1YAK - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   COMPLEX OF BACILLUS SUBTILIS TENA WITH 4-AMINO-2-METHYL-5-HYDROXYMETHYLPYRIMIDINE

Authors :   A. V. Toms, A. L. Haas, J. -H. Park, T. P. Begley, S. E. Ealick

Date :   17 Dec 04 (Deposition) - 22 Feb 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Thiaminase, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. V. Toms, A. L. Haas, J. H. Park, T. P. Begley, S. E. Ealick
Structural Characterization Of The Regulatory Proteins Tena And Teni From Bacillus Subtilis And Identification Of Tena As A Thiaminase Ii.
Biochemistry V. 44 2319 2005
PubMed-ID: 15709744 | Reference-DOI: 10.1021/BI0478648

Molecule 1 - TRANSCRIPTIONAL ACTIVATOR TENA
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PDESTF1
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	TENA
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (2x)	:	A	B
Biological Unit 2 (2x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 4)

No.	Name	Count	Type	Full Name
1	HMH	4	Ligand/Ion	4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	HMH	4	Ligand/Ion	4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	HMH	4	Ligand/Ion	4-AMINO-5-HYDROXYMETHYL-2-METHYLPYRIMIDINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:44 , TYR A:47 , LEU A:48 , CYS A:135 , TYR A:139 , TYR A:163 , GLU A:205	BINDING SITE FOR RESIDUE HMH A 301
2	AC2	SOFTWARE	ASP D:44 , TYR D:47 , LEU D:48 , CYS D:135 , TYR D:139 , TYR D:163 , GLU D:205	BINDING SITE FOR RESIDUE HMH D 302
3	AC3	SOFTWARE	ASP B:44 , TYR B:47 , CYS B:135 , TYR B:139 , TYR B:163 , GLU B:205	BINDING SITE FOR RESIDUE HMH B 303
4	AC4	SOFTWARE	ASP C:44 , TYR C:47 , CYS C:135 , TYR C:139 , TYR C:163 , GLU C:205 , HOH C:2069	BINDING SITE FOR RESIDUE HMH C 304

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

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

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

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

(no "Exon" information available for 1YAK)

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:219
 aligned with TENA_BACSU | P25052 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:219
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         
           TENA_BACSU     2 KFSEECRSAAAEWWEGSFVHPFVQGIGDGTLPIDRFKYYVLQDSYYLTHFAKVQSFGAAYAKDLYTTGRMASHAQGTYEAEMALHREFAELLEISEEERKAFKPSPTAYSYTSHMYRSVLSGNFAEILAALLPCYWLYYEVGEKLLHCDPGHPIYQKWIGTYGGDWFRQQVEEQINRFDELAENSTEEVRAKMKENFVISSYYEYQFWGMAYRKEGWSD 220
               SCOP domains d1yaka_ A: Transcriptional activator TenA                                                                                                                                                                                   SCOP domains
               CATH domains 1yakA00 A:2-220 Heme Oxygenase; Chain A                                                                                                                                                                                     CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yak A   2 KFSEECRSAAAEWWEGSFVHPFVQGIGDGTLPIDRFKYYVLQDSYYLTHFAKVQSFGAAYAKDLYTTGRMASHAQGTYEAEMALHREFAELLEISEEERKAFKPSPTAYSYTSHMYRSVLSGNFAEILAALLPCYWLYYEVGEKLLHCDPGHPIYQKWIGTYGGDWFRQQVEEQINRFDELAENSTEEVRAKMKENFVISSYYEYQFWGMAYRKEGWSD 220
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

Chain B from PDB  Type:PROTEIN  Length:218
 aligned with TENA_BACSU | P25052 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:218
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211        
           TENA_BACSU     2 KFSEECRSAAAEWWEGSFVHPFVQGIGDGTLPIDRFKYYVLQDSYYLTHFAKVQSFGAAYAKDLYTTGRMASHAQGTYEAEMALHREFAELLEISEEERKAFKPSPTAYSYTSHMYRSVLSGNFAEILAALLPCYWLYYEVGEKLLHCDPGHPIYQKWIGTYGGDWFRQQVEEQINRFDELAENSTEEVRAKMKENFVISSYYEYQFWGMAYRKEGWS 219
               SCOP domains d1yakb_ B: Transcriptional activator TenA                                                                                                                                                                                  SCOP domains
               CATH domains 1yakB00 B:2-219 Heme Oxygenase; Chain A                                                                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yak B   2 KFSEECRSAAAEWWEGSFVHPFVQGIGDGTLPIDRFKYYVLQDSYYLTHFAKVQSFGAAYAKDLYTTGRMASHAQGTYEAEMALHREFAELLEISEEERKAFKPSPTAYSYTSHMYRSVLSGNFAEILAALLPCYWLYYEVGEKLLHCDPGHPIYQKWIGTYGGDWFRQQVEEQINRFDELAENSTEEVRAKMKENFVISSYYEYQFWGMAYRKEGWS 219
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

Chain C from PDB  Type:PROTEIN  Length:220
 aligned with TENA_BACSU | P25052 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:220
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222
           TENA_BACSU     3 FSEECRSAAAEWWEGSFVHPFVQGIGDGTLPIDRFKYYVLQDSYYLTHFAKVQSFGAAYAKDLYTTGRMASHAQGTYEAEMALHREFAELLEISEEERKAFKPSPTAYSYTSHMYRSVLSGNFAEILAALLPCYWLYYEVGEKLLHCDPGHPIYQKWIGTYGGDWFRQQVEEQINRFDELAENSTEEVRAKMKENFVISSYYEYQFWGMAYRKEGWSDSA 222
               SCOP domains d1yakc_ C: Transcriptional activator TenA                                                                                                                                                                                    SCOP domains
               CATH domains 1yakC00 C:3-222 Heme Oxygenase; Chain A                                                                                                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..........hhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yak C   3 FSEECRSAAAEWWEGSFVHPFVQGIGDGTLPIDRFKYYVLQDSYYLTHFAKVQSFGAAYAKDLYTTGRMASHAQGTYEAEMALHREFAELLEISEEERKAFKPSPTAYSYTSHMYRSVLSGNFAEILAALLPCYWLYYEVGEKLLHCDPGHPIYQKWIGTYGGDWFRQQVEEQINRFDELAENSTEEVRAKMKENFVISSYYEYQFWGMAYRKEGWSDSA 222
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222

Chain D from PDB  Type:PROTEIN  Length:219
 aligned with TENA_BACSU | P25052 from UniProtKB/Swiss-Prot  Length:236

    Alignment length:219
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211         
           TENA_BACSU     2 KFSEECRSAAAEWWEGSFVHPFVQGIGDGTLPIDRFKYYVLQDSYYLTHFAKVQSFGAAYAKDLYTTGRMASHAQGTYEAEMALHREFAELLEISEEERKAFKPSPTAYSYTSHMYRSVLSGNFAEILAALLPCYWLYYEVGEKLLHCDPGHPIYQKWIGTYGGDWFRQQVEEQINRFDELAENSTEEVRAKMKENFVISSYYEYQFWGMAYRKEGWSD 220
               SCOP domains d1yakd_ D: Transcriptional activator TenA                                                                                                                                                                                   SCOP domains
               CATH domains 1yakD00 D:2-220 Heme Oxygenase; Chain A                                                                                                                                                                                     CATH domains
           Pfam domains (1) ------TENA_THI-4-1yakD01 D:8-215                                                                                                                                                                                      ----- Pfam domains (1)
           Pfam domains (2) ------TENA_THI-4-1yakD02 D:8-215                                                                                                                                                                                      ----- Pfam domains (2)
           Pfam domains (3) ------TENA_THI-4-1yakD03 D:8-215                                                                                                                                                                                      ----- Pfam domains (3)
           Pfam domains (4) ------TENA_THI-4-1yakD04 D:8-215                                                                                                                                                                                      ----- Pfam domains (4)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1yak D   2 KFSEECRSAAAEWWEGSFVHPFVQGIGDGTLPIDRFKYYVLQDSYYLTHFAKVQSFGAAYAKDLYTTGRMASHAQGTYEAEMALHREFAELLEISEEERKAFKPSPTAYSYTSHMYRSVLSGNFAEILAALLPCYWLYYEVGEKLLHCDPGHPIYQKWIGTYGGDWFRQQVEEQINRFDELAENSTEEVRAKMKENFVISSYYEYQFWGMAYRKEGWSD 220
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211

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: All alpha proteins (14657)

Fold: Heme oxygenase-like (107)

Superfamily: Heme oxygenase-like (107)

Family: TENA/THI-4 (15)

Protein domain: Transcriptional activator TenA (5)

Bacillus subtilis [TaxId: 1423] (5)

1a	d1yaka_	A:
1b	d1yakb_	B:
1c	d1yakc_	C:
1d	d1yakd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Up-down Bundle (3216)

Topology: Heme Oxygenase; Chain A (84)

Homologous Superfamily: Heme Oxygenase; Chain A (84)

Bacillus subtilis. Organism_taxid: 1423. (5)

1a	1yakB00	B:2-219
1b	1yakC00	C:3-222
1c	1yakA00	A:2-220
1d	1yakD00	D:2-220

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: HO (49)

Family: TENA_THI-4 (12)

Bacillus subtilis (5)

1a	TENA_THI-4-1yakD01	D:8-215
1b	TENA_THI-4-1yakD02	D:8-215
1c	TENA_THI-4-1yakD03	D:8-215
1d	TENA_THI-4-1yakD04	D:8-215

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (TENA_BACSU | P25052)

molecular function
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0050334	thiaminase activity	Catalysis of the reaction: H(2)O + thiamine = 4-amino-5-hydroxymethyl-2-methylpyrimidine + 5-(2-hydroxyethyl)-4-methylthiazole + H(+).
biological process
	GO:0009228	thiamine biosynthetic process	The chemical reactions and pathways resulting in the formation of thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
	GO:0009229	thiamine diphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of thiamine diphosphate, a derivative of thiamine (vitamin B1) which acts as a coenzyme in a range of processes including the Krebs cycle.
	GO:0006772	thiamine metabolic process	The chemical reactions and pathways involving thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.

Asymmetric Unit
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	1yak
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	TENA_BACSU \| P25052	:	1to9 1tyh 1yaf 2qcx

1yad	STRUCTURE OF TENI FROM BACILLUS SUBTILIS
1yaf	STRUCTURE OF TENA FROM BACILLUS SUBTILIS

Description

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Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

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