2DH5 - JenaLib

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Title :   CRYSTAL STRUCTURE OF E. COLI HOLO-TRPB

Authors :   K. Nishio, Y. Morimoto, K. Ogasahara, K. Yutani, T. Tsukihara, Riken S Genomics/Proteomics Initiative (Rsgi)

Date :   23 Mar 06 (Deposition) - 24 Apr 07 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.90

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

Keywords :   Tryptophan Synthase, Beta-Chain, Plp, 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. Nishio, K. Ogasahara, Y. Morimoto, T. Tsukihara, S. J. Lee, K. Yutan
Large Conformational Changes In The Escherichia Coli Tryptophan Synthase Beta(2) Subunit Upon Pyridoxal 5'-Phosphate Binding
Febs J. V. 277 2157 2010
PubMed-ID: 20370823 | Reference-DOI: 10.1111/J.1742-4658.2010.07631.X

Molecule 1 - TRYPTOPHAN SYNTHASE BETA SUBUNIT
	Chains	:	A
	EC Number	:	4.2.1.20
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PSTECOTB
	Expression System Strain	:	CB149
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	TRYPTOPHAN SYNTHASE BETA-CHAIN

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 4)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	PLP	1	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE
3	SO4	4	Ligand/Ion	SULFATE ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PRO A:23 , ARG A:26 , GLN A:27	BINDING SITE FOR RESIDUE SO4 A 801
2	AC2	SOFTWARE	LYS A:87 , THR A:110 , GLY A:111 , ALA A:112 , GLY A:113 , GLN A:114 , HIS A:115	BINDING SITE FOR RESIDUE SO4 A 802
3	AC3	SOFTWARE	HIS A:86 , LYS A:87 , THR A:190 , CYS A:230 , GLY A:232 , GLY A:233 , GLY A:234 , SER A:235 , ASN A:236 , GLY A:303 , ALA A:348 , GLU A:350 , SER A:377 , GLY A:378	BINDING SITE FOR RESIDUE PLP A 501
4	AC4	SOFTWARE	HIS A:82 , GLY A:83 , VAL A:117 , ILE A:345 , ILE A:346 , ARG A:379 , ASP A:381	BINDING SITE FOR RESIDUE GOL A 901

(no "SS Bond" information available for 2DH5)

Asymmetric Unit

No.	Residues
1	Arg A:55	-	Pro A:56
2	His A:195	-	Pro A:196

Asymmetric Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TRPB_ECOLI_001 *	G	281	R	TRPB_ECOLI	---	---	A	G	281	R
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TRPB_ECOLI_001 *	G	281	R	TRPB_ECOLI	---	---	A	G	281	R
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRP_SYNTHASE_BETA	PS00168	Tryptophan synthase beta chain pyridoxal-phosphate attachment site.	TRPB_ECOLI	80-94	1	A:80-94

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	TRP_SYNTHASE_BETA	PS00168	Tryptophan synthase beta chain pyridoxal-phosphate attachment site.	TRPB_ECOLI	80-94	2	A:80-94

(no "Exon" information available for 2DH5)

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:393
 aligned with TRPB_ECOLI | P0A879 from UniProtKB/Swiss-Prot  Length:397

    Alignment length:395
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392     
           TRPB_ECOLI     3 TLLNPYFGEFGGMYVPQILMPALRQLEEAFVSAQKDPEFQAQFNDLLKNYAGRPTALTKCQNITAGTNTTLYLKREDLLHGGAHKTNQVLGQALLAKRMGKTEIIAETGAGQHGVASALASALLGLKCRIYMGAKDVERQSPNVFRMRLMGAEVIPVHSGSATLKDACNEALRDWSGSYETAHYMLGTAAGPHPYPTIVREFQRMIGEETKAQILEREGRLPDAVIACVGGGSNAIGMFADFINETNVGLIGVEPGGHGIETGEHGAPLKHGRVGIYFGMKAPMMQTEDGQIEESYSISAGLDFPSVGPQHAYLNSTGRADYVSITDDEALEAFKTLCLHEGIIPALESSHALAHALKMMRENPDKEQLLVVNLSGRGDKDIFTVHDILKARGEI 397
               SCOP domains d2dh5a_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ------2dh5A01 A:9-53,A:87-205                      2dh5A02 A:54-86,A:206-391        2dh5A01 A:9-53,A:87-205  [code=3.40.50.1100, no name defined]                                                          2dh5A02 A:54-86,A:206-391  [code=3.40.50.1100, no name defined]                                                                                                                           ------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....ee..ee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeehhhhhh...eeeeeee.hhh....hhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhh..eeeeeeehhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhhh..eee.........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhh.....eeeeeeeee.........hhhhhheeeee..eeeee....--.................hhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh.....eeeeeee...hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------R-------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------TRP_SYNTHASE_BE--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2dh5 A   3 TLLNPYFGEFGGMYVPQILMPALRQLEEAFVSAQKDPEFQAQFNDLLKNYAGRPTALTKCQNITAGTNTTLYLKREDLLHGGAHKTNQVLGQALLAKRMGKTEIIAETGAGQHGVASALASALLGLKCRIYMGAKDVERQSPNVFRMRLMGAEVIPVHSGSATLKDACNEALRDWSGSYETAHYMLGTAAGPHPYPTIVREFQRMIGEETKAQILEREGRLPDAVIACVGGGSNAIGMFADFINETNVGLIGVEPGGHGIETGEHGAPLKHGRVGIYFGMKAPMMQTE--QIEESYSISAGLDFPSVGPQHAYLNSTGRADYVSITDDEALEAFKTLCLHEGIIPALESSHALAHALKMMRENPDKEQLLVVNLSGRGDKDIFTVHDILKARGEI 397
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       | -|      302       312       322       332       342       352       362       372       382       392     
                                                                                                                                                                                                                                                                                                                         290  |                                                                                                        
                                                                                                                                                                                                                                                                                                                            293

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)

Escherichia coli. Organism_taxid: 562. (4)

1a	2dh5A01	A:9-53,A:87-205
1b	2dh5A02	A:54-86,A:206-391

(no "Pfam Domain" information available for 2DH5)

Asymmetric Unit(hide GO term definitions)

Chain A (TRPB_ECOLI | P0A879)

molecular function
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	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: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.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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	Cis Peptide Bonds
		Arg A:55 - Pro A:56	[ RasMol ]
		His A:195 - Pro A:196	[ RasMol ]

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	2dh5
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	TRPB_ECOLI \| P0A879	:	2dh6

2dh6	APO-TRPB RELATED ID: ECO002001253.1 RELATED DB: TARGETDB

Description

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Ligands, Modified Residues, Ions (3, 4)

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SS Bonds (0, 0)

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