2THI - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   THIAMINASE I FROM BACILLUS THIAMINOLYTICUS

Authors :   N. Campobasso, T. P. Begley, S. E. Ealick

Date :   17 Sep 98 (Deposition) - 07 Oct 99 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Thiamine Degradation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Campobasso, C. A. Costello, C. Kinsland, T. P. Begley, S. E. Ealick
Crystal Structure Of Thiaminase-I From Bacillus Thiaminolyticus At 2. 0 A Resolution.
Biochemistry V. 37 15981 1998
PubMed-ID: 9843405 | Reference-DOI: 10.1021/BI981673L
(for further references see the PDB file header)

Molecule 1 - THIAMINASE I
	Chains	:	A, B
	EC Number	:	2.5.1.2
	Engineered	:	YES
	Organism Scientific	:	PAENIBACILLUS THIAMINOLYTICUS
	Organism Taxid	:	49283

		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, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	SO4	-1	Ligand/Ion	SULFATE ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	SO4	1	Ligand/Ion	SULFATE ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:281 , HIS A:282 , GLU A:284 , LEU A:285 , HIS B:282 , PRO B:283 , GLU B:284 , LEU B:285	BINDING SITE FOR RESIDUE SO4 B 380
2	NUC	AUTHOR	CYS A:113	CYS A 113 IS THE ACTIVE SITE NUCLEOPHILE.

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

Asymmetric Unit

No.	Residues
1	Ile A:147	-	Pro A:148
2	Asp A:190	-	Pro A:191
3	Ile B:147	-	Pro B:148
4	Asp B:190	-	Pro B:191

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

(no "PROSITE Motif" information available for 2THI)

(no "Exon" information available for 2THI)

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:362
 aligned with THI1_PANTH | P45741 from UniProtKB/Swiss-Prot  Length:409

    Alignment length:362
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398  
           THI1_PANTH    39 ITLKVAIYPYVPDPARFQAAVLDQWQRQEPGVKLEFTDWDSYSADPPDDLDVFVLDSIFLSHFVDAGYLLPFGSQDIDQAEDVLPFALQGAKRNGEVYGLPQILCTNLLFYRKGDLKIGQVDNIYELYKKIGTSHSEQIPPPQNKGLLINMAGGTTKASMYLEALIDVTGQYTEYDLLPPLDPLNDKVIRGLRLLINMAGEKPSQYVPEDGDAYVRASWFAQGSGRAFIGYSESMMRMGDYAEQVRFKPISSSAGQDIPLFYSDVVSVNSKTAHPELAKKLANVMASADTVEQALRPQADGQYPQYLLPARHQVYEALMQDYPIYSELAQIVNKPSNRVFRLGPEVRTWLKDAKQVLPEALG 400
               SCOP domains d2thia_ A: Thiaminase I                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2thiA01 A:9-116,A:264-330 Periplasmic binding protein-like II                                               2thiA02 A:117-263,A:337-370 Periplasmic binding protein-like II                                                                                    2thiA01 A:9-116,A:264-330 Periplasmic binding protein-like II      ------2thiA02 A:117-263,A:337-370        CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee........hhhhhhhhhhhhhhh....eeee...............eeeeehhhhhhhhh........hhh........hhhhhhh........eeeeee.eeeeee...hhhh....hhhhhhhh...............eee....hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhh.hhhhh.........hhhhhhhh....eeeeehhhhhh.hhhhhheeee.............eeeeeee......hhhhhhhhhhh..hhhhhhhh................hhhhhhhhhh.hhhhhhhhhh...........hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2thi A   9 ITLKVAIYPYVPDPARFQAAVLDQWQRQEPGVKLEFTDWDSYSADPPDDLDVFVLDSIFLSHFVDAGYLLPFGSQDIDQAEDVLPFALQGAKRNGEVYGLPQILCTNLLFYRKGDLKIGQVDNIYELYKKIGTSHSEQIPPPQNKGLLINMAGGTTKASMYLEALIDVTGQYTEYDLLPPLDPLNDKVIRGLRLLINMAGEKPSQYVPEDGDAYVRASWFAQGSGRAFIGYSESMMRMGDYAEQVRFKPISSSAGQDIPLFYSDVVSVNSKTAHPELAKKLANVMASADTVEQALRPQADGQYPQYLLPARHQVYEALMQDYPIYSELAQIVNKPSNRVFRLGPEVRTWLKDAKQVLPEALG 370
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368

Chain B from PDB  Type:PROTEIN  Length:362
 aligned with THI1_PANTH | P45741 from UniProtKB/Swiss-Prot  Length:409

    Alignment length:362
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398  
           THI1_PANTH    39 ITLKVAIYPYVPDPARFQAAVLDQWQRQEPGVKLEFTDWDSYSADPPDDLDVFVLDSIFLSHFVDAGYLLPFGSQDIDQAEDVLPFALQGAKRNGEVYGLPQILCTNLLFYRKGDLKIGQVDNIYELYKKIGTSHSEQIPPPQNKGLLINMAGGTTKASMYLEALIDVTGQYTEYDLLPPLDPLNDKVIRGLRLLINMAGEKPSQYVPEDGDAYVRASWFAQGSGRAFIGYSESMMRMGDYAEQVRFKPISSSAGQDIPLFYSDVVSVNSKTAHPELAKKLANVMASADTVEQALRPQADGQYPQYLLPARHQVYEALMQDYPIYSELAQIVNKPSNRVFRLGPEVRTWLKDAKQVLPEALG 400
               SCOP domains d2thib_ B: Thiaminase I                                                                                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 2thiB01 B:9-116,B:264-330 Periplasmic binding protein-like II                                               2thiB02 B:117-263,B:337-370 Periplasmic binding protein-like II                                                                                    2thiB01 B:9-116,B:264-330 Periplasmic binding protein-like II      ------2thiB02 B:117-263,B:337-370        CATH domains
           Pfam domains (1) -------SBP_bac_1-2thiB01 B:16-300                                                                                                                                                                                                                                                                   ---------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) -------SBP_bac_1-2thiB02 B:16-300                                                                                                                                                                                                                                                                   ---------------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author .eeee........hhhhhhhhhhhhhhh....eeee...............eeeeehhhhhhhhh........hhh........hhhhhhh........eeeeee.eeeeee...hhhh....hhhhhhhh...............eee....hhhhhhhhhhhhhhhh................hhhhhhhhhhhhhh.hhhhh.........hhhhhhhh....eeeeehhhhhh.hhhhhheeeee............eeeeeee......hhhhhhhhhhh..hhhhhhhh................hhhhhhhhhh.hhhhhhhhhh...........hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2thi B   9 ITLKVAIYPYVPDPARFQAAVLDQWQRQEPGVKLEFTDWDSYSADPPDDLDVFVLDSIFLSHFVDAGYLLPFGSQDIDQAEDVLPFALQGAKRNGEVYGLPQILCTNLLFYRKGDLKIGQVDNIYELYKKIGTSHSEQIPPPQNKGLLINMAGGTTKASMYLEALIDVTGQYTEYDLLPPLDPLNDKVIRGLRLLINMAGEKPSQYVPEDGDAYVRASWFAQGSGRAFIGYSESMMRMGDYAEQVRFKPISSSAGQDIPLFYSDVVSVNSKTAHPELAKKLANVMASADTVEQALRPQADGQYPQYLLPARHQVYEALMQDYPIYSELAQIVNKPSNRVFRLGPEVRTWLKDAKQVLPEALG 370
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368

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

Fold: Periplasmic binding protein-like II (813)

Superfamily: Periplasmic binding protein-like II (813)

Family: Phosphate binding protein-like (463)

Protein domain: Thiaminase I (3)

Paenibacillus thiaminolyticus [TaxId: 49283] (3)

1a	d2thia_	A:
1b	d2thib_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: D-Maltodextrin-Binding Protein; domain 2 (600)

Homologous Superfamily: Periplasmic binding protein-like II (486)

Paenibacillus thiaminolyticus. Organism_taxid: 49283 (1)

1a	2thiA01	A:9-116,A:264-330
1b	2thiB01	B:9-116,B:264-330
1c	2thiA02	A:117-263,A:337-370
1d	2thiB02	B:117-263,B:337-370

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PBP (391)

Family: SBP_bac_1 (83)

Paenibacillus thiaminolyticus (Bacillus thiaminolyticus) (2)

1a	SBP_bac_1-2thiB01	B:16-300
1b	SBP_bac_1-2thiB02	B:16-300

Asymmetric Unit(hide GO term definitions)

Chain A,B (THI1_PANTH | P45741)

molecular function
	GO:0050332	thiamine pyridinylase activity	Catalysis of the reaction: pyridine + thiamine = 5-(2-hydroxyethyl)-4-methylthiazole + heteropyrithiamine.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0005215	transporter activity	Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
	GO:0009230	thiamine catabolic process	The chemical reactions and pathways resulting in the breakdown of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
	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.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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	Cis Peptide Bonds
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		Asp B:190 - Pro B:191	[ RasMol ]
		Ile A:147 - Pro A:148	[ RasMol ]
		Ile B:147 - Pro B:148	[ RasMol ]

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	THI1_PANTH \| P45741	:	3thi 4thi

(no "Related Entries Specified in the PDB File" available for 2THI)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

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SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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