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(-) Description

Title :  CRYSTAL STRUCTURE OF A GERANYLGERANYL BACTERIOCHLOROPHYLL REDUCTASE-LIKE (TA0516) FROM THERMOPLASMA ACIDOPHILUM AT 1.60 A RESOLUTION
 
Authors :  Joint Center For Structural Genomics (Jcsg)
Date :  24 Sep 10  (Deposition) - 27 Oct 10  (Release) - 20 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi-Biology, Flavoprotein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Q. Xu, T. Eguchi, I. I. Mathews, C. L. Rife, H. J. Chiu, C. L. Farr, J. Feuerhelm, L. Jaroszewski, H. E. Klock, M. W. Knuth, M. D. Miller, D. Weekes, M. A. Elsliger, A. M. Deacon, A. Godzik, S. A. Lesley, I. A. Wilson
Insights Into Substrate Specificity Of Geranylgeranyl Reductases Revealed By The Structure Of Digeranylgeranylglycerophospholipid Reductase, An Essential Enzyme In The Biosynthesis Of Archaeal Membrane Lipids.
J. Mol. Biol. V. 404 403 2010
PubMed-ID: 20869368  |  Reference-DOI: 10.1016/J.JMB.2010.09.032

(-) Compounds

Molecule 1 - DIGERANYLGERANYLGLYCEROPHOSPHOLIPID REDUCTASE
    Chains: A
    EC Number: 1.3.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: SPEEDET
    Expression System Strain: HK100
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TA0516
    Organism Common: ARCHAEA
    Organism Scientific: THERMOPLASMA ACIDOPHILUM
    Organism Taxid: 2303
    Synonym: DGGGPL REDUCTASE, 2,3-DI-O-GERANYLGERANYLGLYCERYL PHOSPHATE REDUCTASE, GERANYLGERANYL REDUCTASE, GGR

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 27)

Asymmetric/Biological Unit (5, 27)
No.NameCountTypeFull Name
1EDO11Ligand/Ion1,2-ETHANEDIOL
2FAD1Ligand/IonFLAVIN-ADENINE DINUCLEOTIDE
3GOL2Ligand/IonGLYCEROL
4MSE12Mod. Amino AcidSELENOMETHIONINE
5OZ21Ligand/Ion(2R)-3-{[(R)-{[(2S)-2,3-DIHYDROXYPROPYL]OXY}(HYDROXY)PHOSPHORYL]OXY}-2-[(6Z)-TRIDEC-6-ENOYLOXY]PROPYL (9Z)-OCTADEC-9-ENOATE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:10 , GLY A:12 , PRO A:13 , GLY A:14 , GLU A:33 , LYS A:34 , ARG A:35 , ARG A:43 , CYS A:44 , GLY A:45 , GLU A:46 , GLY A:47 , ARG A:100 , PRO A:123 , ALA A:124 , ALA A:156 , ASP A:157 , GLY A:158 , GLU A:162 , PHE A:213 , VAL A:264 , GLY A:282 , ASP A:283 , GLY A:294 , GLY A:295 , ILE A:296 , ALA A:299 , OZ2 A:502 , HOH A:517 , HOH A:518 , HOH A:524 , HOH A:528 , HOH A:622 , HOH A:623 , HOH A:628 , HOH A:630 , HOH A:687BINDING SITE FOR RESIDUE FAD A 501
02AC2SOFTWARESER A:49 , TYR A:209 , TRP A:211 , PRO A:290 , ILE A:291 , THR A:292 , GLY A:293 , LYS A:338 , LEU A:349 , ILE A:372 , SER A:373 , VAL A:374 , FAD A:501 , EDO A:508 , GOL A:515 , HOH A:655 , HOH A:805 , HOH A:836BINDING SITE FOR RESIDUE OZ2 A 502
03AC3SOFTWAREVAL A:118 , TRP A:119 , VAL A:120 , HIS A:141 , HOH A:575 , HOH A:790BINDING SITE FOR RESIDUE EDO A 503
04AC4SOFTWARELYS A:138 , GLU A:312 , GLU A:315 , HOH A:616BINDING SITE FOR RESIDUE EDO A 504
05AC5SOFTWAREGLY A:132 , LYS A:133 , VAL A:134 , MSE A:275 , HOH A:585BINDING SITE FOR RESIDUE EDO A 505
06AC6SOFTWARETYR A:4 , HOH A:670 , HOH A:747BINDING SITE FOR RESIDUE EDO A 506
07AC7SOFTWAREASN A:177 , SER A:227 , LYS A:346 , GLU A:347 , HOH A:617 , HOH A:785BINDING SITE FOR RESIDUE EDO A 507
08AC8SOFTWAREASP A:289 , THR A:292 , GLY A:294 , ASN A:298 , OZ2 A:502 , EDO A:509BINDING SITE FOR RESIDUE EDO A 508
09AC9SOFTWAREASN A:298 , VAL A:301 , ARG A:334 , LYS A:338 , EDO A:508 , HOH A:666BINDING SITE FOR RESIDUE EDO A 509
10BC1SOFTWAREASP A:117 , TRP A:119 , HOH A:635BINDING SITE FOR RESIDUE EDO A 510
11BC2SOFTWAREHOH A:558 , HOH A:684 , HOH A:769 , HOH A:788BINDING SITE FOR RESIDUE EDO A 511
12BC3SOFTWAREALA A:23 , LEU A:27 , HOH A:557 , HOH A:633 , HOH A:705BINDING SITE FOR RESIDUE EDO A 512
13BC4SOFTWAREGLY A:254 , LYS A:270 , MSE A:271 , HOH A:589 , HOH A:626 , HOH A:672 , HOH A:765BINDING SITE FOR RESIDUE EDO A 513
14BC5SOFTWAREPRO A:272 , THR A:274 , MSE A:275 , PRO A:321 , MSE A:324 , GLN A:325 , GLU A:328 , HOH A:604BINDING SITE FOR RESIDUE GOL A 514
15BC6SOFTWAREGLY A:47 , LEU A:48 , SER A:49 , VAL A:69 , THR A:197 , OZ2 A:502BINDING SITE FOR RESIDUE GOL A 515

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OZ2)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:40 -Pro A:41
2Mse A:271 -Pro A:272

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OZ2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OZ2)

(-) Exons   (0, 0)

(no "Exon" information available for 3OZ2)

(-) 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:397
 aligned with GGR_THEAC | Q9HKS9 from UniProtKB/Swiss-Prot  Length:396

    Alignment length:397
                             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       
            GGR_THEAC     - -METYDVLVVGGGPGGSTAARYAAKYGLKTLMIEKRPEIGSPVRCGEGLSKGILNEADIKADRSFIANEVKGARIYGPSEKRPIILQSEKAGNEVGYVLERDKFDKHLAALAAKAGADVWVKSPALGVIKENGKVAGAKIRHNNEIVDVRAKMVIAADGFESEFGRWAGLKSVILARNDIISALQYRMINVDVDPDYTDFYLGSIAPAGYIWVFPKGEGMANVGIGSSINWIHNRFELKNYLDRFIENHPGLKKGQDIQLVTGGVSVSKVKMPITMPGLMLVGDAARLIDPITGGGIANAIVSGMYAAQVTKEAIESNDYSPQMMQKYEKLIKERFERKHLRNWVAKEKLAMLSDDTLDKLVDIVSEQVLTTISVEAILKAIAEKYPEVVKELEDLI 396
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---FAD_binding_3-3oz2A01 A:3-221                                                                                                                                                                                              ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee..hhhhhhhhhhhhhh...eeee..............eeehhhhhhh........eeeee.eeeee.......eeee........eeeehhhhhhhhhhhhhhhhh.eee....eeeeeee..eeeeeeeee..eeeeeeeeeeee.....hhhhhhhhhhhhh.hhh.eeeeeeeeee.......eeeee.......eeeeeeeee..eeeeeeeee.....hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeee........ee..eee.hhhhh........hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oz2 A   0 GmETYDVLVVGGGPGGSTAARYAAKYGLKTLmIEKRPEIGSPVRCGEGLSKGILNEADIKADRSFIANEVKGARIYGPSEKRPIILQSEKAGNEVGYVLERDKFDKHLAALAAKAGADVWVKSPALGVIKENGKVAGAKIRHNNEIVDVRAKmVIAADGFESEFGRWAGLKSVILARNDIISALQYRmINVDVDPDYTDFYLGSIAPAGYIWVFPKGEGmANVGIGSSINWIHNRFELKNYLDRFIENHPGLKKGQDIQLVTGGVSVSKVKmPITmPGLmLVGDAARLIDPITGGGIANAIVSGmYAAQVTKEAIESNDYSPQmmQKYEKLIKERFERKHLRNWVAKEKLAmLSDDTLDKLVDIVSEQVLTTISVEAILKAIAEKYPEVVKELEDLI 396
                             |       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       
                             |                            31-MSE                                                                                                                  152-MSE                            187-MSE                         219-MSE                                             271-MSE   |                      304-MSE            323-MSE                     351-MSE                                         
                             1-MSE                                                                                                                                                                                                                                                                           275-MSE                                          324-MSE                                                                    
                                                                                                                                                                                                                                                                                                                 279-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 3OZ2)

(-) CATH Domains  (0, 0 ; only for superseded entry 3CGV: 2,2)

(no "CATH Domain" information available for 3OZ2, only for superseded entry 3CGV replaced by 3OZ2)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: NADP_Rossmann (1239)

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (GGR_THEAC | Q9HKS9)
molecular function
    GO:0071949    FAD binding    Interacting selectively and non-covalently with the oxidized form, FAD, of flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes.
    GO:0051287    NAD binding    Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0050660    flavin adenine dinucleotide binding    Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
    GO:0045550    geranylgeranyl reductase activity    Catalysis of the formation of phytyl group from the stepwise reduction of a geranylgeranyl group.
    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:0016628    oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-CH group acts as a hydrogen or electron donor and reduces NAD or NADP.
biological process
    GO:0006650    glycerophospholipid metabolic process    The chemical reactions and pathways involving glycerophospholipids, any derivative of glycerophosphate that contains at least one O-acyl, O-alkyl, or O-alkenyl group attached to the glycerol residue.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    GO:0046467    membrane lipid biosynthetic process    The chemical reactions and pathways resulting in the formation of membrane lipids, any lipid found in or associated with a biological membrane.
    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.
    GO:0008654    phospholipid biosynthetic process    The chemical reactions and pathways resulting in the formation of phospholipids, any lipid containing phosphoric acid as a mono- or diester.
cellular component
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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