1K3U - JenaLib

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Title :   CRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE COMPLEXED WITH N-[1H-INDOL-3-YL-ACETYL]ASPARTIC ACID

Authors :   M. Weyand, I. Schlichting, A. Marabotti, A. Mozzarelli

Date :   04 Oct 01 (Deposition) - 03 Jul 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Carbon-Oxygen Lyase, Tryptophan Biosynthesis, Pyridoxal Phosphate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Weyand, I. Schlichting, A. Marabotti, A. Mozzarelli
Crystal Structures Of A New Class Of Allosteric Effectors Complexed To Tryptophan Synthase.
J. Biol. Chem. V. 277 10647 2002
PubMed-ID: 11756456 | Reference-DOI: 10.1074/JBC.M111285200

Molecule 1 - TRYPTOPHAN SYNTHASE ALPHA CHAIN
	Chains	:	A
	EC Number	:	4.2.1.20
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSTB7
	Expression System Strain	:	CB149
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TRPA/TRPB
	Organism Scientific	:	SALMONELLA TYPHIMURIUM
	Organism Taxid	:	602

Molecule 2 - TRYPTOPHAN SYNTHASE BETA CHAIN
	Chains	:	B
	EC Number	:	4.2.1.20
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSTB7
	Expression System Strain	:	CB149
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TRPA/TRPB
	Organism Scientific	:	SALMONELLA TYPHIMURIUM
	Organism Taxid	:	602

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 3)

No.	Name	Count	Type	Full Name
1	IAD	1	Ligand/Ion	N-[1H-INDOL-3-YL-ACETYL]ASPARTIC ACID
2	NA	1	Ligand/Ion	SODIUM ION
3	PLP	1	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Biological Unit 1 (2, 4)

No.	Name	Count	Type	Full Name
1	IAD	2	Ligand/Ion	N-[1H-INDOL-3-YL-ACETYL]ASPARTIC ACID
2	NA	-1	Ligand/Ion	SODIUM ION
3	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY B:232 , PHE B:306 , SER B:308 , HOH B:828 , HOH B:870	BINDING SITE FOR RESIDUE NA B 803
2	AC2	SOFTWARE	PHE A:22 , ASP A:60 , ILE A:64 , LEU A:100 , TYR A:175 , THR A:183 , GLY A:184 , GLY A:211 , PHE A:212 , GLY A:213 , ILE A:214 , ILE A:232 , SER A:233 , GLY A:234 , SER A:235 , HOH A:857	BINDING SITE FOR RESIDUE IAD A 801
3	AC3	SOFTWARE	ALA B:85 , HIS B:86 , LYS B:87 , THR B:190 , CYS B:230 , GLY B:232 , GLY B:233 , GLY B:234 , SER B:235 , ASN B:236 , GLY B:303 , GLU B:350 , SER B:377 , GLY B:378 , HOH B:804 , HOH B:816 , HOH B:848	BINDING SITE FOR RESIDUE PLP B 802

(no "SS Bond" information available for 1K3U)

Asymmetric Unit

No.	Residues
1	Asp A:27	-	Pro A:28
2	Arg B:55	-	Pro B:56
3	His B:195	-	Pro B:196

(no "SAP(SNP)/Variant" information available for 1K3U)

Asymmetric Unit (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRP_SYNTHASE_ALPHA	PS00167	Tryptophan synthase alpha chain signature.	TRPA_SALTY	48-61	1	A:48-61
2	TRP_SYNTHASE_BETA	PS00168	Tryptophan synthase beta chain pyridoxal-phosphate attachment site.	TRPB_SALTY	80-94	1	B:80-94

Biological Unit 1 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRP_SYNTHASE_ALPHA	PS00167	Tryptophan synthase alpha chain signature.	TRPA_SALTY	48-61	2	A:48-61
2	TRP_SYNTHASE_BETA	PS00168	Tryptophan synthase beta chain pyridoxal-phosphate attachment site.	TRPB_SALTY	80-94	2	B:80-94

(no "Exon" information available for 1K3U)

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:268
 aligned with TRPA_SALTY | P00929 from UniProtKB/Swiss-Prot  Length:268

    Alignment length:268
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260        
           TRPA_SALTY     1 MERYENLFAQLNDRREGAFVPFVTLGDPGIEQSLKIIDTLIDAGADALELGVPFSDPLADGPTIQNANLRAFAAGVTPAQCFEMLALIREKHPTIPIGLLMYANLVFNNGIDAFYARCEQVGVDSVLVADVPVEESAPFRQAALRHNIAPIFICPPNADDDLLRQVASYGRGYTYLLSRSGVTGAENRGALPLHHLIEKLKEYHAAPALQGFGISSPEQVSAAVRAGAAGAISGSAIVKIIEKNLASPKQMLAELRSFVSAMKAASRA 268
               SCOP domains d1k3ua_ A: Trp synthase alpha-subunit                                                                                                                                                                                                                                        SCOP domains
               CATH domains 1k3uA00 A:1-268 Aldolase class I                                                                                                                                                                                                                                             CATH domains
               Pfam domains -------Trp_syntA-1k3uA01 A:8-267                                                                                                                                                                                                                                           - Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhhhhh....eeee.........hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh....eeeeehhhhhhh.hhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh..eee.ee....hhhhhhhhhhhh...eeee...............hhhhhhhhhhh....eeee....hhhhhhhhhhh...eeeehhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------TRP_SYNTHASE_A--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k3u A   1 MERYENLFAQLNDRREGAFVPFVTLGDPGIEQSLKIIDTLIDAGADALELGVPFSDPLADGPTIQNANLRAFAAGVTPAQCFEMLALIREKHPTIPIGLLMYANLVFNNGIDAFYARCEQVGVDSVLVADVPVEESAPFRQAALRHNIAPIFICPPNADDDLLRQVASYGRGYTYLLSRSGVTGAENRGALPLHHLIEKLKEYHAAPALQGFGISSPEQVSAAVRAGAAGAISGSAIVKIIEKNLASPKQMLAELRSFVSAMKAASRA 268
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260

Chain B from PDB  Type:PROTEIN  Length:394
 aligned with TRPB_SALTY | P0A2K1 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:394
                                    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       311       321       331       341       351       361       371       381       391    
           TRPB_SALTY     2 TTLLNPYFGEFGGMYVPQILMPALNQLEEAFVSAQKDPEFQAQFADLLKNYAGRPTALTKCQNITAGTRTTLYLKREDLLHGGAHKTNQVLGQALLAKRMGKSEIIAETGAGQHGVASALASALLGLKCRIYMGAKDVERQSPNVFRMRLMGAEVIPVHSGSATLKDACNEALRDWSGSYETAHYMLGTAAGPHPYPTIVREFQRMIGEETKAQILDKEGRLPDAVIACVGGGSNAIGMFADFINDTSVGLIGVEPGGHGIETGEHGAPLKHGRVGIYFGMKAPMMQTADGQIEESYSISAGLDFPSVGPQHAYLNSIGRADYVSITDDEALEAFKTLCRHEGIIPALESSHALAHALKMMREQPEKEQLLVVNLSGRGDKDIFTVHDILKARG 395
               SCOP domains d1k3ub_ B: Tryptophan synthase, beta-subunit                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------1k3uB01 B:9-53,B:87-205                      1k3uB02 B:54-86,B:206-391        1k3uB01 B:9-53,B:87-205  [code=3.40.50.1100, no name defined]                                                          1k3uB02 B:54-86,B:206-391  [code=3.40.50.1100, no name defined]                                                                                                                           ---- CATH domains
               Pfam domains ------------------------------------------------PALP-1k3uB01 B:50-378                                                                                                                                                                                                                                                                                                                    ----------------- Pfam domains
         Sec.struct. author ......ee..eeeee.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeehhhhhh...eeeeeee.hhh.....hhhhhhhhhhhhhhh...eeeeee..hhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhh..eee.........hhhhhhhhh.hhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh.....eeeeeeeee.hhhhh...hhhhhheeeee.eeeeee.......................hhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------TRP_SYNTHASE_BE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1k3u B   2 TTLLNPYFGEFGGMYVPQILMPALNQLEEAFVSAQKDPEFQAQFADLLKNYAGRPTALTKCQNITAGTRTTLYLKREDLLHGGAHKTNQVLGQALLAKRMGKSEIIAETGAGQHGVASALASALLGLKCRIYMGAKDVERQSPNVFRMRLMGAEVIPVHSGSATLKDACNEALRDWSGSYETAHYMLGTAAGPHPYPTIVREFQRMIGEETKAQILDKEGRLPDAVIACVGGGSNAIGMFADFINDTSVGLIGVEPGGHGIETGEHGAPLKHGRVGIYFGMKAPMMQTADGQIEESYSISAGLDFPSVGPQHAYLNSIGRADYVSITDDEALEAFKTLCRHEGIIPALESSHALAHALKMMREQPEKEQLLVVNLSGRGDKDIFTVHDILKARG 395
                                    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       311       321       331       341       351       361       371       381       391

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.1100, no name defined] (77)

Salmonella typhimurium. Organism_taxid: 602. (9)

1a	1k3uB01	B:9-53,B:87-205
1b	1k3uB02	B:54-86,B:206-391

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Salmonella typhimurium. Organism_taxid: 602. (13)

1k3uA00

A:1-268

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: TIM_barrel (694)

Family: Trp_syntA (28)

Salmonella typhimurium (21)

Trp_syntA-1k3uA01

A:8-267

Clan: no clan defined [family: PALP] (67)

Family: PALP (67)

Salmonella typhimurium (25)

PALP-1k3uB01

B:50-378

Asymmetric Unit(hide GO term definitions)

Chain A (TRPA_SALTY | P00929)

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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0030170	pyridoxal phosphate binding	Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
	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.
cellular component
	GO:0009507	chloroplast	A chlorophyll-containing plastid with thylakoids organized into grana and frets, or stroma thylakoids, and embedded in a stroma.
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Chain B (TRPB_SALTY | P0A2K1)

molecular function
	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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0030170	pyridoxal phosphate binding	Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
	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: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.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
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	Cis Peptide Bonds
		Arg B:55 - Pro B:56	[ RasMol ]
		Asp A:27 - Pro A:28	[ RasMol ]
		His B:195 - Pro B:196	[ RasMol ]

Biological Unit
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1k7e	CRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE COMPLEXED WITH N-[1H-INDOL-3-YL-ACETYL]GLYCINE ACID
1k7f	CRYSTAL STRUCTURE OF WILD-TYPE TRYPTOPHAN SYNTHASE COMPLEXED WITH N-[1H-INDOL-3-YL-ACETYL]VALINE ACID

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