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(-) Description

Title :  CRYSTAL STRUCTURE OF AN AMIDE BOND FORMING F420-GAMMA GLUTAMYL LIGASE FROM ARCHAEOGLOBUS FULGIDUS
 
Authors :  B. Nocek, E. Evdokimova, M. Kudritska, A. Edwards, A. Savchenko, A. Joa Midwest Center For Structural Genomics (Mcsg)
Date :  11 Apr 07  (Deposition) - 15 May 07  (Release) - 19 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Gamma-Glutamyl Ligase, Coenzyme F420 Biosynthesis, Amide Bond Forming Enzyme, Metal Dependent, New Fold, Gdp Binding, Mcsg, Structural Genomics, Psi-2, Protein Structure Initiative, Midwest Center For Structural Genomics, 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):Gammagamma-Glutamyl Ligase From Archaeoglobus Fulgidus - A Member Of A New Family Of Non-Ribosomal Peptid Synthases.
J. Mol. Biol. V. 372 456 2007
PubMed-ID: 17669425  |  Reference-DOI: 10.1016/J.JMB.2007.06.063

(-) Compounds

Molecule 1
    Atcc: 49558
    Chains: A, B
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET15B
    Expression System Strain: BL21GOLD
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: COFE, AF_2256
    Organism Scientific: ARCHAEOGLOBUS FULGIDUS DSM 4304
    Organism Taxid: 224325
    Strain: DSM 4304, VC-16, JCM 9628, NBRC 100126

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric/Biological Unit (5, 15)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2EDO4Ligand/Ion1,2-ETHANEDIOL
3GDP2Ligand/IonGUANOSINE-5'-DIPHOSPHATE
4GOL1Ligand/IonGLYCEROL
5MN4Ligand/IonMANGANESE (II) ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:151 , GLU A:208 , GDP A:2696 , HOH A:4042 , HOH A:4080BINDING SITE FOR RESIDUE MN A 2001
02AC2SOFTWAREASP A:109 , ASP A:150 , GDP A:2696 , HOH A:4008 , HOH A:4065 , HOH A:4092BINDING SITE FOR RESIDUE MN A 2002
03AC3SOFTWAREPHE A:6 , VAL A:28 , ARG A:29 , ARG A:219 , HOH A:4208 , ARG B:2BINDING SITE FOR RESIDUE ACT A 3001
04AC4SOFTWAREPHE A:92 , ACT A:3003 , HOH A:4044 , ARG B:234 , GLU B:238 , ASP B:239 , VAL B:240 , ILE B:241BINDING SITE FOR RESIDUE ACT A 3002
05AC5SOFTWAREGLY A:153 , ARG A:154 , CYS A:155 , ACT A:3002 , HOH A:4124 , HOH A:4209 , PHE B:156 , ILE B:241BINDING SITE FOR RESIDUE ACT A 3003
06AC6SOFTWARETHR B:151 , GLU B:208 , GDP B:2697 , HOH B:3045 , HOH B:3061BINDING SITE FOR RESIDUE MN B 2001
07AC7SOFTWAREASP B:109 , ASP B:150 , GDP B:2697 , HOH B:3052 , HOH B:3066 , HOH B:3167BINDING SITE FOR RESIDUE MN B 2002
08AC8SOFTWAREVAL B:104 , GLY B:153 , ARG B:154 , CYS B:155 , HOH B:3128BINDING SITE FOR RESIDUE ACT B 3001
09AC9SOFTWARELEU A:11 , PRO A:12 , LEU A:13 , ILE A:14 , CYS A:39 , SER A:40 , THR A:41 , VAL A:42 , LYS A:45 , ASP A:109 , ASN A:112 , THR A:149 , ASP A:150 , THR A:151 , MET A:206 , GLY A:207 , GLU A:208 , GLY A:209 , ASP A:211 , GLY A:212 , ILE A:213 , PRO A:214 , MN A:2001 , MN A:2002 , HOH A:4008 , HOH A:4028 , HOH A:4042 , HOH A:4080 , HOH A:4091 , HOH A:4188 , LEU B:182BINDING SITE FOR RESIDUE GDP A 2696
10BC1SOFTWARELYS A:174 , LEU A:221 , ASN A:222 , HOH A:4113BINDING SITE FOR RESIDUE EDO A 1001
11BC2SOFTWARELEU A:204 , LYS B:174 , ASN B:222 , HOH B:3118BINDING SITE FOR RESIDUE EDO A 1002
12BC3SOFTWARELEU A:88 , PHE A:90 , GLU A:237 , HOH A:4166 , VAL B:240 , CYS B:244BINDING SITE FOR RESIDUE EDO A 1003
13BC4SOFTWAREHOH A:4015 , HOH A:4029 , HOH A:4045 , HOH A:4062BINDING SITE FOR RESIDUE EDO A 1004
14BC5SOFTWARELEU A:182 , LEU B:11 , PRO B:12 , LEU B:13 , ILE B:14 , CYS B:39 , SER B:40 , THR B:41 , VAL B:42 , LYS B:45 , ASP B:109 , ASN B:112 , THR B:149 , ASP B:150 , THR B:151 , MET B:206 , GLY B:207 , GLU B:208 , GLY B:209 , ASP B:211 , GLY B:212 , ILE B:213 , PRO B:214 , MN B:2001 , MN B:2002 , HOH B:3017 , HOH B:3033 , HOH B:3045 , HOH B:3061 , HOH B:3167 , HOH B:3269BINDING SITE FOR RESIDUE GDP B 2697
15BC6SOFTWAREGLU A:9 , GLY A:10 , LEU A:11 , ASP A:211 , GLY A:212 , ILE A:213 , HOH A:4052 , HOH A:4086 , HOH A:4290BINDING SITE FOR RESIDUE GOL A 4001

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:155 -B:155
2A:244 -B:248
3A: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 2PHN)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2PHN)

(-) 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:248
 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 d2phna_ A: F420-0:gamma-glutamyl ligase CofE                                                                                                                                                                                                             SCOP domains
               CATH domains 2phnA01 A:2-49,A:122-228 CofE-like              2phnA02 A:50-121,A:229-249 CofE-like domain                             2phnA01 A:2-49,A:122-228 CofE-like                                                                         2phnA02               CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee...........hhhhhhhh........eeeeehhhhhhhh..eee.hhh..hhhhhhhhhhhh.hhhhhhhhhhheeeeee.....eeee....eee.hhh........eee....hhhhhhhhhhhhhhhhhh...eeeeeeeeee..eeeeeeeeeeee.....ee...............eehhhhhhhhhhhhhhh.......eeeee........hhhhh......hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2phn A   2 RVEVFPVEGLPLIKEGDDLAELISSRVRFEDGDVLVVCSTVISKAEGRIRRLEEFNPSERAKEIAARIGKPAEFVQAVLEESEEVLLDFPFLLVKAKFGNVCVNAGIDASNVEEGSLLLPPLDPDGSAEKLRRRILELTGKRVGVIITDTNGRCFRRGVVGFAIGISGVKAMKDWIGRKDLYGRELEVTVECVADEIAAFANLLMGEGGDGIPAVVVRGLNVAGEGSMEEIYRSEEEDVIRRCLKRCL 249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241        


Chain B from PDB  Type:PROTEIN  Length:249
 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 d2phnb_ B: F420-0:gamma-glutamyl ligase CofE                                                                                                                                                                                                              SCOP domains
               CATH domains 2phnB01 B:1-49,B:122-228 CofE-like               2phnB02 B:50-121,B:229-249 CofE-like domain                             2phnB01 B:1-49,B:122-228 CofE-like                                                                         2phnB02               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...........hhhhhhhh........eeeeehhhhhhhh..eee.hhh..hhhhhhhhhhhh.hhhhhhhhhhheeeeee.....eeee....eee.hhh........eee....hhhhhhhhhhhhhhhhhh...eeeeeeeeee..eeeeeeeeeeee.....ee...............eehhhhhhhhhhhhhhh.......eeeee........hhhhh......hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2phn B   1 MRVEVFPVEGLPLIKEGDDLAELISSRVRFEDGDVLVVCSTVISKAEGRIRRLEEFNPSERAKEIAARIGKPAEFVQAVLEESEEVLLDFPFLLVKAKFGNVCVNAGIDASNVEEGSLLLPPLDPDGSAEKLRRRILELTGKRVGVIITDTNGRCFRRGVVGFAIGISGVKAMKDWIGRKDLYGRELEVTVECVADEIAAFANLLMGEGGDGIPAVVVRGLNVAGEGSMEEIYRSEEEDVIRRCLKRCL 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
   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 2PHN)

(-) 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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 Related Entries

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

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        COFE_ARCFU | O28028: 2g9i

(-) Related Entries Specified in the PDB File

2g9i APO-COFE STRUCTURE