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(-) Description

Title :  THREE-DIMENSIONAL STRUCTURE OF YAAE FROM BACILLUS SUBTILIS
 
Authors :  J. A. Bauer, E. M. Bennett, T. P. Begley, S. E. Ealick
Date :  29 Oct 03  (Deposition) - 27 Jan 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Triad Amidotransferase, Glutaminase, Alpha/Beta Protein, Cofactor Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. A. Bauer, E. M. Bennett, T. P. Begley, S. E. Ealick
Three-Dimensional Structure Of Yaae From Bacillus Subtilis, A Glutaminase Implicated In Pyridoxal-5'-Phosphate Biosynthesis.
J. Biol. Chem. V. 279 2704 2004
PubMed-ID: 14585832  |  Reference-DOI: 10.1074/JBC.M310311200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN YAAE
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainB834(DE3)
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneYAAE, BSU00120
    Organism ScientificBACILLUS SUBTILIS
    Organism Taxid1423

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 10)

Asymmetric Unit (1, 10)
No.NameCountTypeFull Name
1MSE10Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 5)
No.NameCountTypeFull Name
1MSE5Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 1R9G)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R9G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R9G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R9G)

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDXT_SNO_2PS51130 PdxT/SNO family profile.PDXT_BACSU3-188
 
  2A:3-188
B:3-188
2PDXT_SNO_1PS01236 PdxT/SNO family family signature.PDXT_BACSU41-51
 
  2A:41-51
B:41-51
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDXT_SNO_2PS51130 PdxT/SNO family profile.PDXT_BACSU3-188
 
  1A:3-188
-
2PDXT_SNO_1PS01236 PdxT/SNO family family signature.PDXT_BACSU41-51
 
  1A:41-51
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDXT_SNO_2PS51130 PdxT/SNO family profile.PDXT_BACSU3-188
 
  1-
B:3-188
2PDXT_SNO_1PS01236 PdxT/SNO family family signature.PDXT_BACSU41-51
 
  1-
B:41-51

(-) Exons   (0, 0)

(no "Exon" information available for 1R9G)

(-) 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:196
 aligned with PDXT_BACSU | P37528 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:196
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190      
           PDXT_BACSU     1 MLTIGVLGLQGAVREHIHAIEACGAAGLVVKRPEQLNEVDGLILPGGESTTMRRLIDTYQFMEPLREFAAQGKPMFGTCAGLIILAKEIAGSDNPHLGLLNVVVERNSFGRQVDSFEADLTIKGLDEPFTGVFIRAPHILEAGENVEVLSEHNGRIVAAKQGQFLGCSFHPELTEDHRVTQLFVEMVEEYKQKALV 196
               SCOP domains d1r9ga_ A: Hypothetical protein YaaE                                                                                                                                                                 SCOP domains
               CATH domains -1r9gA00 A:2-196  [code=3.40.50.880, no name defined]                                                                                                                                                CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee......hhhhhhhhhhh..eee...hhhhhhhh.eeee...hhhhhhhhhhhh.hhhhhhhhhhh...eeeehhhhhhhhee.............eeee.........eeeeee........eeeeee...eeeee....eeeeee..eeeeeee..eeee..hhhhh..hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --PDXT_SNO_2  PDB: A:3-188 UniProt: 3-188                                                                                                                                                   -------- PROSITE (1)
                PROSITE (2) ----------------------------------------PDXT_SNO_1 ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r9g A   1 mLTIGVLGLQGAVREHIHAIEACGAAGLVVKRPEQLNEVDGLILPGGESTTmRRLIDTYQFmEPLREFAAQGKPmFGTCAGLIILAKEIAGSDNPHLGLLNVVVERNSFGRQVDSFEADLTIKGLDEPFTGVFIRAPHILEAGENVEVLSEHNGRIVAAKQGQFLGCSFHPELTEDHRVTQLFVEmVEEYKQKALV 196
                            |       10        20        30        40        50 |      60 |      70    |   80        90       100       110       120       130       140       150       160       170       180     | 190      
                            |                                                 52-MSE    62-MSE       75-MSE                                                                                                        186-MSE      
                            1-MSE                                                                                                                                                                                               

Chain B from PDB  Type:PROTEIN  Length:196
 aligned with PDXT_BACSU | P37528 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:196
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190      
           PDXT_BACSU     1 MLTIGVLGLQGAVREHIHAIEACGAAGLVVKRPEQLNEVDGLILPGGESTTMRRLIDTYQFMEPLREFAAQGKPMFGTCAGLIILAKEIAGSDNPHLGLLNVVVERNSFGRQVDSFEADLTIKGLDEPFTGVFIRAPHILEAGENVEVLSEHNGRIVAAKQGQFLGCSFHPELTEDHRVTQLFVEMVEEYKQKALV 196
               SCOP domains d1r9gb_ B: Hypothetical protein YaaE                                                                                                                                                                 SCOP domains
               CATH domains -1r9gB00 B:2-196  [code=3.40.50.880, no name defined]                                                                                                                                                CATH domains
           Pfam domains (1) -----SNO-1r9gB01 B:6-189                                                                                                                                                                     ------- Pfam domains (1)
           Pfam domains (2) -----SNO-1r9gB02 B:6-189                                                                                                                                                                     ------- Pfam domains (2)
         Sec.struct. author ..eeee.....hhhhhhhhhhhh..eee...hhhhhhhh.eeee.....hhhhhhhhh..hhhhhhhhhhh...eeeehhhhhhhhee.............eeee.........eeeeee........eeeeee...eeeee....eeeeee..eeeeeee..eeee.........hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --PDXT_SNO_2  PDB: B:3-188 UniProt: 3-188                                                                                                                                                   -------- PROSITE (1)
                PROSITE (2) ----------------------------------------PDXT_SNO_1 ------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r9g B   1 mLTIGVLGLQGAVREHIHAIEACGAAGLVVKRPEQLNEVDGLILPGGESTTmRRLIDTYQFmEPLREFAAQGKPmFGTCAGLIILAKEIAGSDNPHLGLLNVVVERNSFGRQVDSFEADLTIKGLDEPFTGVFIRAPHILEAGENVEVLSEHNGRIVAAKQGQFLGCSFHPELTEDHRVTQLFVEmVEEYKQKALV 196
                            |       10        20        30        40        50 |      60 |      70    |   80        90       100       110       120       130       140       150       160       170       180     | 190      
                            1-MSE                                             52-MSE    62-MSE       75-MSE                                                                                                        186-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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Family: SNO (5)
1aSNO-1r9gB01B:6-189
1bSNO-1r9gB02B:6-189

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (PDXT_BACSU | P37528)
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.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0036381    pyridoxal 5'-phosphate synthase (glutamine hydrolysing) activity    Catalysis of the reaction: D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + L-glutamine = pyridoxal 5'-phosphate + L-glutamate + 3 H2O + phosphate. The reaction occurs in two steps: L-glutamine + H2O = L-glutamate + NH3, and subsequently D-ribose 5-phosphate + D-glyceraldehyde 3-phosphate + NH3 = pyridoxal 5'-phosphate + 4 H2O + phosphate.
biological process
    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.
    GO:0042823    pyridoxal phosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of pyridoxal phosphate, pyridoxal phosphorylated at the hydroxymethyl group of C-5, the active form of vitamin B6.
    GO:0008614    pyridoxine metabolic process    The chemical reactions and pathways involving pyridoxine, 2-methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine, one of the vitamin B6 compounds. Pyridoxal, pyridoxamine and pyridoxine are collectively known as vitamin B6, and are efficiently converted to the biologically active form of vitamin B6, pyridoxal phosphate.
    GO:0042819    vitamin B6 biosynthetic process    The chemical reactions and pathways resulting in the formation of any of the vitamin B6 compounds; pyridoxal, pyridoxamine and pyridoxine and the active form, pyridoxal phosphate.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:1903600    glutaminase complex    A protein complex which is capable of glutaminase activity.

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        PDXT_BACSU | P375282nv0 2nv2

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