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Title :   STRUCTURE OF MUTANT TRYPTOPHAN SYNTHASE ALPHA-SUBUNIT (D110N) FROM A HYPERTHERMOPHILE, PYROCOCCUS FURIOSUS

Authors :   K. Ogasahara, Y. Yamagata, K. Yutani, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   30 Sep 06 (Deposition) - 28 Aug 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.46

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   Tryptophan Synthase Alpha-Subunit, Hyperthermophile, Pyrococcus Furiosus, X-Ray Analysis, Stability, Calorimetry, Lyase, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Ogasahara, Y. Yamagata, K. Yutani
Structures Of Mutant Tryptophan Synthase Alpha-Subunits From A Hyperthermophile, Pyrococcus Furiosus
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - TRYPTOPHAN SYNTHASE ALPHA CHAIN
	Chains	:	A, B
	EC Number	:	4.2.1.20
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PS1974
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TRPA
	Mutation	:	YES
	Organism Scientific	:	PYROCOCCUS FURIOSUS
	Organism Taxid	:	2261
	Synonym	:	TRYPTOPHAN SYNTHASE ALPHA-SUBUNIT

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

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

(no "Site" information available for 2DZU)

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

Asymmetric Unit

No.	Residues
1	Asp A:15	-	Pro A:16
2	Asp B:15	-	Pro B:16

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRP_SYNTHASE_ALPHA	PS00167	Tryptophan synthase alpha chain signature.	TRPA_PYRFU	35-48	2	A:35-48 B:35-48

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRP_SYNTHASE_ALPHA	PS00167	Tryptophan synthase alpha chain signature.	TRPA_PYRFU	35-48	1	A:35-48 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRP_SYNTHASE_ALPHA	PS00167	Tryptophan synthase alpha chain signature.	TRPA_PYRFU	35-48	1	- B:35-48

(no "Exon" information available for 2DZU)

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
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Chain A from PDB  Type:PROTEIN  Length:244
 aligned with TRPA_PYRFU | Q8U094 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:248
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240        
           TRPA_PYRFU     1 MFKDGSLIPYLTAGDPDKQSTLNFLLALDEYAGAIELGIPFSDPIADGKTIQESHYRALKNGFKLREAFWIVKEFRRHSSTPIVLMTYYNPIYRAGVRNFLAEAKASGVDGILVVDLPVFHAKEFTEIAREEGIKTVFLAAPNTPDERLKVIDDMTTGFVYLVSLYGTTGAREEIPKTAYDLLRRAKRICRNKVAVGFGVSKREHVVSLLKEGANGVVVGSALVKIIGEKGREATEFLKKKVEELLGI 248
               SCOP domains d2dzua_ A: Trp synthase alpha-subunit                                                                                                                                                                                                                    SCOP domains
               CATH domains 2dzuA00 A:1-248 Aldolase class I                                                                                                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee....hhhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhh....hhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh..eeeeee....hhhhhhhhhhhh..eeeee.....----...hhhhhhhhhhhhhhh...eeee....hhhhhhhhhhh...eeeehhhhhhhhhhhh..hhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------TRP_SYNTHASE_A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dzu A   1 MFKDGSLIPYLTAGDPDKQSTLNFLLALDEYAGAIELGIPFSDPIADGKTIQESHYRALKNGFKLREAFWIVKEFRRHSSTPIVLMTYYNPIYRAGVRNFLAEAKASGVNGILVVDLPVFHAKEFTEIAREEGIKTVFLAAPNTPDERLKVIDDMTTGFVYLVSLYGT----EEIPKTAYDLLRRAKRICRNKVAVGFGVSKREHVVSLLKEGANGVVVGSALVKIIGEKGREATEFLKKKVEELLGI 248
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       | -  |    180       190       200       210       220       230       240        
                                                                                                                                                                                                 168  173

Chain B from PDB  Type:PROTEIN  Length:245
 aligned with TRPA_PYRFU | Q8U094 from UniProtKB/Swiss-Prot  Length:248

    Alignment length:248
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240        
           TRPA_PYRFU     1 MFKDGSLIPYLTAGDPDKQSTLNFLLALDEYAGAIELGIPFSDPIADGKTIQESHYRALKNGFKLREAFWIVKEFRRHSSTPIVLMTYYNPIYRAGVRNFLAEAKASGVDGILVVDLPVFHAKEFTEIAREEGIKTVFLAAPNTPDERLKVIDDMTTGFVYLVSLYGTTGAREEIPKTAYDLLRRAKRICRNKVAVGFGVSKREHVVSLLKEGANGVVVGSALVKIIGEKGREATEFLKKKVEELLGI 248
               SCOP domains d2dzub_ B: Trp synthase alpha-subunit                                                                                                                                                                                                                    SCOP domains
               CATH domains 2dzuB00 B:1-248 Aldolase class I                                                                                                                                                                                                                         CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeee....hhhhhhhhhhhhhhhh..eeee.........hhhhhhhhhhhhhh....hhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhhh.eeeeee....hhhhhhhhhhhh..eeeee......---...hhhhhhhhhhhhh.....eeee....hhhhhhhhhhh...eeeehhhhhhhhhhhh..hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------TRP_SYNTHASE_A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dzu B   1 MFKDGSLIPYLTAGDPDKQSTLNFLLALDEYAGAIELGIPFSDPIADGKTIQESHYRALKNGFKLREAFWIVKEFRRHSSTPIVLMTYYNPIYRAGVRNFLAEAKASGVNGILVVDLPVFHAKEFTEIAREEGIKTVFLAAPNTPDERLKVIDDMTTGFVYLVSLYGTT---EEIPKTAYDLLRRAKRICRNKVAVGFGVSKREHVVSLLKEGANGVVVGSALVKIIGEKGREATEFLKKKVEELLGI 248
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160        |-  |    180       190       200       210       220       230       240        
                                                                                                                                                                                                  169 173

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Ribulose-phoshate binding barrel (356)

Family: Tryptophan biosynthesis enzymes (108)

Protein domain: Trp synthase alpha-subunit (62)

Pyrococcus furiosus [TaxId: 2261] (10)

1a	d2dzua_	A:
1b	d2dzub_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Pyrococcus furiosus. Organism_taxid: 2261. (11)

1a	2dzuB00	B:1-248
1b	2dzuA00	A:1-248

(no "Pfam Domain" information available for 2DZU)

Asymmetric Unit(hide GO term definitions)

Chain A,B (TRPA_PYRFU | Q8U094)

molecular function
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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:0004834	tryptophan synthase activity	Catalysis of the reaction: L-serine + (1S,2R)-1-C-(indol-3-yl)glycerol 3-phosphate = L-tryptophan + glyceraldehyde 3-phosphate + H2O.
biological process
	GO:0009073	aromatic amino acid family biosynthetic process	The chemical reactions and pathways resulting in the formation of aromatic amino acid family, amino acids with aromatic ring (phenylalanine, tyrosine, tryptophan).
	GO:0008652	cellular amino acid biosynthetic process	The chemical reactions and pathways resulting in the formation of amino acids, organic acids containing one or more amino substituents.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0000162	tryptophan biosynthetic process	The chemical reactions and pathways resulting in the formation of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid; tryptophan is synthesized from chorismate via anthranilate.
	GO:0006568	tryptophan metabolic process	The chemical reactions and pathways involving tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3-yl)propanoic acid.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2dzu)

	Sites
(no "Sites" information available for 2dzu)

	Cis Peptide Bonds
		Asp A:15 - Pro A:16	[ RasMol ]
		Asp B:15 - Pro B:16	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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	2dzu
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	TRPA_PYRFU \| Q8U094
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	4.2.1.20
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	TRPA_PYRFU \| Q8U094
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UniProtKB/Swiss-Prot
	TRPA_PYRFU \| Q8U094	:	1geq 1wdw 2dzp 2dzs 2dzt 2dzv 2dzw 2dzx 2e09 5e0k

1geq	WILD-TYPE
2dzp	THE SAME PROTEIN, D17N MUTANT
2dzs	THE SAME PROTEIN, E103A MUTANT
2dzt	THE SAME PROTEIN, D110A MUTANT
2dzv	THE SAME PROTEIN, D146A MUTANT
2dzw	THE SAME PROTEIN, E244A MUTANT
2dzx	THE SAME PROTEIN, E131A,E132A MUTANT RELATED ID: MY_001000046.5 RELATED DB: TARGETDB

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Cis Peptide Bonds (2, 2)

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