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(-) Description

Title :  X-RAY STRUCTURE OF THE GLYCEROL-3-PHOSPHATE DEHYDROGENASE FROM BACILLUS HALODURANS COMPLEXED WITH FAD. NORTHEAST STRUCTURAL GENOMICS CONSORTIUM TARGET BHR167.
 
Authors :  A. P. Kuzin, M. Abashidze, J. Seetharaman, D. Wang, H. Janjua, L. Owens, R. Xiao, R. Nair, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt, L. Tong, Northeast Structural Genomics Consortium (Nesg)
Date :  28 May 08  (Deposition) - 29 Jul 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A
Keywords :  Nesg Bhr167 Q9Kdw6 X-Ray, Structural Genomics, Psi-2, Protein Structure Initiative, Northeast Structural Genomics Consortium, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. Kuzin, M. Abashidze, J. Seetharaman, D. Wang, H. Janjua, L. Owens, R. Xiao, R. Nair, M. C. Baran, T. B. Acton, B. Rost, G. T. Montelione, J. F. Hunt, L. Tong
X-Ray Structure Of The Glycerol-3-Phosphate Dehydrogenase From Bacillus Halodurans Complexed With Fad. Northeast Structural Genomics Consortium Target Bhr167.
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLYCEROL-3-PHOSPHATE DEHYDROGENASE
    Chains: A
    Organism Scientific: BACILLUS HALODURANS

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 15)

Asymmetric/Biological Unit (2, 15)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2MSE14Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:24 , GLY A:27 , ILE A:28 , THR A:29 , GLU A:48 , ASN A:50 , ASP A:51 , SER A:54 , GLY A:55 , THR A:56 , SER A:57 , SER A:60 , THR A:61 , LEU A:63 , HIS A:65 , GLY A:229 , PRO A:230 , TRP A:231 , LEU A:235 , GLY A:252 , HIS A:254 , THR A:292 , GLY A:338 , ARG A:340 , GLY A:372 , LYS A:373 , LEU A:374 , THR A:375 , HOH A:613 , HOH A:635BINDING SITE FOR RESIDUE FAD A 609

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DA1)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DA1)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DA1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3DA1)

(-) Exons   (0, 0)

(no "Exon" information available for 3DA1)

(-) 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:496
 aligned with Q9KDW6_BACHD | Q9KDW6 from UniProtKB/TrEMBL  Length:553

    Alignment length:549
                                    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       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540         
         Q9KDW6_BACHD     1 MFSAKKRDKCIGEMSEKQLDLLVIGGGITGAGIALDAQVRGIQTGLVEMNDFASGTSSRSTKLVHGGLRYLKQFEIKLVAEVGKERAIVYENAPHVTTPEWMLLPIFKDGTFGKFSTSLGLKVYDYLADVRKDERRYMLNEKQTLEKEPLLRKENLKGGGIYVEYRTDDARLTLEIMKEAVARGAVALNYMKVESFIYDQGKVVGVVAKDRLTDTTHTIYAKKVVNAAGPWVDTLREKDRSKHGKYLKLSKGVHLVVDQSRFPLRQAVYFDTESDGRMIFAIPREGKTYIGTTDTFYDKDIASPRMTVEDRDYILAAANYMFPSLNLTADDVESSWAGLRPLIHEEGKKASEISRKDEIFFSDSGLISIAGGKLTGYRKMAERTVDAVAQGLNVNEPCTTAAIRLSGGLAEGAQGFPRFLDEASRKGAKLGFDADEVRRLAKLYGSNVDHVLNYAYEGKEEAEHYGLPALLLGQLQYGVEQEMVATPLDFFVRRTGALFFNISLVHQWKEAVLRWMAEEFSWTEEEKTRFQNELETELKMAVDPLFQVE 549
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....hhhhhhhhhh...eeeeee..hhhhhhhhhhhhh....eeeee......hhhhh...ee..---------------hhhhhhhhhhhh....eeeeeeeee..---------------------------.eeehhhhhhhhh.........eeeeeeeee.hhhhhhhhhhhhhhhh..eeee.eeeeeeeee..eeeeeeeee.....eeeeeeeeeee.hhhhhhhhhhh.......eeeeeeeeeeeee.hhh....eeee........eeeeee..eeee....eee.........hhhhhhhhhhhhhhhh.........eeeeeeeeeeeee.-----------..eee.....eee......hhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh...hhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3da1 A   1 mFSAKKRDKCIGEmSEKQLDLLVIGGGITGAGIALDAQVRGIQTGLVEmNDFASGTSSRSTKLVHG---------------VGKERAIVYENAPHVTTPEWmLLPIFK---------------------------RYmLNEKQTLEKEPLLRKENLKGGGIYVEYRTDDARLTLEImKEAVARGAVALNYmKVESFIYDQGKVVGVVAKDRLTDTTHTIYAKKVVNAAGPWVDTLREKDRSKHGKYLKLSKGVHLVVDQSRFPLRQAVYFDTESDGRmIFAIPREGKTYIGTTDTFYDKDIASPRmTVEDRDYILAAANYmFPSLRLTADDVESSWAGLRPLIHE-----------DEIFFSDSGLISIAGGKLTGYRKmAERTVDAVAQGLNVNEPCTTAAIRLSGGLAEGAQGFPRFLDEASRKGAKLGFDADEVRRLAKLYGSNVDHVLNYAYEGKEEAEHYGLPALLLGQLQYGVEQEmVATPLDFFVRRTGALFFNISLVHQWKEAVLRWmAEEFSWTEEEKTRFQNELETELKmAVDPLFQVE 549
                            |       10   |    20        30        40        50        60     |   -         - |      90       100 |     | -         -         -     | 140       150       160       170      |180       190|      200       210       220       230       240       250       260       270       280       290       300     | 310       320|      330       340    |    -      |360       370       380       390       400       410       420       430       440       450       460       470       480  |    490       500       510     | 520       530       540         
                            |           14-MSE                             49-MSE           66              82                 102-MSE08                         136 |                                    177-MSE       191-MSE                                                                                278-MSE                     306-MSE        321-MSE                 345         357                    380-MSE                                                                                                483-MSE                          516-MSE                 540-MSE     
                            1-MSE                                                                                                                                  138-MSE
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3DA1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DA1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DA1)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9KDW6_BACHD | Q9KDW6)
molecular function
    GO:0004368    glycerol-3-phosphate dehydrogenase activity    Catalysis of the reaction: sn-glycerol 3-phosphate + a quinone = glycerone phosphate + a quinol.
    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:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0052590    sn-glycerol-3-phosphate:ubiquinone oxidoreductase activity    Catalysis of the reaction: sn-glycerol 3-phosphate + a ubiquinone = glycerone phosphate + a ubiquinol.
    GO:0052591    sn-glycerol-3-phosphate:ubiquinone-8 oxidoreductase activity    Catalysis of the reaction: sn-glycerol 3-phosphate + ubiquinone-8 = glycerone phosphate + ubiquinol-8.
biological process
    GO:0006072    glycerol-3-phosphate metabolic process    The chemical reactions and pathways involving glycerol-3-phosphate, a phosphoric monoester of glycerol.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
    GO:0009331    glycerol-3-phosphate dehydrogenase complex    An enzyme complex that catalyzes the dehydrogenation of sn-glycerol 3-phosphate to form glycerone phosphate.

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