhh............hhhhhhhhhhhhhhh.hhhhhhhhhhhh...eee....eeeeee...eeeeee.........hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pby B   4 YNQEELVRFVEEAKQYARYGKVADYIPALGKANPNELSIAIYTPDDEVVSAGDVTVKVTLQSISKIIALALVLIDRGEDEVFHKVGMEP---------------AKPLNPMINAGALVVTSMIQGGSVSERLERLLAFVRRLAGNERISYSDEVARSEFETAFLNRSLCYFLKQHRIIDEDVEELMELYTKQCAIEMTCIDLARIGLVLALDGRDPHSSEPLMPLDVARICKTFMVTCGMYNSSGEFAIKVGIPAKSGVSGGILAAVPGRCGIGVFGPALDDKGNSLTGVKLLERLSKTYSLSIF 308
                                    13        23        33        43        53        63        73        83        |-         -    |  113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303     
                                                                                                                   92             108                                                                                                                                                                                                        


Chain C from PDB  Type:PROTEIN  Length:288
 aligned with GLSA_GEOKA | Q5KY26 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:304
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303    
           GLSA_GEOKA     4 YNQEELVRFVEEAKQYARYGKVADYIPALGKANPNELSIAIYTPDDEVVSAGDVTVKVTLQSISKIIALALVLIDRGEDEVFHKVGMEPTDYPFHSIAKLEEKPAKPLNPMINAGALVVTSMIQGGSVSERLERLLAFVRRLAGNERISYSDEVARSEFETAFLNRSLCYFLKQHRIIDEDVEELMELYTKQCAIEMTCIDLARIGLVLALDGRDPHSSEPLMPLDVARICKTFMVTCGMYNSSGEFAIKVGIPAKSGVSGGILAAVPGRCGIGVFGPALDDKGNSLTGVKLLERLSKTYSLSI 307
               SCOP domains d2pbyc_ C: automated matches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2pbyC01 C:4-61,C:200-302                                  2pbyC02 C:62-199  [code=1.10.15                00.10, no name defined]                                                                    2pbyC01 C:4-61,C:200-302 Probable glutaminase ybgj; domain 1                                           ----- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh.....hhhhhhh.....eeeee.....eeeee.....ee...hhhhhhhhhhhhhhhhhhhhhhh....----------------......hhhhhhhhhhh....hhhhhhhhhhhhhhhhhh....eehhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhheeehhhhhhhhhhhhhh............hhhhhhhhhhhhhhh....hhhhhhhhh...eee....eeeeee...eeeeee.........hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pby C   4 YNQEELVRFVEEAKQYARYGKVADYIPALGKANPNELSIAIYTPDDEVVSAGDVTVKVTLQSISKIIALALVLIDRGEDEVFHKVGMEP----------------KPLNPMINAGALVVTSMIQGGSVSERLERLLAFVRRLAGNERISYSDEVARSEFETAFLNRSLCYFLKQHRIIDEDVEELMELYTKQCAIEMTCIDLARIGLVLALDGRDPHSSEPLMPLDVARICKTFMVTCGMYNSSGEFAIKVGIPAKSGVSGGILAAVPGRCGIGVFGPALDDKGNSLTGVKLLERLSKTYSLSI 307
                                    13        23        33        43        53        63        73        83        |-         -     | 113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303    
                                                                                                                   92              109                                                                                                                                                                                                      


Chain D from PDB  Type:PROTEIN  Length:286
 aligned with GLSA_GEOKA | Q5KY26 from UniProtKB/Swiss-Prot  Length:308

    Alignment length:304
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304    
           GLSA_GEOKA     5 NQEELVRFVEEAKQYARYGKVADYIPALGKANPNELSIAIYTPDDEVVSAGDVTVKVTLQSISKIIALALVLIDRGEDEVFHKVGMEPTDYPFHSIAKLEEKPAKPLNPMINAGALVVTSMIQGGSVSERLERLLAFVRRLAGNERISYSDEVARSEFETAFLNRSLCYFLKQHRIIDEDVEELMELYTKQCAIEMTCIDLARIGLVLALDGRDPHSSEPLMPLDVARICKTFMVTCGMYNSSGEFAIKVGIPAKSGVSGGILAAVPGRCGIGVFGPALDDKGNSLTGVKLLERLSKTYSLSIF 308
               SCOP domains d2pbyd_ D: automated matches                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2pbyD01 D:5-61,D:200-302                                 2pbyD02 D:62-199  [code=1.10.15                  00.10, no name defined]                                                                  2pbyD01 D:5-61,D:200-302 Probable glutaminase ybgj; domain 1                                           ------ CATH domains
           Pfam domains (1) ------------------Glutaminase-2pbyD01 D:23-308                                                                                                                                                                                                                                                                   Pfam domains (1)
           Pfam domains (2) ------------------Glutaminase-2pbyD02 D:23-308                                                                                                                                                                                                                                                                   Pfam domains (2)
           Pfam domains (3) ------------------Glutaminase-2pbyD03 D:23-308                                                                                                                                                                                                                                                                   Pfam domains (3)
           Pfam domains (4) ------------------Glutaminase-2pbyD04 D:23-308                                                                                                                                                                                                                                                                   Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.......hhhhh.....eeeee.....eeeee.....ee..hhhhhhhhhhhhhhhhhhhhhhhh....------------------....hhhhhhhhhh.....hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.eehhhhhhhhhhhhhh............hhhhhhhhhhhhhhh....hhhhhhhhh...eee....eeeeee...eeeeee.........hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pby D   5 NQEELVRFVEEAKQYARYGKVADYIPALGKANPNELSIAIYTPDDEVVSAGDVTVKVTLQSISKIIALALVLIDRGEDEVFHKVGMEP------------------LNPMINAGALVVTSMIQGGSVSERLERLLAFVRRLAGNERISYSDEVARSEFETAFLNRSLCYFLKQHRIIDEDVEELMELYTKQCAIEMTCIDLARIGLVLALDGRDPHSSEPLMPLDVARICKTFMVTCGMYNSSGEFAIKVGIPAKSGVSGGILAAVPGRCGIGVFGPALDDKGNSLTGVKLLERLSKTYSLSIF 308
                                    14        24        34        44        54        64        74        84       | -         -      |114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304    
                                                                                                                  92                111
   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/Biological Unit
(-)
Class: Multi-domain proteins (alpha and beta) (2421)

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (GLSA_GEOKA | Q5KY26)
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:0006541    glutamine metabolic process    The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.

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(-) Related Entries Specified in the PDB File

1mki CRYSTAL STRUCTURE OF BACILLUS SUBTILIS PROBABLE GLUTAMINASE, APC1040