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(-) Description

Title :  STRUCTURE OF ALPHA-GLYCEROPHOSPHATE OXIDASE FROM STREPTOCOCCUS SP.: A TEMPLATE FOR THE MITOCHONDRIAL ALPHA-GLYCEROPHOSPHATE DEHYDROGENASE
 
Authors :  T. Colussi, W. Boles, T. C. Mallett, P. A. Karplus, A. Claiborne
Date :  01 Oct 07  (Deposition) - 15 Jan 08  (Release) - 29 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Flavoprotein Oxidase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Colussi, D. Parsonage, W. Boles, T. Matsuoka, T. C. Mallett, P. A. Karplus, A. Claiborne
Structure Of Alpha-Glycerophosphate Oxidase From Streptococcus Sp. : A Template For The Mitochondrial Alpha-Glycerophosphate Dehydrogenase.
Biochemistry V. 47 965 2008
PubMed-ID: 18154320  |  Reference-DOI: 10.1021/BI701685U
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALPHA-GLYCEROPHOSPHATE OXIDASE
    Chains: A
    EC Number: 1.1.3.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE30
    Expression System Strain: B834
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: DELETION OF RESIDUES 356-405
    Gene: GLPO
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS SP.
    Organism Taxid: 1306
    Other Details: CONSTRUCT WITH RESIDUES 356-405 OF STREPTOCOCCUS SP. ALPHA-GLYCEROPHOSPHATE OXIDASE DELETED
    Synonym: FAD DEPENDENT OXIDOREDUCTASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
1FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2MSE12Mod. Amino AcidSELENOMETHIONINE
3SO41Ligand/IonSULFATE ION
Biological Unit 1 (3, 28)
No.NameCountTypeFull Name
1FAD2Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
2MSE24Mod. Amino AcidSELENOMETHIONINE
3SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:235 , LYS A:238 , ASP A:306 , PHE A:307 , THR A:308 , HOH A:655BINDING SITE FOR RESIDUE SO4 A 608
2AC2SOFTWAREGLY A:25 , GLY A:27 , ILE A:28 , THR A:29 , ILE A:47 , GLU A:48 , MSE A:49 , GLN A:50 , GLY A:55 , THR A:56 , SER A:57 , SER A:60 , THR A:61 , LEU A:63 , MSE A:195 , LYS A:196 , ALA A:197 , SER A:232 , GLY A:233 , PRO A:234 , TRP A:235 , GLY A:257 , HIS A:259 , THR A:298 , GLY A:344 , LEU A:345 , ARG A:346 , PRO A:347 , GLY A:428 , LYS A:429 , ILE A:430 , THR A:431 , HOH A:624 , HOH A:734 , HOH A:736 , HOH A:780 , HOH A:786BINDING SITE FOR RESIDUE FAD A 609

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gly A:297 -Thr A:298

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2RGH)

(-) Sequences/Alignments

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:546
 aligned with D0VWY7_STRSP | D0VWY7 from UniProtKB/TrEMBL  Length:557

    Alignment length:557
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       
         D0VWY7_STRSP     - -MFSNKTRQDSIQKMQQEELDLLIIGGGITGAGVAVQAAASGIKTGLIEMQDFAEGTSSRSTKLVHGGIRYLKTFDVEVVADTVGERAVVQGIAPHIPKPDPMLLPIYEDEGATTFNMFSVKVAMDLYDKLANVTGTKYENYTLTPEEVLEREPFLKKEGLKGAGVYLDFRNNDARLVIDNIKKAAEDGAYLVSKMKAVGFLYEGDQIVGVKARDLLTDEVIEIKAKLVINTSGPWVDKVRNLNFTRPVSPKMRPTKGIHLVVDAKKLPVPQPTYFDTGKQDGRMVFAIPRENKTYFGTTDTDYQGDFTDPKVTQEDVDYLLDVINHRYPEANITLADIEASWAGLRPLLIGNSGSPSTISRGSSLEREPDGLLTLSGGKITDYRKMAEGALRLIRQLLKEEYGIETKEIDSKKYQISGGNFDPTKLEETVTELAKEGVAAGLEEEDATYIADFYGTNARRIFELAKEMAPYPGLSLAESARLRYGLEEEMVLAPGDYLIRRTNHLLFERDQLDEIKQPVIDAIAEYFGWTEEEKAQQTKRLEALIAESDLRELKGE 556
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhh...eeee..hhhhhhhhhhhhhh...eeee.......hhhhh...ee..hhhhhhhhhhhhhhhhhhhhhhhhhhh....ee..eeeeee........hhhhhhhhhhhhhhhh.........eeehhhhhhhhh.......eeeeeee..ee.hhhhhhhhhhhhhhhh..eee..eeeeeeeee..eeeeeeeee.....eeeee...eee.hhhhhhhhhh.............eeeeeeeee.hhh.....eeee.......eeeeeee..eeee....ee..........hhhhhhhhhhhhhhhh.....hhhhh.eeeeeee....-----------.eeeee.....eeeee.hhhhhhhhhhhhhhhhhhhhhhhhh.....................hhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhh.......hhhhhhhhhhhhhhh...hhhhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2rgh A   0 CmFSNKTRQDSIQKmQQEELDLLIIGGGITGAGVAVQAAASGIKTGLIEmQDFAEGTSSRSTKLVHGGIRYLKTFDVEVVADTVGERAVVQGIAPHIPKPDPmLLPIYEDEGATTFNmFSVKVAmDLYDKLANVTGTKYENYTLTPEEVLEREPFLKKEGLKGAGVYLDFRNNDARLVIDNIKKAAEDGAYLVSKmKAVGFLYEGDQIVGVKARDLLTDEVIEIKAKLVINTSGPWVDKVRNLNFTRPVSPKmRPTKGIHLVVDAKKLPVPQPTYFDTGKQDGRmVFAIPRENKTYFGTTDTDYQGDFTDPKVTQEDVDYLLDVINHRYPEANITLADIEASWAGLRPLLI-----------GSSLEREPDGLLTLSGGKITDYRKmAEGALRLIRQLLKEEYGIETKEIDSKKYQISGGNFDPTKLEETVTELAKEGVAAGLEEEDATYIADFYGTNARRIFELAKEmAPYPGLSLAESARLRYGLEEEmVLAPGDYLIRRTNHLLFERDQLDEIKQPVIDAIAEYFGWTEEEKAQQTKRLEALIAESDLRELKGE 606
                             |       9    |   19        29        39        49        59        69        79        89        99  |    109       119    |  129       139       149       159       169       179       189     | 199       209       219       229       239       249  |    259       269       279    |  289       299       309       319       329       339       349|        -  |    419       429      |439       449       459       469       479       489       499       509       519       529       539|      549       559       569       579       589       599       
                             |           14-MSE                             49-MSE                                              102-MSE        117-MSE  |                                                                    195-MSE                                                  252-MSE                         284-MSE                                                           350         412                     436-MSE                                                                           518-MSE               540-MSE                                                              
                             1-MSE                                                                                                                    124-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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2RGH)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2RGH)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A   (D0VWY7_STRSP | D0VWY7)
molecular function
    GO:0004368    glycerol-3-phosphate dehydrogenase activity    Catalysis of the reaction: sn-glycerol 3-phosphate + a quinone = glycerone phosphate + a quinol.
    GO:0004369    glycerol-3-phosphate oxidase activity    Catalysis of the reaction: sn-glycerol 3-phosphate + O(2) = glycerone phosphate + H(2)O(2).
    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.
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.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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2rgo SAME PROTEIN, NO DELETION