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(-) Description

Title :  CRYSTAL STRUCTURE OF HOMOLOG OF F420-0:GAMMA-GLUTAMYL LIGASE FROM ARCHAEOGLOBUS FULGIDUS REVEALS A NOVEL FOLD.
 
Authors :  B. Nocek, E. Evdokimova, M. Kudritska, A. Savchenko, A. Edwards, A. Joa Midwest Center For Structural Genomics (Mcsg)
Date :  06 Mar 06  (Deposition) - 04 Apr 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cofe Homolog, Homolog Of F420-0:Gamma-Glutamyl Ligase, Gamma-Glutamyl Ligase, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. Nocek, E. Evdokimova, M. Proudfoot, M. Kudritska, L. L. Grochowski R. H. White, A. Savchenko, A. F. Yakunin, A. Edwards, A. Joachimiak
Structure Of An Amide Bond Forming F(420):Gamma-Glutamyl Ligase From Archaeoglobus Fulgidus -- A Member Of A New Family Of Non-Ribosomal Peptide Synthases.
J. Mol. Biol. V. 372 456 2007
PubMed-ID: 17669425  |  Reference-DOI: 10.1016/J.JMB.2007.06.063

(-) Compounds

Molecule 1
    Chains: A, B
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET15B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: COFE
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS
    Organism Taxid: 224325
    Strain: DSM 4304

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 7)

Asymmetric/Biological Unit (1, 7)
No.NameCountTypeFull Name
1MSE7Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 2G9I)

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:155 -B:155
2A:248 -B:244

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:90 -Pro A:91
2Phe B:90 -Pro B:91

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2G9I)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2G9I)

(-) Exons   (0, 0)

(no "Exon" information available for 2G9I)

(-) 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:233
 aligned with COFE_ARCFU | O28028 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:249
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240         
           COFE_ARCFU     1 MRVEVFPVEGLPLIKEGDDLAELISSRVRFEDGDVLVVCSTVISKAEGRIRRLEEFNPSERAKEIAARIGKPAEFVQAVLEESEEVLLDFPFLLVKAKFGNVCVNAGIDASNVEEGSLLLPPLDPDGSAEKLRRRILELTGKRVGVIITDTNGRCFRRGVVGFAIGISGVKAMKDWIGRKDLYGRELEVTVECVADEIAAFANLLMGEGGDGIPAVVVRGLNVAGEGSMEEIYRSEEEDVIRRCLKRCL 249
               SCOP domains d2g9ia1 A:1-249 F420-0:gamma-glutamyl ligase CofE                                                                                                                                                                                                         SCOP domains
               CATH domains -2g9iA01 A:2-49,A:122-228 CofE-like              2g9iA02 A:50-121,A:230-249 CofE-like domain                             2g9iA01 A:2-49,A:122-228 CofE-like                                                                         -2g9iA02              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee..........hhhhhhhhhh......eeeeehhhhhhhh..eee.hhh..hhhhhhhhhhhh.hhhhhhhhhhheeeeee.....eeee....eee.hhh........eee....hhhhhhhhhhhhhhhhhh...eeeeeeee........eeeeeeee....eee.------------..eeehhhhhhhhhhhhh.----...eeeee........hhhhh......hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g9i A   1 mRVEVFPVEGLPLIKEGDDLAELISSRVRFEDGDVLVVCSTVISKAEGRIRRLEEFNPSERAKEIAARIGKPAEFVQAVLEESEEVLLDFPFLLVKAKFGNVCVNAGIDASNVEEGSLLLPPLDPDGSAEKLRRRILELTGKRVGVIITDTNGRCFRRGVVGFAIGISGVKAmKDW------------VTVECVADEIAAFANLLmG----GIPAVVVRGLNVAGEGSmEEIYRSEEEDVIRRCLKRCL 249
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170  |  |   -       190       200     ||  - |     220       230       240         
                            |                                                                                                                                                                         173-MSE         189              206-MSE12              229-MSE                
                            1-MSE                                                                                                                                                                        176                            207                                          


Chain B from PDB  Type:PROTEIN  Length:232
 aligned with COFE_ARCFU | O28028 from UniProtKB/Swiss-Prot  Length:249

    Alignment length:248
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241        
           COFE_ARCFU     2 RVEVFPVEGLPLIKEGDDLAELISSRVRFEDGDVLVVCSTVISKAEGRIRRLEEFNPSERAKEIAARIGKPAEFVQAVLEESEEVLLDFPFLLVKAKFGNVCVNAGIDASNVEEGSLLLPPLDPDGSAEKLRRRILELTGKRVGVIITDTNGRCFRRGVVGFAIGISGVKAMKDWIGRKDLYGRELEVTVECVADEIAAFANLLMGEGGDGIPAVVVRGLNVAGEGSMEEIYRSEEEDVIRRCLKRCL 249
               SCOP domains d2g9ib_ B: F420-0:gamma-glutamyl ligase CofE                                                                                                                                                                                                             SCOP domains
               CATH domains 2g9iB01 B:2-49,B:122-228 CofE-like              2g9iB02 B:50-121,B:230-249 CofE-like domain                             2g9iB01 B:2-49,B:122-228 CofE-like                                                                         -2g9iB02              CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...........hhhhhhhhhh......eeeeehhhhhhhh..eee.hhh..hhhhhhhhhhhh.hhhhhhhhhhheeeeee.....eeee....eee.hhh........eee....hhhhhhhhhhhhhhhhhh...eeeeeeee........eeeeeeee.....ee.------------..eehhhhhhhhhhhhhh.----...eeeee........hhhhh......hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2g9i B   2 RVEVFPVEGLPLIKEGDDLAELISSRVRFEDGDVLVVCSTVISKAEGRIRRLEEFNPSERAKEIAARIGKPAEFVQAVLEESEEVLLDFPFLLVKAKFGNVCVNAGIDASNVEEGSLLLPPLDPDGSAEKLRRRILELTGKRVGVIITDTNGRCFRRGVVGFAIGISGVKAmKDW------------VTVECVADEIAAFANLLmG----GIPAVVVRGLNVAGEGSmEEIYRSEEEDVIRRCLKRCL 249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171 |  |    -       191       201    ||   -|      221       231       241        
                                                                                                                                                                                                     173-MSE         189              206-MSE12              229-MSE                
                                                                                                                                                                                                        176                            207
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2G9I)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (COFE_ARCFU | O28028)
molecular function
    GO:0005525    GTP binding    Interacting selectively and non-covalently with GTP, guanosine triphosphate.
    GO:0043773    coenzyme F420-0 gamma-glutamyl ligase activity    Catalysis of the reactions: (1) GTP + F420-0 + L-glutamate = GDP + phosphate + F420-1, and (2) GTP + F420-1 + L-glutamate = GDP + phosphate + gamma-F420-2. This is the GTP-dependent successive addition of two L-glutamates to the L-lactyl phosphodiester of 7,8-didemethyl-8-hydroxy-5-deazariboflavin (F420-0) to form F420-0-glutamyl-glutamate (F420-2), with a gamma-linkage between the two glutamates.
    GO:0052618    coenzyme F420-0:L-glutamate ligase activity    Catalysis of the reaction: GTP + L-glutamate + factor F420-0 = GDP + H+ + factor gamma-F420-1 + phosphate.
    GO:0052619    coenzyme F420-1:gamma-L-glutamate ligase activity    Catalysis of the reaction: GTP + L-glutamate + factor gamma-F420-1 = GDP + H+ + factor gamma-F420-2 + phosphate.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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.
biological process
    GO:0052645    F420-0 metabolic process    The chemical reactions and pathways involving F420-0 (5-O-{[(1S)-1-carboxyethoxy](hydroxy)phosphoryl}-1-deoxy-1-(8-hydroxy-2,4-dioxo-2H-pyrimido[4,5-b]quinolin-10(4H)-yl)-D-ribitol), the fragment of coenzyme F420 remaining after formal hydrolytic removal of all of the glutamate residues.
    GO:0009108    coenzyme biosynthetic process    The chemical reactions and pathways resulting in the formation of coenzymes, any of various nonprotein organic cofactors that are required, in addition to an enzyme and a substrate, for an enzymatic reaction to proceed.
    GO:0051188    cofactor biosynthetic process    The chemical reactions and pathways resulting in the formation of a cofactor, a substance that is required for the activity of an enzyme or other protein.

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