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(-) Description

Title :  X-RAY CRYSTALLOGRAPHIC ANALYSIS OF A PREDICTED AMIDOTRANSFERASE FROM B. STEAROTHERMOPHILUS AT 1.9 A RESOLUTION
 
Authors :  D. J. Miller, W. F. Anderson, Midwest Center For Structural Genomics (Mcsg)
Date :  19 Aug 03  (Deposition) - 11 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Yaae, Pdx2, Predicted Glutamine Amidotransferase, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. J. Miller, W. F. Anderson
X-Ray Structure Analysis Of A Predicted Amidotransferase From B. Stearothermophilus At 1. 9 A Resolution
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PREDICTED AMIDOTRANSFERASE
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System StrainBL21-DE3
    Expression System Taxid469008
    Organism ScientificGEOBACILLUS STEAROTHERMOPHILUS
    Organism Taxid1422

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2EDO1Ligand/Ion1,2-ETHANEDIOL
3MSE8Mod. Amino AcidSELENOMETHIONINE
4SO41Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:105 , ASN A:106 , SER A:107 , ARG A:134 , HOH A:512 , HOH A:589BINDING SITE FOR RESIDUE SO4 A 400
2AC2SOFTWAREHOH A:505BINDING SITE FOR RESIDUE CL A 500
3AC3SOFTWARELYS A:122 , VAL A:145 , ASP A:146 , VAL A:147BINDING SITE FOR RESIDUE EDO A 300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Q7R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1Q7R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Q7R)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PDXT_SNO_2PS51130 PdxT/SNO family profile.PDXT_GEOSE2-187  1A:2-187
2PDXT_SNO_1PS01236 PdxT/SNO family family signature.PDXT_GEOSE40-50  1A:40-50

(-) Exons   (0, 0)

(no "Exon" information available for 1Q7R)

(-) 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:202
 aligned with PDXT_GEOSE | P83813 from UniProtKB/Swiss-Prot  Length:196

    Alignment length:202
                                  1                                                                                                                                                                                                   
                                  |  4        14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194  
           PDXT_GEOSE     - ------MKIGVLGLQGAVREHVRAIEACGAEAVIVKKSEQLEGLDGLVLPGGESTTXRRLIDRYGLXEPLKQFAAAGKPXFGTCAGLILLAKRIVGYDEPHLGLXDITVERNSFGRQRESFEAELSIKGVGDGFVGVFIRAPHIVEAGDGVDVLATYNDRIVAARQGQFLGCSFHPELTDDHRLXQYFLNXVKEAKXASSLK 196
               SCOP domains d1q7ra_ A: Hypothetical protein YaaE                                                                                                                                                                       SCOP domains
               CATH domains 1q7rA00 A:-5-196  [code=3.40.50.880, no name defined]                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eeeee.hhhhhhhhhhhhhhh..eeeee.hhhhhh...eeee...hhhhhhhhhhhh.hhhhhhhhhhh...eeee.hhhhhheeeee.........eeeeeehhhhhh....eeeeeee...eeeeeeee....eeeee....eeeeee..eeeeeee..eeee..hhhhh..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------PDXT_SNO_2  PDB: A:2-187 UniProt: 2-187                                                                                                                                                   --------- PROSITE (1)
                PROSITE (2) ---------------------------------------------PDXT_SNO_1 -------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1q7r A  -5 LYFQSNmKIGVLGLQGAVREHVRAIEACGAEAVIVKKSEQLEGLDGLVLPGGESTTmRRLIDRYGLmEPLKQFAAAGKPmFGTCAGLILLAKRIVGYDEPHLGLmDITVERNSFGRQRESFEAELSIKGVGDGFVGVFIRAPHIVEAGDGVDVLATYNDRIVAARQGQFLGCSFHPELTDDHRLmQYFLNmVKEAKmASSLK 196
                                  |  4        14        24        34        44      | 54      | 64        74        84        94    |  104       114       124       134       144       154       164       174    |  184|     |194  
                                  1-MSE                                            51-MSE    61-MSE       74-MSE                   99-MSE                                                                         179-MSE |     |     
                                                                                                                                                                                                                        185-MSE |     
                                                                                                                                                                                                                              191-MSE 

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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Q7R)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PDXT_GEOSE | P83813)
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: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.

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