1TLW - JenaLib

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Title :   TSX STRUCTURE COMPLEXED WITH THYMIDINE

Authors :   J. Ye, B. Van Den Berg

Date :   10 Jun 04 (Deposition) - 24 Aug 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.10

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

Keywords :   Nucleoside Transporter, Beta Barrel, Thymidine, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Ye, B. Van Den Berg
Crystal Structure Of The Bacterial Nucleoside Transporter Tsx.
Embo J. V. 23 3187 2004
PubMed-ID: 15272310 | Reference-DOI: 10.1038/SJ.EMBOJ.7600330
(for further references see the PDB file header)

Molecule 1 - NUCLEOSIDE-SPECIFIC CHANNEL-FORMING PROTEIN TSX
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBAD
	Expression System Strain	:	C43
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	TSX, NUPA, B0411, Z0512, ECS0464, SF0348, S0356
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	THM	4	Ligand/Ion	THYMIDINE

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	THM	2	Ligand/Ion	THYMIDINE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	THM	2	Ligand/Ion	THYMIDINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	PHE A:27 , ARG A:32 , TYR A:53 , ASP A:55 , PHE A:77 , GLU A:79 , ILE A:109	BINDING SITE FOR RESIDUE THM A 798
2	AC2	SOFTWARE	PHE B:27 , ARG B:32 , TYR B:36 , ASP B:55 , PHE B:77 , GLU B:79 , ILE B:109	BINDING SITE FOR RESIDUE THM B 799
3	AC3	SOFTWARE	GLU A:38 , TYR A:51 , TYR A:53 , LYS A:168 , PHE A:186 , ILE A:219 , ARG A:234	BINDING SITE FOR RESIDUE THM A 800
4	AC4	SOFTWARE	GLU B:38 , TYR B:51 , TYR B:53 , LYS B:168 , PHE B:186 , ARG B:234	BINDING SITE FOR RESIDUE THM B 801

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

(no "Cis Peptide Bond" information available for 1TLW)

Asymmetric Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TSX_ECOLI_001 *	N	276	Y	TSX_ECOLI	---	---	A/B	N	254	Y
	* ID not provided by source

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

Biological Unit 1 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TSX_ECOLI_001 *	N	276	Y	TSX_ECOLI	---	---	A	N	254	Y
	* ID not provided by source

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

Biological Unit 2 (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_TSX_ECOLI_001 *	N	276	Y	TSX_ECOLI	---	---	B	N	254	Y
	* ID not provided by source

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

(no "PROSITE Motif" information available for 1TLW)

(no "Exon" information available for 1TLW)

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:251
 aligned with TSX_ECOLI | P0A927 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:267
                                                                                                                                                                                                                                                                                                 294   
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290   |   
            TSX_ECOLI    31 LSDWWHQSVNVVGSYHTRFGPQIRNDTYLEYEAFAKKDWFDFYGYADAPVFFGGNSDAKGIWNHGSPLFMEIEPRFSIDKLTNTDLSFGPFKEWYFANNYIYDMGRNKDGRQSTWYMGLGTDIDTGLPMSLSMNVYAKYQWQNYGAANENEWDGYRFKIKYFVPITDLWGGQLSYIGFTNFDWGSDLGDDSGNAINGIKTRTNNSIASSHILALNYDHWHYSVVARYWHDGGQWNDDAELNFGNGNFNVRSTGWGGYLVVGYNF---   -
               SCOP domains d1tlwa_ A: Nucleoside-specific channel-forming pro                tein tsx (NupA)                                                                                                                                                                                           SCOP domains
               CATH domains 1tlwA00 A:9-275 Tsx-like channel                                                                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeee...........eeeeeeeeeee..eeeeeeeeee.----------------..eeeeeeeeehhhhhh.......eeeeeeeeeeeee........eeeeeeeeeeee......eeeeeeeeeeeeee.......eeeeeeeeeeeeeeeeee..eeeeeeeeeeeee.....................eeeeeeeeeee...eeeeeeeeeeehhhhh....ee......ee....eeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y--------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1tlw A   9 LSDWWHQSVNVVGSYHTRFGPQIRNDTYLEYEAFAKKDWFDFYGYADAPV----------------PLFMEIEPRFSIDKLTNTDLSFGPFKEWYFANNYIYDMGRNKDGRQSTWYMGLGTDIDTGLPMSLSMNVYAKYQWQNYGAANENEWDGYRFKIKYFVPITDLWGGQLSYIGFTNFDWGSDLGDDSGNAINGIKTRTNNSIASSHILALNYDHWHYSVVARYWHDGGQWNDDAELNFGNGNFNVRSTGWGGYLVVGYNFHHH 275
                                    18        28        38        48        58         -      | 78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       
                                                                            58               75

Chain B from PDB  Type:PROTEIN  Length:248
 aligned with TSX_ECOLI | P0A927 from UniProtKB/Swiss-Prot  Length:294

    Alignment length:264
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290    
            TSX_ECOLI    31 LSDWWHQSVNVVGSYHTRFGPQIRNDTYLEYEAFAKKDWFDFYGYADAPVFFGGNSDAKGIWNHGSPLFMEIEPRFSIDKLTNTDLSFGPFKEWYFANNYIYDMGRNKDGRQSTWYMGLGTDIDTGLPMSLSMNVYAKYQWQNYGAANENEWDGYRFKIKYFVPITDLWGGQLSYIGFTNFDWGSDLGDDSGNAINGIKTRTNNSIASSHILALNYDHWHYSVVARYWHDGGQWNDDAELNFGNGNFNVRSTGWGGYLVVGYNF 294
               SCOP domains d1tlwb_ B: Nucleoside-specific channel-forming pro                tein tsx (NupA)                                                                                                                                                                                        SCOP domains
               CATH domains 1tlwB00 B:9-272 Tsx-like channel                                                                                                                                                                                                                                         CATH domains
           Pfam domains (1) Channel_Tsx-1tlwB01 B:9-272                                                                                                                                                                                                                                              Pfam domains (1)
           Pfam domains (2) Channel_Tsx-1tlwB02 B:9-272                                                                                                                                                                                                                                              Pfam domains (2)
         Sec.struct. author .....eeeeeeeeee...........eeeeeeeeeee..eeeeeeeeee.----------------..eeeeeeeeehhhhhh.......eeeeeeeeeeeee........eeeeeeeeeeee......eeeeeeeeeeeeee.......eeeeeeeeeeeeeeeeee..eeeeeeeeeeeee.....................eeeeeeeeeee...eeeeeeeeeeehhhhh....ee......ee....eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1tlw B   9 LSDWWHQSVNVVGSYHTRFGPQIRNDTYLEYEAFAKKDWFDFYGYADAPV----------------PLFMEIEPRFSIDKLTNTDLSFGPFKEWYFANNYIYDMGRNKDGRQSTWYMGLGTDIDTGLPMSLSMNVYAKYQWQNYGAANENEWDGYRFKIKYFVPITDLWGGQLSYIGFTNFDWGSDLGDDSGNAINGIKTRTNNSIASSHILALNYDHWHYSVVARYWHDGGQWNDDAELNFGNGNFNVRSTGWGGYLVVGYNF 272
                                    18        28        38        48        58         -      | 78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268    
                                                                            58               75

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Membrane and cell surface proteins and peptides (2046)

Fold: Transmembrane beta-barrels (143)

Superfamily: Tsx-like channel (3)

Family: Tsx-like channel (3)

Protein domain: Nucleoside-specific channel-forming protein tsx (NupA) (3)

Escherichia coli [TaxId: 562] (3)

1a	d1tlwa_	A:
1b	d1tlwb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Outer membrane phospholipase (ompla); Chain C (12)

Homologous Superfamily: Tsx-like channel (3)

Escherichia coli. Organism_taxid: 562. (3)

1a	1tlwA00	A:9-275
1b	1tlwB00	B:9-272

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: MBB (97)

Family: Channel_Tsx (3)

Escherichia coli (strain K12) (3)

1a	Channel_Tsx-1tlwB01	B:9-272
1b	Channel_Tsx-1tlwB02	B:9-272

Asymmetric Unit(hide GO term definitions)

Chain A,B (TSX_ECOLI | P0A927)

molecular function
	GO:0005337	nucleoside transmembrane transporter activity	Enables the transfer of a nucleoside, a nucleobase linked to either beta-D-ribofuranose (ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleotide) from one side of a membrane to the other.
	GO:0015471	nucleoside-specific channel forming porin activity	Enables the energy independent passage of nucleoside, sized less than 1000 Da, across a membrane. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria.
	GO:0015288	porin activity	Catalysis of the transfer of substances, sized less than 1000 Da, from one side of the membrane to the other. The transmembrane portions of porins consist exclusively of beta-strands which form a beta-barrel. They are found in the outer membranes of Gram-negative bacteria, mitochondria, plastids and possibly acid-fast Gram-positive bacteria.
biological process
	GO:0006811	ion transport	The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:1901642	nucleoside transmembrane transport	The directed movement of nucleoside across a membrane.
	GO:0015858	nucleoside transport	The directed movement of a nucleoside, a nucleobase linked to either beta-D-ribofuranose (ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleotide), into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
	GO:0055085	transmembrane transport	The process in which a solute is transported across a lipid bilayer, from one side of a membrane to the other
	GO:0006810	transport	The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
cellular component
	GO:0009279	cell outer membrane	A lipid bilayer that forms the outermost membrane of the cell envelope; enriched in polysaccharide and protein; the outer leaflet of the membrane contains specific lipopolysaccharide structures.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0046930	pore complex	Any small opening in a membrane that allows the passage of gases and/or liquids.

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Description

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