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Title :   THE STRUCTURE AND FUNCTION OF B. SUBTILIS YKOF GENE PRODUCT: THE COMPLEX WITH THIAMIN

Authors :   Y. Devedjiev, Y. Surendranath, U. Derewenda, Z. S. Derewenda

Date :   11 Feb 04 (Deposition) - 05 Oct 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Ykof, Thiamin-Binding Protein, Act-Domain Family, X-Ray Structure, Ligand Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Y. Devedjiev, Y. Surendranath, U. Derewenda, A. Gabrys, D. R. Cooper, R. G. Zhang, L. Lezondra, A. Joachimiak, Z. S. Derewenda
The Structure And Ligand Binding Properties Of The B. Subtilis Ykof Gene Product, A Member Of A Novel Family Of Thiamin/Hmp-Binding Proteins
J. Mol. Biol. V. 343 395 2004
PubMed-ID: 15451668 | Reference-DOI: 10.1016/J.JMB.2004.08.037
(for further references see the PDB file header)

Molecule 1 - YKOF
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PMCSG7
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	YKOF
	Mutation	:	YES
	Organism Scientific	:	BACILLUS SUBTILIS
	Organism Taxid	:	1423

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 19)

No.	Name	Count	Type	Full Name
1	CA	1	Ligand/Ion	CALCIUM ION
2	MSE	14	Mod. Amino Acid	SELENOMETHIONINE
3	VIB	4	Ligand/Ion	3-(4-AMINO-2-METHYL-PYRIMIDIN-5-YLMETHYL)-5-(2-HYDROXY-ETHYL)-4-METHYL-THIAZOL-3-IUM

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ALA A:33 , THR A:35 , HOH A:802 , ALA B:33 , THR B:35 , HOH B:803	BINDING SITE FOR RESIDUE CA A 801
2	AC2	SOFTWARE	PHE A:15 , SER A:16 , LEU A:17 , ILE A:28 , THR A:44 , ASP A:45 , HIS A:46 , ILE A:47 , SER A:48 , THR A:49	BINDING SITE FOR RESIDUE VIB A 501
3	AC3	SOFTWARE	PHE A:119 , ALA A:120 , LEU A:121 , MSE A:130 , ILE A:133 , SER A:154 , HOH A:828	BINDING SITE FOR RESIDUE VIB A 502
4	AC4	SOFTWARE	PHE B:15 , SER B:16 , LEU B:17 , ILE B:25 , THR B:44 , ASP B:45 , HIS B:46 , ILE B:47 , SER B:48 , THR B:49	BINDING SITE FOR RESIDUE VIB B 503
5	AC5	SOFTWARE	PRO A:87 , HIS A:180 , PHE B:119 , ALA B:120 , LEU B:121 , MSE B:130 , ILE B:133 , ALA B:153 , SER B:154	BINDING SITE FOR RESIDUE VIB B 504

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

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

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

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

(no "Exon" information available for 1SBR)

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:182
 aligned with YKOF_BACSU | O34911 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:186
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188      
           YKOF_BACSU     9 RIAGFRFSLYPMTDDFISVIKSALKKTDTSKVWTKTDHISTVLRGSIDHVFDAAKAIYLHAANSEQHIVMNGTFSIGCPGDTQGDTYLSKGDKRVNEDAVRGLKAEAPCQFALYPMNEPDYMGLIMEAVDIAKAQGTFVQGVHYASELDGDAHDVFSTLEAVFRMAEQQTNHITMTVNLSANSPSR 194
               SCOP domains d1sbra_ A: Putative thiamin/HMP-binding protein YkoF                                                                                                                                       SCOP domains
               CATH domains 1sbrA01 A:9-87  [code=3.30.70.930, no name defined]                            ------------------------1sbrA02 A:112-194  [code=3.30.70.930, no name defined]                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhhhh.....eeee....eeeeehhhhhhhhhhhhhhhhhh.....eeeeeee.............----................eeeeee.....hh.hhh.hhhhhhhhh..eeeee..eeee..hhhhhhhhhhhhhh.hhhh....eeeeee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1sbr A   9 RIAGFRFSLYPmTDDFISVIKSALAATDTSKVWTKTDHISTVLRGSIDHVFDAAKAIYLHAANSEQHIVmNGTFSIGCPGDTQGDTYL----KRVNEDAVRGLKAEAPCQFALYPmNEPDYmGLImEAVDIAKAQGTFVQGVHYASELDGDAHDVFSTLEAVFRmAEQQTNHITmTVNLSANSPSR 194
                                    18 |      28        38        48        58        68        78        88       | -  |    108       118     | 128 |   | 138       148       158       168    |  178    |  188      
                                      20-MSE                                                    78-MSE            96  101                    124-MSE |   |                                    173-MSE   183-MSE       
                                                                                                                                                   130-MSE                                                            
                                                                                                                                                       134-MSE

Chain B from PDB  Type:PROTEIN  Length:182
 aligned with YKOF_BACSU | O34911 from UniProtKB/Swiss-Prot  Length:200

    Alignment length:184
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188    
           YKOF_BACSU     9 RIAGFRFSLYPMTDDFISVIKSALKKTDTSKVWTKTDHISTVLRGSIDHVFDAAKAIYLHAANSEQHIVMNGTFSIGCPGDTQGDTYLSKGDKRVNEDAVRGLKAEAPCQFALYPMNEPDYMGLIMEAVDIAKAQGTFVQGVHYASELDGDAHDVFSTLEAVFRMAEQQTNHITMTVNLSANSP 192
               SCOP domains d1sbrb_ B: Putative thiamin/HMP-binding protein YkoF                                                                                                                                     SCOP domains
               CATH domains 1sbrB01 B:9-87  [code=3.30.70.930, no name defined]                            ------------------------1sbrB02 B:112-192  [code=3.30.70.930, no name defined]                            CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------Ykof-1sbrB01 B:114-192                                                          Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------Ykof-1sbrB02 B:114-192                                                          Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------Ykof-1sbrB03 B:114-192                                                          Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------Ykof-1sbrB04 B:114-192                                                          Pfam domains (4)
         Sec.struct. author ..eeeeeeee....hhhhhhhhhhhhh.....eeee....eeeeehhhhhhhhhhhhhhhhhhh....eeeeeeee.............--.....hhhhh.......eee........hh.hhh.hhhhhhhhh..eeeee..eeee..hhhhhhhhhhhhhh.hhh....eeeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sbr B   9 RIAGFRFSLYPmTDDFISVIKSALAATDTSKVWTKTDHISTVLRGSIDHVFDAAKAIYLHAANSEQHIVmNGTFSIGCPGDTQGDTYLS--DKRVNEDAVRGLKAEAPCQFALYPmNEPDYmGLImEAVDIAKAQGTFVQGVHYASELDGDAHDVFSTLEAVFRmAEQQTNHITmTVNLSANSP 192
                                    18 |      28        38        48        58        68        78        88        |- |     108       118     | 128 |   | 138       148       158       168    |  178    |  188    
                                      20-MSE                                                    78-MSE             97  |                     124-MSE |   |                                    173-MSE   183-MSE     
                                                                                                                     100                           130-MSE                                                          
                                                                                                                                                       134-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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Ferredoxin-like (1795)

Superfamily: MTH1187/YkoF-like (11)

Family: Putative thiamin/HMP-binding protein YkoF (3)

Protein domain: Putative thiamin/HMP-binding protein YkoF (3)

Bacillus subtilis [TaxId: 1423] (3)

1a	d1sbra_	A:
1b	d1sbrb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Alpha-Beta Plaits (1688)

Homologous Superfamily: [code=3.30.70.930, no name defined] (10)

Bacillus subtilis. Organism_taxid: 1423. (2)

1a	1sbrA02	A:112-194
1b	1sbrB02	B:112-192
1c	1sbrA01	A:9-87
1d	1sbrB01	B:9-87

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: MTH1187-YkoF (6)

Family: Ykof (2)

Bacillus subtilis (2)

1a	Ykof-1sbrB01	B:114-192
1b	Ykof-1sbrB02	B:114-192
1c	Ykof-1sbrB03	B:114-192
1d	Ykof-1sbrB04	B:114-192

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (YKOF_BACSU | O34911)

molecular function
	GO:0030975	thiamine binding	Interacting selectively and non-covalently with thiamine (vitamin B1), a water soluble vitamin present in fresh vegetables and meats, especially liver.
biological process
	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.

Asymmetric/Biological Unit
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	YKOF_BACSU \| O34911	:	1s7h 1s99

1lxj	SHARES SIMILAR FOLD
1lxn	SHARES SIMILAR FOLD
1s99	THE SAME PROTEIN, LIGAND FREE

Description

Compounds

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Ligands, Modified Residues, Ions (3, 19)

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