1X1Q - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF TRYPTOPHAN SYNTHASE BETA CHAIN FROM THERMUS THERMOPHILUS HB8

Authors :   Y. Asada, N. Kunishima, Riken Structural Genomics/Proteomics Ini (Rsgi)

Date :   11 Apr 05 (Deposition) - 01 Aug 06 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym./Biol. Unit : A,B

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

Reference :   Y. Asada, N. Kunishima
Crystal Structure Of Tryptophan Synthase Beta Chain From Thermus Thermophilus Hb8
To Be Published
PubMed: search

Molecule 1 - TRYPTOPHAN SYNTHASE BETA CHAIN
	Chains	:	A, B
	EC Number	:	4.2.1.20
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11A
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	300852
	Strain	:	HB8

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 16)

No.	Name	Count	Type	Full Name
1	CL	1	Ligand/Ion	CHLORIDE ION
2	MSE	15	Mod. Amino Acid	SELENOMETHIONINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SER A:257 , ALA A:259 , ILE A:260 , HIS A:337	BINDING SITE FOR RESIDUE CL A 1001

(no "SS Bond" information available for 1X1Q)

Asymmetric/Biological Unit

No.	Residues
1	Leu A:23	-	Pro A:24
2	Arg A:76	-	Pro A:77
3	His A:217	-	Pro A:218
4	Leu B:23	-	Pro B:24
5	Arg B:76	-	Pro B:77
6	His B:217	-	Pro B:218

(no "SAP(SNP)/Variant" information available for 1X1Q)

Asymmetric/Biological Unit (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_THET2	88-102	2	A:102-116 B:102-116

(no "Exon" information available for 1X1Q)

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:385
 aligned with TRPB_THET2 | P16609 from UniProtKB/Swiss-Prot  Length:404

    Alignment length:401
                                    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       401 
           TRPB_THET2     2 LTLPDFPLPDARGRFGPYGGRYVPETLIPALEELEAAYREAKKDPAFLEELDHYLRQFAGRPTPLYHAKRLSEYWGGAQVFLKREDLLHTGAHKINNTLGQALLARRMGKRRVIAETGAGQHGVSVATVAALFGLECVVYMGEEDVRRQALNVFRMKLLGAEVRPVAAGSRTLKDATNEAIRDWITNVRTTFYILGSVVGPHPYPMMVRDFQSVIGEEVKRQSLELFGRLPDALIAAVGGGSNAIGLFAPFAYLPEGRPKLIGVEAAGEGLSTGRHAASIGAGKRGVLHGSYMYLLYDHDGQITPAHSVSAGLDYPGVGPEHSYYADAGVAEYASVTDEEALEGFKLLARLEGIIPALESAHAIAYAAKVVPEMDKDQVVVINLSGRGDKDVTEVMRLLGG 402
               SCOP domains d1x1qa_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains --------------1x1qA01 A:30-74,A:109-227                    1x1qA02 A:75-108,A:228-410        1x1qA01 A:30-74,A:109-227  [code=3.40.50.1100, no name defined]                                                        1x1qA02 A:75-108,A:228-410  [code=3.40.50.1100, no name defined]                                                                                                                       ------ CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............ee..ee.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeehhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhhhhhhh.eeeeeeehhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhhhh...eee.........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhh......eeeeeee.......hhhhhhhhhh.eeee..eeee...----------------.....hhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh.......eeeeee..hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------TRP_SYNTHASE_BE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x1q A  16 LTLPDFPLPDARGRFGPYGGRYVPETLIPALEELEAAYREAKKDPAFLEELDHYLRQFAGRPTPLYHAKRLSEYWGGAQVFLKREDLLHTGAHKINNTLGQALLARRmGKRRVIAETGAGQHGVSVATVAALFGLECVVYmGEEDVRRQALNVFRmKLLGAEVRPVAAGSRTLKDATNEAIRDWITNVRTTFYILGSVVGPHPYPmmVRDFQSVIGEEVKRQSLELFGRLPDALIAAVGGGSNAIGLFAPFAYLPEGRPKLIGVEAAGEGLSTGRHAASIGAGKRGVLHGSYmYLLY----------------DYPGVGPEHSYYADAGVAEYASVTDEEALEGFKLLARLEGIIPALESAHAIAYAAKVVPEmDKDQVVVINLSGRGDKDVTEVmRLLGG 416
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155|      165     | 175       185       195       205       215     ||225       235       245       255       265       275       285       295       305  |   |  -         -   |   335       345       355       365       375       385   |   395       405     | 415 
                                                                                                                                     123-MSE                          156-MSE        171-MSE                                           221-MSE                                                                                308-MSE              329                                                         389-MSE               411-MSE 
                                                                                                                                                                                                                                        222-MSE

Chain B from PDB  Type:PROTEIN  Length:354
 aligned with TRPB_THET2 | P16609 from UniProtKB/Swiss-Prot  Length:404

    Alignment length:400
                                    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       401
           TRPB_THET2     2 LTLPDFPLPDARGRFGPYGGRYVPETLIPALEELEAAYREAKKDPAFLEELDHYLRQFAGRPTPLYHAKRLSEYWGGAQVFLKREDLLHTGAHKINNTLGQALLARRMGKRRVIAETGAGQHGVSVATVAALFGLECVVYMGEEDVRRQALNVFRMKLLGAEVRPVAAGSRTLKDATNEAIRDWITNVRTTFYILGSVVGPHPYPMMVRDFQSVIGEEVKRQSLELFGRLPDALIAAVGGGSNAIGLFAPFAYLPEGRPKLIGVEAAGEGLSTGRHAASIGAGKRGVLHGSYMYLLYDHDGQITPAHSVSAGLDYPGVGPEHSYYADAGVAEYASVTDEEALEGFKLLARLEGIIPALESAHAIAYAAKVVPEMDKDQVVVINLSGRGDKDVTEVMRLLG 401
               SCOP domains d1x1qb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1x1qB01 B:16-74,B:109-223                                  1x1qB02 B:75-108,B:224-415        1x1qB01 B:16-74,B:109-223  [code=3.40.50.1100, no name defined]                                                    1x1qB02 B:75-108,B:224-415  [code=3.40.50.1100, no name def                                        ined]                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........................hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh......eeehhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhh..eee.------.hhhhhhhhhhhhhhh...eee.........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhh......eeeeee..----------------------------------------...........hhhhhhhhhhh..eeee.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhh..........eeeee......hhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------TRP_SYNTHASE_BE----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1x1q B  16 LTLPDFPLPDARGRFGPYGGRYVPETLIPALEELEAAYREAKKDPAFLEELDHYLRQFAGRPTPLYHAKRLSEYWGGAQVFLKREDLLHTGAHKINNTLGQALLARRmGKRRVIAETGAGQHGVSVATVAALFGLECVVYmGEEDVRRQALNVFRmKLLGAEVRP------TLKDATNEAIRDWITNVRTTFYILGSVVGPHPYPmmVRDFQSVIGEEVKRQSLELFGRLPDALIAAVGGGSNAIGLFAPFAYLPEGRPKLIGVEAA----------------------------------------SVSAGLDYPGVGPEHSYYADAGVAEYASVTDEEALEGFKLLARLEGIIPALESAHAIAYAAKVVPEmDKDQVVVINLSGRGDKDVTEVmRLLG 415
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155|      165     | 175    |    - |     195       205       215     ||225       235       245       255       265       275      |  -         -         -         -       325       335       345       355       365       375       385   |   395       405     | 415
                                                                                                                                     123-MSE                          156-MSE        171-MSE  180    187                               221-MSE                                                      282                                      323                                                               389-MSE               411-MSE
                                                                                                                                                                                                                                        222-MSE

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/Biological 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)

Thermus thermophilus hb8. Organism_taxid: 300852. Strain: hb8. (1)

1a	1x1qB01	B:16-74,B:109-223
1b	1x1qA01	A:30-74,A:109-227
1c	1x1qB02	B:75-108,B:224-415
1d	1x1qA02	A:75-108,A:228-410

(no "Pfam Domain" information available for 1X1Q)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (TRPB_THET2 | P16609)

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: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.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Arg A:76 - Pro A:77	[ RasMol ]
		Arg B:76 - Pro B:77	[ RasMol ]
		His A:217 - Pro A:218	[ RasMol ]
		His B:217 - Pro B:218	[ RasMol ]
		Leu A:23 - Pro A:24	[ RasMol ]
		Leu B:23 - Pro B:24	[ RasMol ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1x1q
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	TRPB_THET2 \| P16609
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	4.2.1.20
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	TRPB_THET2 \| P16609
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

(no "Entries Sharing at Least One Protein Chain" available for 1X1Q)

(no "Related Entries Specified in the PDB File" available for 1X1Q)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 16)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 2)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (6, 6)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File