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(-) Description

Title :  CRYSTAL STRUCTURE OF ADP BOUND TM379
 
Authors :  D. H. Shin, W. Wang, R. Kim, H. Yokota, S. -H. Kim, Berkeley Structural Genomics Center (Bsgc)
Date :  07 May 04  (Deposition) - 10 Aug 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.29
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Crystal; Fad Synthetase; Adp; X-Ray Crystallography; Structural Genomics, Bsgc Structure Funded By Nih, Protein Structure Initiative, Psi, Berkeley Structural Genomics Center, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. H. Shin, W. Wang, R. Kim, H. Yokota, S. -H. Kim
Crystal Structure Of Adp Bound Fad Synthetase
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - RIBOFLAVIN KINASE/FMN ADENYLYLTRANSFERASE
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PSJS1244
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: THERMOTOGA MARITIMA
    Organism Taxid: 2336
    Synonym: FAD SYNTHETASE;
FLAVIN BINDING PROTEIN;
TM379

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1ADP2Ligand/IonADENOSINE-5'-DIPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:179 , THR A:180 , ALA A:181 , ASN A:182 , VAL A:232 , ILE A:234 , PHE A:237 , GLY A:239 , ASP A:240 , LEU A:241 , TYR A:242BINDING SITE FOR RESIDUE ADP A 294
2AC2SOFTWAREPRO B:479 , THR B:480 , ALA B:481 , ASN B:482 , GLU B:531 , VAL B:532 , TYR B:533 , ILE B:534 , PHE B:537 , GLY B:539 , ASP B:540 , LEU B:541 , TYR B:542BINDING SITE FOR RESIDUE ADP B 594

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1T6X)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:178 -Pro A:179

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1T6X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1T6X)

(-) Exons   (0, 0)

(no "Exon" information available for 1T6X)

(-) Sequences/Alignments

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:266
 aligned with Q9WZW1_THEMA | Q9WZW1 from UniProtKB/TrEMBL  Length:293

    Alignment length:287
                                    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 VVSIGVFDGVHIGHQKVLRTMKEIAFFRKDDSLIYTISYPPEYFLPDFPGLLMTVESRVEMLSRYARTVVLDFFRIKDLTPEGFVERYLSGVSAVVVGRDFRFGKNASGNASFLRKKGVEVYEIEDVVVQGKRVSSSLIRNLVQEGRVEEIPAYLGRYFEIEGIVHKDREFGRKLGFPTANIDRGNEKLVDLKRGVYLVRVHLPDGKKKFGVMNVGFRPTVGDARNVKYEVYILDFEGDLYGQRLKLEVLKFMRDEKKFDSIEELKAAIDQDVKSARNMIDDIINSK 288
               SCOP domains d1t6xa2 A:2-158 FMN adenylyltransferase domain of bifunctional FAD synthetase                                                                                d1t6xa1            A:159-288 Riboflavin kinase domain of bifu      nctional FAD synthetase                                         SCOP domains
               CATH domains 1t6xA01 A:2-159 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                         1t6xA02            A:160-288 Riboflavin kinase-like                                                                               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.....hhhhhhhhhhhhhhhhhhh...eeeee..hhhhhh........hhhhhhhhhh...eeeeehhhhhh..hhhhhhhhhh....eeeee.....hhhhh.hhhhhhhh..eeeee...ee..ee.hhhhhhhhhhh.....hhhhhh...eeeee.-----------...ee.............eeeeeeee.....eeeeeeeee..------...eeeeeee.........eeeeeeeeeeee...----.hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t6x A   2 VVSIGVFDGVHIGHQKVLRTMKEIAFFRKDDSLIYTISYPPEYFLPDFPGLLMTVESRVEMLSRYARTVVLDFFRIKDLTPEGFVERYLSGVSAVVVGRDFRFGKNASGNASFLRKKGVEVYEIEDVVVQGKRVSSSLIRNLVQEGRVEEIPAYLGRYFEIEGIV-----------FPTANIDRGNEKLVDLKRGVYLVRVHLPDGKKKFGVMNVGFR------RNVKYEVYILDFEGDLYGQRLKLEVLKFMRDEKK----EELKAAIDQDVKSARNMIDDIINSK 288
                                    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       
                                                                                                                                                                                              166         178                                      219    226                              259  264                        


Chain B from PDB  Type:PROTEIN  Length:270
 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 d1t6xb2 B:302-458 FMN adenylyltransferase domain of bifunctional FAD synthetase                                                                              d1t6xb1 B          :459-589 Riboflavin kinase domain of bifu        nctional FAD synthetase                                         SCOP domains
               CATH domains 1t6xB01 B:302-459 Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1                                                                                       1t6xB02           B:460-589 Riboflavin kinase-like                                                                                 CATH domains
           Pfam domains (1) FAD_syn-1t6xB01 B:302-439                                                                                                                 ---------------Flavokinase-1          t6xB03 B:455-582                                                                                         ------- Pfam domains (1)
           Pfam domains (2) FAD_syn-1t6xB02 B:302-439                                                                                                                 ---------------Flavokinase-1          t6xB04 B:455-582                                                                                         ------- Pfam domains (2)
         Sec.struct. author .eeee.....hhhhhhhhhhhhhhhhhhh...eeeee..hhhhhh........hhhhhhhhhhh...eeeehhhhh...hhhhhhhhhh....eeee......hhhhh.hhhhhhh...eeee....ee..ee.hhhhhhhhhhh.....hhhhhh...eeeeee.----------...eeee...........eeeeeeee.....eeeeeeeee.--------..eeeeee..........eeeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1t6x B 302 VVSIGVFDGVHIGHQKVLRTMKEIAFFRKDDSLIYTISYPPEYFLPDFPGLLMTVESRVEMLSRYARTVVLDFFRIKDLTPEGFVERYLSGVSAVVVGRDFRFGKNASGNASFLRKKGVEVYEIEDVVVQGKRVSSSLIRNLVQEGRVEEIPAYLGRYFEIEGIVH----------FPTANIDRGNEKLVDLKRGVYLVRVHLPDGKKKFGVMNVGF--------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        
                                                                                                                                                                                               467        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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: HUP (230)
(-)
Clan: no clan defined [family: Flavokinase] (12)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological 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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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q9WZW1_THEMA | Q9WZW1: 1mrz 1s4m 1t6y 1t6z 2i1l

(-) Related Entries Specified in the PDB File

1mrz NATIVE
1t6x
1t6y
1t6z
1t70
1t71 RELATED ID: BSGCAIR30409 RELATED DB: TARGETDB