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Title :   CRYSTAL STRUCTURE OF THIAMIN PYROPHOSPHOKINASE FAMILY PROTEIN FROM ENTEROCOCCUS FAECALIS, NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET EFR150

Authors :   A. Kuzin, M. Abasidze, J. Seetharaman, M. Mao, R. Xiao, C. Ciccosanti, E M. Maglaqui, L. Zhao, J. K. Everett, R. Nair, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomic Consortium (Nesg)

Date :   31 Mar 10 (Deposition) - 05 May 10 (Release) - 05 May 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.79

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

Keywords :   Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Nesg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Kuzin, M. Abasidze, J. Seetharaman, M. Mao, R. Xiao, C. Ciccosanti, E. L. Foote, M. Maglaqui, L. Zhao, J. K. Everett, R. Nair, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt, L. Tong
Northeast Structural Genomics Consortium Target Efr150
To Be Published
PubMed: search

Molecule 1 - THIAMIN PYROPHOSPHOKINASE FAMILY PROTEIN
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET 21-23C
	Expression System Strain	:	BL21(DE3)+ MAGIC
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	EF_3117
	Organism Common	:	STREPTOCOCCUS FAECALIS
	Organism Scientific	:	ENTEROCOCCUS FAECALIS
	Organism Taxid	:	1351

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 24)

No.	Name	Count	Type	Full Name
1	MG	11	Ligand/Ion	MAGNESIUM ION
2	MSE	9	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	2	Ligand/Ion	PHOSPHATE ION
4	TPP	2	Ligand/Ion	THIAMINE DIPHOSPHATE

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	1	Ligand/Ion	PHOSPHATE ION
4	TPP	1	Ligand/Ion	THIAMINE DIPHOSPHATE

Biological Unit 2 (3, 7)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	MSE	5	Mod. Amino Acid	SELENOMETHIONINE
3	PO4	1	Ligand/Ion	PHOSPHATE ION
4	TPP	1	Ligand/Ion	THIAMINE DIPHOSPHATE

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LYS A:75 , ASP A:76 , THR A:78 , ASP A:79 , THR A:80 , HIS A:108 , MG A:223 , TYR B:174 , LEU B:176 , TYR B:187 , SER B:189 , ASN B:190	BINDING SITE FOR RESIDUE TPP A 902
02	AC2	SOFTWARE	TYR C:174 , LEU C:176 , TYR C:187 , SER C:189 , LYS D:75 , ASP D:76 , THR D:78 , ASP D:79 , THR D:80 , HIS D:108 , MG D:223	BINDING SITE FOR RESIDUE TPP D 902
03	AC3	SOFTWARE	ARG B:55 , GLY C:9 , ASP C:30 , ARG C:31 , SER C:52 , HOH C:226	BINDING SITE FOR RESIDUE PO4 C 223
04	AC4	SOFTWARE	GLY B:9 , ASP B:30 , ARG B:31 , SER B:52	BINDING SITE FOR RESIDUE PO4 B 223
05	AC5	SOFTWARE	ASP D:30 , ASP D:49 , ASP D:51 , ASP D:79 , TPP D:902	BINDING SITE FOR RESIDUE MG D 223
06	AC6	SOFTWARE	ASP A:30 , ASP A:49 , ASP A:51 , ASP A:79 , TPP A:902	BINDING SITE FOR RESIDUE MG A 223
07	AC7	SOFTWARE	ASP B:30 , ASP B:49 , ASP B:51 , ASP B:79	BINDING SITE FOR RESIDUE MG B 224
08	AC8	SOFTWARE	ASP C:30 , ASP C:49 , ASP C:79	BINDING SITE FOR RESIDUE MG C 224
09	AC9	SOFTWARE	MG B:225 , ASP C:51	BINDING SITE FOR RESIDUE MG C 225
10	BC1	SOFTWARE	PHE B:50 , LEU B:53 , TYR B:58 , MG C:225	BINDING SITE FOR RESIDUE MG B 225
11	BC2	SOFTWARE	HIS A:59	BINDING SITE FOR RESIDUE MG A 224
12	BC3	SOFTWARE	ASN A:166 , SER A:200	BINDING SITE FOR RESIDUE MG A 225
13	BC4	SOFTWARE	ASP A:76	BINDING SITE FOR RESIDUE MG A 226
14	BC5	SOFTWARE	SER D:2 , GLN D:93 , ALA D:94	BINDING SITE FOR RESIDUE MG D 224

(no "SS Bond" information available for 3MEL)

Asymmetric Unit

No.	Residues
1	Mse C:1	-	Ser C:2

(no "SAP(SNP)/Variant" information available for 3MEL)

(no "PROSITE Motif" information available for 3MEL)

(no "Exon" information available for 3MEL)

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:213
 aligned with Q82ZE3_ENTFA | Q82ZE3 from UniProtKB/TrEMBL  Length:214

    Alignment length:213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   
         Q82ZE3_ENTFA     2 SRVLLVAGGNPSDWPTIEPATYDYFVGIDRGCLHLLEADLPLQLAVGDFDSLSREEYHFVQETTETLIQAPAEKDDTDTQLALQEALQRFPQAEMTIIGATGGRIDHLLANLWLPFEPRFQGVLRQIRLCDRQNSIQYYAPGSYIVPKEPDKEYLAYCCLTPVENLTLRRSKYLLTNQDVPYPTSYASNEFIEEAAAFSFDAGMIAVIQSKDK 214
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhh...hhhhh..eeee.hhhhhhhh......eeee.......hhhhhhhhhh..eee.......hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhhhh.eeee...eeeeee...eeeee......eeeeee...eeeeeee.....eeeeee...eeeeee.....eeeee.....eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mel A   2 SRVLLVAGGNPSDWPTIEPATYDYFVGIDRGCLHLLEADLPLQLAVGDFDSLSREEYHFVQETTETLIQAPAEKDDTDTQLALQEALQRFPQAEmTIIGATGGRIDHLLANLWLPFEPRFQGVLRQIRLCDRQNSIQYYAPGSYIVPKEPDKEYLAYCCLTPVENLTLRRSKYLLTNQDVPYPTSYASNEFIEEAAAFSFDAGmIAVIQSKDK 214
                                    11        21        31        41        51        61        71        81        91    |  101       111       121       131       141       151       161       171       181       191       201   |   211   
                                                                                                                         96-MSE                                                                                                      205-MSE

Chain B from PDB  Type:PROTEIN  Length:213
 aligned with Q82ZE3_ENTFA | Q82ZE3 from UniProtKB/TrEMBL  Length:214

    Alignment length:213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   
         Q82ZE3_ENTFA     2 SRVLLVAGGNPSDWPTIEPATYDYFVGIDRGCLHLLEADLPLQLAVGDFDSLSREEYHFVQETTETLIQAPAEKDDTDTQLALQEALQRFPQAEMTIIGATGGRIDHLLANLWLPFEPRFQGVLRQIRLCDRQNSIQYYAPGSYIVPKEPDKEYLAYCCLTPVENLTLRRSKYLLTNQDVPYPTSYASNEFIEEAAAFSFDAGMIAVIQSKDK 214
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...hhhhh...hhhhh.eeeee.hhhhhhhh......eeee.....hhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhh....eeeee..eeeeee..eeeeee......eeeeee...eeeeeee.....eeeeee...eeeeee.....eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mel B   2 SRVLLVAGGNPSDWPTIEPATYDYFVGIDRGCLHLLEADLPLQLAVGDFDSLSREEYHFVQETTETLIQAPAEKDDTDTQLALQEALQRFPQAEmTIIGATGGRIDHLLANLWLPFEPRFQGVLRQIRLCDRQNSIQYYAPGSYIVPKEPDKEYLAYCCLTPVENLTLRRSKYLLTNQDVPYPTSYASNEFIEEAAAFSFDAGmIAVIQSKDK 214
                                    11        21        31        41        51        61        71        81        91    |  101       111       121       131       141       151       161       171       181       191       201   |   211   
                                                                                                                         96-MSE                                                                                                      205-MSE

Chain C from PDB  Type:PROTEIN  Length:214
 aligned with Q82ZE3_ENTFA | Q82ZE3 from UniProtKB/TrEMBL  Length:214

    Alignment length:214
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210    
         Q82ZE3_ENTFA     1 MSRVLLVAGGNPSDWPTIEPATYDYFVGIDRGCLHLLEADLPLQLAVGDFDSLSREEYHFVQETTETLIQAPAEKDDTDTQLALQEALQRFPQAEMTIIGATGGRIDHLLANLWLPFEPRFQGVLRQIRLCDRQNSIQYYAPGSYIVPKEPDKEYLAYCCLTPVENLTLRRSKYLLTNQDVPYPTSYASNEFIEEAAAFSFDAGMIAVIQSKDK 214
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...hhhhh...hhhhh.eeeeehhhhhhhhhh.....eeee.....hhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhh....eeeee..eeeeee..eeeeee......eeeeee...eeeeeee.....eeeeee....eeeee.....eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mel C   1 mSRVLLVAGGNPSDWPTIEPATYDYFVGIDRGCLHLLEADLPLQLAVGDFDSLSREEYHFVQETTETLIQAPAEKDDTDTQLALQEALQRFPQAEmTIIGATGGRIDHLLANLWLPFEPRFQGVLRQIRLCDRQNSIQYYAPGSYIVPKEPDKEYLAYCCLTPVENLTLRRSKYLLTNQDVPYPTSYASNEFIEEAAAFSFDAGmIAVIQSKDK 214
                            |       10        20        30        40        50        60        70        80        90     | 100       110       120       130       140       150       160       170       180       190       200    |  210    
                            1-MSE                                                                                         96-MSE                                                                                                      205-MSE

Chain D from PDB  Type:PROTEIN  Length:213
 aligned with Q82ZE3_ENTFA | Q82ZE3 from UniProtKB/TrEMBL  Length:214

    Alignment length:213
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211   
         Q82ZE3_ENTFA     2 SRVLLVAGGNPSDWPTIEPATYDYFVGIDRGCLHLLEADLPLQLAVGDFDSLSREEYHFVQETTETLIQAPAEKDDTDTQLALQEALQRFPQAEMTIIGATGGRIDHLLANLWLPFEPRFQGVLRQIRLCDRQNSIQYYAPGSYIVPKEPDKEYLAYCCLTPVENLTLRRSKYLLTNQDVPYPTSYASNEFIEEAAAFSFDAGMIAVIQSKDK 214
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ----------TPK_catalytic-3melD05 D:12-132                                                                                           ----------TPK_B1_binding-3melD01 D:143-207                                 ------- Pfam domains (1)
           Pfam domains (2) ----------TPK_catalytic-3melD06 D:12-132                                                                                           ----------TPK_B1_binding-3melD02 D:143-207                                 ------- Pfam domains (2)
           Pfam domains (3) ----------TPK_catalytic-3melD07 D:12-132                                                                                           ----------TPK_B1_binding-3melD03 D:143-207                                 ------- Pfam domains (3)
           Pfam domains (4) ----------TPK_catalytic-3melD08 D:12-132                                                                                           ----------TPK_B1_binding-3melD04 D:143-207                                 ------- Pfam domains (4)
         Sec.struct. author .eeeee...hhhhh...hhhhh.eeeee.hhhhhhhhh.....eeee.....hhhhhhhhhhhh.eeee.......hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhhhhhh.eeee...eeeeee..eeeeee......eeeeee...eeeeeee.....eeeeee....eeeee.....eeeeee....eeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mel D   2 SRVLLVAGGNPSDWPTIEPATYDYFVGIDRGCLHLLEADLPLQLAVGDFDSLSREEYHFVQETTETLIQAPAEKDDTDTQLALQEALQRFPQAEmTIIGATGGRIDHLLANLWLPFEPRFQGVLRQIRLCDRQNSIQYYAPGSYIVPKEPDKEYLAYCCLTPVENLTLRRSKYLLTNQDVPYPTSYASNEFIEEAAAFSFDAGmIAVIQSKDK 214
                                    11        21        31        41        51        61        71        81        91    |  101       111       121       131       141       151       161       171       181       191       201   |   211   
                                                                                                                         96-MSE                                                                                                      205-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 '\|'

(no "SCOP Domain" information available for 3MEL)

(no "CATH Domain" information available for 3MEL)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Q82ZE3_ENTFA | Q82ZE3)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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.
	GO:0004788	thiamine diphosphokinase activity	Catalysis of the reaction: ATP + thiamine = AMP + thiamine diphosphate.
biological process
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
	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.

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	Cis Peptide Bonds
		Mse C:1 - Ser C:2	[ RasMol ]

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gtr2	HOMOLOG RELATED ID: SR677 RELATED DB: TARGETDB HOMOLOG RELATED ID: SMR83 RELATED DB: TARGETDB HOMOLOG RELATED ID: EFR150 RELATED DB: TARGETDB

Description

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Ligands, Modified Residues, Ions (4, 24)

Sites (14, 14)

SS Bonds (0, 0)

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