2YWD - JenaLib

Title :   CRYSTAL STRUCTURE OF GLUTAMINE AMIDOTRANSFERASE

Authors :   M. Manzoku, A. Ebihara, S. Yokoyama, S. Kuramitsu, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   20 Apr 07 (Deposition) - 23 Oct 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym./Biol. Unit : A

Keywords :   Pyridoxine Biosynthesis, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Manzoku, A. Ebihara, Y. Fujimoto, S. Yokoyama, S. Kuramitsu
Crystal Structure Of Glutamine Amidotransferase
To Be Published
PubMed: search

Compounds

Molecule 1 - GLUTAMINE AMIDOTRANSFERASE SUBUNIT PDXT
	Chains	:	A
	EC Number	:	2.6.-.-
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-11A
	Expression System Strain	:	ROSETTA(DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PDXT
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8
	Synonym	:	GLUTAMINE AMIDOTRANSFERASE GLUTAMINASE SUBUNIT PDXT

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 2)

Exons (0, 0)

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)
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Chain A from PDB  Type:PROTEIN  Length:189
 aligned with PDXT_THET8 | Q5SKD6 from UniProtKB/Swiss-Prot  Length:191

    Alignment length:189
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182         
           PDXT_THET8     3 GVVGVLALQGDFREHKEALKRLGIEAKEVRKKEHLEGLKALIVPGGESTTIGKLAREYGIEDEVRKRVEEGSLALFGTCAGAIWLAKEIVGYPEQPRLGVLEAWVERNAFGRQVESFEEDLEVEGLGSFHGVFIRAPVFRRLGEGVEVLARLGDLPVLVRQGKVLASSFHPELTEDPRLHRYFLELAGV 191
               SCOP domains d2ywda_ A: Hypothetical protein YaaE                                                                                                                                                          SCOP domains
               CATH domains 2ywdA00 A:3-191  [code=3.40.50.880, no name defined]                                                                                                                                          CATH domains
               Pfam domains ----SNO-2ywdA01 A:7-190                                                                                                                                                                     - Pfam domains
         Sec.struct. author ..eeee....hhhhhhhhhhh.....eee.hhhhhh...eeee...hhhhhhhhhhhhhhhhhhhhhhhh...eeeeehhhhhhheeee...........eeeeee.........eeeeeeee...eeeeeeee...eeeee....eeeeee..eeeeeee..eeee..hhhhh..hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -PDXT_SNO_2  PDB: A:4-190 UniProt: 4-190                                                                                                                                                    - PROSITE (1)
                PROSITE (2) ---------------------------------------PDXT_SNO_1 ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ywd A   3 GVVGVLALQGDFREHKEALKRLGIEAKEVRKKEHLEGLKALIVPGGESTTIGKLAREYGIEDEVRKRVEEGSLALFGTCAGAIWLAKEIVGYPEQPRLGVLEAWVERNAFGRQVESFEEDLEVEGLGSFHGVFIRAPVFRRLGEGVEVLARLGDLPVLVRQGKVLASSFHPELTEDPRLHRYFLELAGV 191
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

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		→ 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, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PDXT_THET8 | Q5SKD6)

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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