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Title :   CRYSTAL STRUCTURE OF FLAVIN BINDING TO FAD SYNTHETASE FROM THERMOTOGA MARITINA

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

Date :   16 Jan 04 (Deposition) - 19 Oct 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Fad, Flavin, Riboflavin Kinase, Structural Genomics, Bsgc Structure Funded By Nih, Protein Structure Initiative, Psi, Berkeley Structural Genomics Center, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. Wang, R. Kim, H. Yokota, S. -H. Kim
Crystal Structure Of Flavin Binding To Fad Synthetase Of Thermotoga Maritima
Proteins V. 58 246 2005
PubMed-ID: 15468322 | Reference-DOI: 10.1002/PROT.20207
(for further references see the PDB file header)

Molecule 1 - RIBOFLAVIN KINASE/FMN ADENYLYLTRANSFERASE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	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 (2, 3)

No.	Name	Count	Type	Full Name
1	LUM	2	Ligand/Ion	LUMICHROME
2	MG	1	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	LUM	1	Ligand/Ion	LUMICHROME
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	LUM	1	Ligand/Ion	LUMICHROME
2	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:119 , HOH A:738 , HOH A:739 , HOH A:740 , HOH A:741 , HOH B:652	BINDING SITE FOR RESIDUE MG A 295
2	AC2	SOFTWARE	VAL A:197 , VAL A:213 , ASN A:215 , ARG A:255 , GLU A:257 , LYS A:258 , PHE A:260 , ASP A:273 , ILE B:563	BINDING SITE FOR RESIDUE LUM A 294
3	AC3	SOFTWARE	VAL B:497 , VAL B:513 , ASN B:515 , ARG B:555 , GLU B:557 , LYS B:558 , PHE B:560 , LEU B:566 , ILE B:570 , ASP B:573	BINDING SITE FOR RESIDUE LUM B 594

(no "SS Bond" information available for 1S4M)

(no "Cis Peptide Bond" information available for 1S4M)

(no "SAP(SNP)/Variant" information available for 1S4M)

(no "PROSITE Motif" information available for 1S4M)

(no "Exon" information available for 1S4M)

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
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Chain A from PDB  Type:PROTEIN  Length:277
 aligned with Q9WZW1_THEMA | Q9WZW1 from UniProtKB/TrEMBL  Length:293

    Alignment length:288
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280        
         Q9WZW1_THEMA     1 MVVSIGVFDGVHIGHQKVLRTMKEIAFFRKDDSLIYTISYPPEYFLPDFPGLLMTVESRVEMLSRYARTVVLDFFRIKDLTPEGFVERYLSGVSAVVVGRDFRFGKNASGNASFLRKKGVEVYEIEDVVVQGKRVSSSLIRNLVQEGRVEEIPAYLGRYFEIEGIVHKDREFGRKLGFPTANIDRGNEKLVDLKRGVYLVRVHLPDGKKKFGVMNVGFRPTVGDARNVKYEVYILDFEGDLYGQRLKLEVLKFMRDEKKFDSIEELKAAIDQDVKSARNMIDDIINSK 288
               SCOP domains d1s4ma2 A:1-158 FMN adenylyltransferase domain of bifunctional FAD synthetase                                                                                 d1s4ma1 A:         159-288 Riboflavin kinase domain of bifuncti  onal FAD synthetase                                               SCOP domains
               CATH domains 1s4mA01 A:1-159 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                          1s4mA02 A         :160-288 Riboflavin kinase-like                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhh........hhhhhhhhhh....eeeehhhhhh..hhhhhhhhhh....eeeee.....hhhhh.hhhhhhhh..eeeee...ee..ee.hhhhhhhhhhh.....hhhhhh...eeeeee..---------...eeee...........eeeeeeee.hhh.eeeeeeeeee...--....eeeeeee..........eeeeeeeeeee........hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1s4m A   1 MVVSIGVFDGVHIGHQKVLRTMKEIAFFRKDDSLIYTISYPPEYFLPDFPGLLMTVESRVEMLSRYARTVVLDFFRIKDLTPEGFVERYLSGVSAVVVGRDFRFGKNASGNASFLRKKGVEVYEIEDVVVQGKRVSSSLIRNLVQEGRVEEIPAYLGRYFEIEGIVHK---------FPTANIDRGNEKLVDLKRGVYLVRVHLPDGKKKFGVMNVGFRPT--DARNVKYEVYILDFEGDLYGQRLKLEVLKFMRDEKKFDSIEELKAAIDQDVKSARNMIDDIINSK 288
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       | -       180       190       200       210       220|  |   230       240       250       260       270       280        
                                                                                                                                                                                                 168       178                                        221  |                                                                
                                                                                                                                                                                                                                                         224

Chain B from PDB  Type:PROTEIN  Length:272
 aligned with Q9WZW1_THEMA | Q9WZW1 from UniProtKB/TrEMBL  Length:293

    Alignment length:289
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280         
         Q9WZW1_THEMA     1 MVVSIGVFDGVHIGHQKVLRTMKEIAFFRKDDSLIYTISYPPEYFLPDFPGLLMTVESRVEMLSRYARTVVLDFFRIKDLTPEGFVERYLSGVSAVVVGRDFRFGKNASGNASFLRKKGVEVYEIEDVVVQGKRVSSSLIRNLVQEGRVEEIPAYLGRYFEIEGIVHKDREFGRKLGFPTANIDRGNEKLVDLKRGVYLVRVHLPDGKKKFGVMNVGFRPTVGDARNVKYEVYILDFEGDLYGQRLKLEVLKFMRDEKKFDSIEELKAAIDQDVKSARNMIDDIINSKF 289
               SCOP domains d1s4mb2 B:301-458 FMN adenylyltransferase domain of bifunctional FAD synthetase                                                                               d1s4mb1 B:         459-589 Riboflavin kinase domain of bifun        ctional FAD synthetase                                          SCOP domains
               CATH domains 1s4mB01 B:301-459 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                        1s4mB02 B         :460-589 Riboflavin kinase-like                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhh........hhhhhhhhhh....eeeehhhhhhhhhhhhhhhhhh....eeeee.....hhhhh.hhhhhhhh..eeeee...ee..ee.hhhhhhhhhhh.....hhhhhh...eeeeee..---------...eeee...........eeeeeeee.....eeeeeeeee.--------..eeeeee..........eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s4m B 301 MVVSIGVFDGVHIGHQKVLRTMKEIAFFRKDDSLIYTISYPPEYFLPDFPGLLMTVESRVEMLSRYARTVVLDFFRIKDLTPEGFVERYLSGVSAVVVGRDFRFGKNASGNASFLRKKGVEVYEIEDVVVQGKRVSSSLIRNLVQEGRVEEIPAYLGRYFEIEGIVHK---------FPTANIDRGNEKLVDLKRGVYLVRVHLPDGKKKFGVMNVGF--------NVKYEVYILDFEGDLYGQRLKLEVLKFMRDEKKFDSIEELKAAIDQDVKSARNMIDDIINSKF 589
                                   310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       | -       480       490       500       510       | -      |530       540       550       560       570       580         
                                                                                                                                                                                                 468       478                                     518      527

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

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. (5)

1a	1s4mA01	A:1-159
1b	1s4mB01	B:301-459

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. (4)

2a	1s4mA02	A:160-288
2b	1s4mB02	B:460-589

(no "Pfam Domain" information available for 1S4M)

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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1mrz	APO STRUCTURE RELATED ID: BSGCAIR30409 RELATED DB: TARGETDB

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