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Title :   CRYSTAL STRUCTURE OF THE C2 FORM OF FAD SYNTHETASE FROM THERMOTOGA MARITIMA

Authors :   W. Wang, D. H. Shin, H. Yokota, R. Kim, S. -H. Kim, Berkeley Structural Genomics Center (Bsgc)

Date :   14 Aug 06 (Deposition) - 07 Nov 06 (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 :   Fad Synthetase, Crystal Structure, Structural Genomics, Psi, Protein Structure Initiative, Berkeley Structural Genomics Center, Bsgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Wang, D. H. Shin, H. Yokota, R. Kim, S. -H. Kim
Crystal Structure Of The C2 Form Of Fad Synthetase From Thermotoga Maritima
To Be Published
PubMed: search
(for further references see the PDB file header)

Molecule 1 - RIBOFLAVIN KINASE/FMN ADENYLYLTRANSFERASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET21, PSJS1240
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Gene	:	TM_0857
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336

		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, 12)

No.	Name	Count	Type	Full Name
1	MSE	12	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 2I1L)

(no "SS Bond" information available for 2I1L)

(no "Cis Peptide Bond" information available for 2I1L)

(no "SAP(SNP)/Variant" information available for 2I1L)

(no "PROSITE Motif" information available for 2I1L)

(no "Exon" information available for 2I1L)

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:267
 aligned with Q9WZW1_THEMA | Q9WZW1 from UniProtKB/TrEMBL  Length:293

    Alignment length:289
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281         
         Q9WZW1_THEMA     2 VVSIGVFDGVHIGHQKVLRTMKEIAFFRKDDSLIYTISYPPEYFLPDFPGLLMTVESRVEMLSRYARTVVLDFFRIKDLTPEGFVERYLSGVSAVVVGRDFRFGKNASGNASFLRKKGVEVYEIEDVVVQGKRVSSSLIRNLVQEGRVEEIPAYLGRYFEIEGIVHKDREFGRKLGFPTANIDRGNEKLVDLKRGVYLVRVHLPDGKKKFGVMNVGFRPTVGDARNVKYEVYILDFEGDLYGQRLKLEVLKFMRDEKKFDSIEELKAAIDQDVKSARNMIDDIINSKFE 290
               SCOP domains d2i1la2 A:2-158 FMN adenylyltransferase domain of bifunctional FAD synthetase                                                                                d2i1la1            A:159-290 Riboflavin kinase domain of bif       unctional FAD synthetase                                          SCOP domains
               CATH domains 2i1lA01 A:2-159 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                         2i1lA02            A:160-290 Riboflavin kinase-like                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhhhhhhh.....eeeee................hhhhhhhhhhh..eeeeehhhhhh..hhhhhhhhhh....eeeee.....hhhhh.hhhhhhhh..eeeee...ee..ee.hhhhhhhhhhh.hhhhhhhhhh...eeeee.-----------..eee.............eeeeeeee.....eeeeeeeee.-------...eeeeee..........eeeeeeeee......----.hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2i1l A   2 VVSIGVFDGVHIGHQKVLRTmKEIAFFRKDDSLIYTISYPPEYFLPDFPGLLmTVESRVEmLSRYARTVVLDFFRIKDLTPEGFVERYLSGVSAVVVGRDFRFGKNASGNASFLRKKGVEVYEIEDVVVQGKRVSSSLIRNLVQEGRVEEIPAYLGRYFEIEGIV-----------FPTANIDRGNEKLVDLKRGVYLVRVHLPDGKKKFGVmNVGF-------RNVKYEVYILDFEGDLYGQRLKLEVLKFmRDEKK----EELKAAIDQDVKSARNmIDDIINSKFE 290
                                    11        21|       31        41        51  |     61|       71        81        91       101       111       121       131       141       151       161    |    -      |181       191       201       211  |   |  -    |  231       241       251  |    | -  |    271       281         
                                               22-MSE                          54-MSE  62-MSE                                                                                                 166         178                                 214-MSE     226                         254-MSE9  264             280-MSE

Chain B from PDB  Type:PROTEIN  Length:269
 aligned with Q9WZW1_THEMA | Q9WZW1 from UniProtKB/TrEMBL  Length:293

    Alignment length:288
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281        
         Q9WZW1_THEMA     2 VVSIGVFDGVHIGHQKVLRTMKEIAFFRKDDSLIYTISYPPEYFLPDFPGLLMTVESRVEMLSRYARTVVLDFFRIKDLTPEGFVERYLSGVSAVVVGRDFRFGKNASGNASFLRKKGVEVYEIEDVVVQGKRVSSSLIRNLVQEGRVEEIPAYLGRYFEIEGIVHKDREFGRKLGFPTANIDRGNEKLVDLKRGVYLVRVHLPDGKKKFGVMNVGFRPTVGDARNVKYEVYILDFEGDLYGQRLKLEVLKFMRDEKKFDSIEELKAAIDQDVKSARNMIDDIINSKF 289
               SCOP domains d2i1lb2 B:302-458 FMN adenylyltransferase domain of bifunctional FAD synthetase                                                                              d2i1lb1 B           :459-589 Riboflavin kinase domain of bif        unctional FAD synthetase                                        SCOP domains
               CATH domains 2i1lB01 B:302-459 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                       2i1lB02            B:460-589 Riboflavin kinase-like                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhhhhhhhhh...eeeee................hhhhhhhhhh...eeeee........hhhhhhhhhh....eeeee.....hhhhh.hhhhhhh...eeeee...ee..ee.hhhhhhhhhhhhhhhhhhhhhh..eeeeeee.-----------..eeee...........eeeeeeee.....eeeeeeeee.--------..eeeeee..........eeeeeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2i1l B 302 VVSIGVFDGVHIGHQKVLRTmKEIAFFRKDDSLIYTISYPPEYFLPDFPGLLmTVESRVEmLSRYARTVVLDFFRIKDLTPEGFVERYLSGVSAVVVGRDFRFGKNASGNASFLRKKGVEVYEIEDVVVQGKRVSSSLIRNLVQEGRVEEIPAYLGRYFEIEGIVH-----------PTANIDRGNEKLVDLKRGVYLVRVHLPDGKKKFGVmNVGF--------NVKYEVYILDFEGDLYGQRLKLEVLKFmRDEKKFDSIEELKAAIDQDVKSARNmIDDIINSKF 589
                                   311       321|      331       341       351  |    361|      371       381       391       401       411       421       431       441       451       461     |   -       481       491       501       511  |   |  -     | 531       541       551  |    561       571       581        
                                              322-MSE                         354-MSE 362-MSE                                                                                                  467         479                                514-MSE      527                        554-MSE                   580-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 Unit

Classes(

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Architectures( (-)

)

Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

)

Class: Alpha Beta (26913)

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

Topology: Rossmann fold (7312)

Homologous Superfamily: Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1 (328)

Thermotoga maritima. Organism_taxid: 2336. (6)

1a	2i1lA01	A:2-159
1b	2i1lB01	B:302-459

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Elongation Factor Tu (Ef-tu); domain 3 (323)

Homologous Superfamily: Riboflavin kinase-like (22)

Thermotoga maritima. Organism_taxid: 2336. (2)

2a	2i1lB02	B:460-589
2b	2i1lA02	A:160-290

(no "Pfam Domain" information available for 2I1L)

Asymmetric Unit(hide GO term definitions)

Chain A,B (Q9WZW1_THEMA | Q9WZW1)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003919	FMN adenylyltransferase activity	Catalysis of the reaction: ATP + FMN = diphosphate + FAD.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0008531	riboflavin kinase activity	Catalysis of the reaction: ATP + riboflavin = ADP + FMN + 2 H(+).
	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.
biological process
	GO:0006747	FAD biosynthetic process	The chemical reactions and pathways resulting in the formation of FAD, the oxidized form of flavin-adenine dinucleotide.
	GO:0009398	FMN biosynthetic process	The chemical reactions and pathways resulting in the formation of FMN, the oxidized form of flavin mononucleotide (riboflavin 5'-(dihydrogen phosphate)), which acts as a coenzyme for a number of oxidative enzymes including NADH dehydrogenase.
	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:0009231	riboflavin biosynthetic process	The chemical reactions and pathways resulting in the formation of riboflavin (vitamin B2), the precursor for the coenzymes flavin mononucleotide (FMN) and flavin adenine dinucleotide (FAD).

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	Q9WZW1_THEMA \| Q9WZW1	:	1mrz 1s4m 1t6x 1t6y 1t6z

1mrz	CRYSTAL STRUCTURE OF A FLAVIN BINDING PROTEIN FROM THERMOTOGA MARITIMA, TM379
1s4m	CRYSTAL STRUCTURE OF FLAVIN BINDING TO FAD SYNTHETASE FROM THERMOTOGA MARITINA
1t6x	CRYSTAL STRUCTURE OF ADP BOUND TM379
1t6y	CRYSTAL STRUCTURE OF ADP, AMP, AND FMN BOUND TM379
1t6z	CRYSTAL STRUCTURE OF RIBOFLAVIN BOUND TM379 RELATED ID: BSGCAIR30409 RELATED DB: TARGETDB

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