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(-) Description

Title :  CRYSTAL STRUCTURE OF METHYLENETETRAHYDROMETHANOPTERIN REDUCTASE (MER) IN COMPLEX WITH COENZYME F420
 
Authors :  S. W. Aufhammer, E. Warkentin, U. Ermler, C. H. Hagemeier, R. K. Thauer, S. Shima
Date :  22 Mar 05  (Deposition) - 21 Jun 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.61
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  (Alpha, Beta)8 Barrel, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. W. Aufhammer, E. Warkentin, U. Ermler, C. H. Hagemeier, R. K. Thauer, S. Shima
Crystal Structure Of Methylenetetrahydromethanopterin Reductase (Mer) In Complex With Coenzyme F420: Architecture Of The F420/Fmn Binding Site Of Enzymes Within The Nonprolyl Cis-Peptide Containing Bacterial Luciferase Family
Protein Sci. V. 14 1840 2005
PubMed-ID: 15937276  |  Reference-DOI: 10.1110/PS.041289805
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - COENZYME F420-DEPENDENT N(5),N(10)- METHYLENETETRAHYDROMETHANOPTERIN REDUCTASE
    Chains: A, B, C, D
    EC Number: 1.5.99.11
    Organism Scientific: METHANOSARCINA BARKERI
    Organism Taxid: 2208
    Strain: FUSARO (DSMZ 804)
    Synonym: COG2141;
METHYLENE-H(4)MPT REDUCTASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
11PG1Ligand/Ion2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
2CL2Ligand/IonCHLORIDE ION
3F424Ligand/IonCOENZYME F420

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA B:50 , LEU B:51 , THR B:53 , ASN B:54 , ALA C:50 , LEU C:51 , THR C:53BINDING SITE FOR RESIDUE CL B 4001
2AC2SOFTWAREALA A:50 , LEU A:51 , THR A:53 , ASN A:54 , ALA D:50 , LEU D:51 , THR D:53 , ASN D:54BINDING SITE FOR RESIDUE CL D 4002
3AC3SOFTWARETHR A:34 , ASP A:35 , HIS A:36 , GLY A:61 , VAL A:62 , PRO A:94 , GLY A:95 , ASP A:96 , TRP A:107 , LYS A:109 , PRO A:110 , LEU A:111 , ALA A:112 , GLY A:156 , ALA A:157 , GLN A:158 , GLY A:159 , PRO A:160 , LYS A:161 , MET A:162 , LEU A:174 , ASN A:176 , HOH A:4047 , HOH A:4118BINDING SITE FOR RESIDUE F42 A 328
4AC4SOFTWARETHR B:34 , ASP B:35 , HIS B:36 , GLY B:61 , VAL B:62 , GLY B:95 , ASP B:96 , TRP B:107 , LYS B:109 , LEU B:111 , ALA B:157 , GLN B:158 , GLY B:159 , PRO B:160 , LYS B:161 , MET B:162 , LEU B:174 , ASN B:176 , TYR B:209 , HOH B:4054BINDING SITE FOR RESIDUE F42 B 1328
5AC5SOFTWARETHR C:34 , ASP C:35 , HIS C:36 , GLY C:61 , VAL C:62 , PRO C:94 , GLY C:95 , ASP C:96 , LYS C:109 , PRO C:110 , LEU C:111 , ALA C:112 , ALA C:157 , GLN C:158 , GLY C:159 , PRO C:160 , LYS C:161 , MET C:162 , LEU C:174 , ASN C:176 , TYR C:209 , HOH C:4043BINDING SITE FOR RESIDUE F42 C 2328
6AC6SOFTWARETHR D:34 , ASP D:35 , HIS D:36 , GLY D:61 , VAL D:62 , PRO D:94 , GLY D:95 , ASP D:96 , TRP D:107 , LYS D:109 , PRO D:110 , LEU D:111 , ALA D:112 , GLY D:156 , ALA D:157 , GLN D:158 , GLY D:159 , PRO D:160 , LYS D:161 , MET D:162 , LEU D:174 , ASN D:176 , TYR D:209 , HOH D:4108 , HOH D:4204 , HOH D:4515BINDING SITE FOR RESIDUE F42 D 3328
7AC7SOFTWAREALA C:145 , VAL D:8 , SER D:10 , HIS D:36 , ASN D:38 , ASN D:39 , SER D:307BINDING SITE FOR RESIDUE 1PG D 4003

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1Z69)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric/Biological Unit
No.Residues
1Gly A:61 -Val A:62
2Ser A:307 -Pro A:308
3Gly B:61 -Val B:62
4Ser B:307 -Pro B:308
5Gly C:61 -Val C:62
6Ser C:307 -Pro C:308
7Gly D:61 -Val D:62
8Ser D:307 -Pro D:308

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1Z69)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1Z69)

(-) Exons   (0, 0)

(no "Exon" information available for 1Z69)

(-) 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:327
 aligned with MER_METBF | Q46FV4 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:327
                                    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       
            MER_METBF     1 MKFGIEFVPSDPALKIAYYAKLSEQQGFDHVWITDHYNNRDVYSTLTVLALNTNSIKIGPGVTNSYTRNPAITASSIASIAEISGGRAVLGLGPGDKATFDAMGIAWKKPLATTKEAIQAIRDFISGKKVSMDGEMIKFAGAKLAFKAGNIPIYMGAQGPKMLELAGEIADGVLINASHPKDFEVAVEQIKKGAEKAGRDPSEVDVTAYACFSIDKDPVKAVNAAKVVVAFIVAGSPDLVLERHGIPVEAKSQIGAAIAKGDFGALMGGLVTPQMIEAFSICGTPDDCMKRIKDLEAIGVTQIVAGSPIGPAKEKAIKLIGKEIIAK 327
               SCOP domains d1z69a_ A: automated matches                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1z69A00 A:1-327 FMN dependent fluorescent proteins                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh....eeee..ee....hhhhhhhhhhhhhhhhh....eeee..hhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeee....eeeee..........eeee..hhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhh.hhhhheeeeeeeeee..hhhhhhhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhheeehhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z69 A   1 MKFGIEFVPSDPALKIAYYAKLSEQQGFDHVWITDHYNNRDVYSTLTVLALNTNSIKIGPGVTNSYTRNPAITASSIASIAEISGGRAVLGLGPGDKATFDAMGIAWKKPLATTKEAIQAIRDFISGKKVSMDGEMIKFAGAKLAFKAGNIPIYMGAQGPKMLELAGEIADGVLINASHPKDFEVAVEQIKKGAEKAGRDPSEVDVTAYACFSIDKDPVKAVNAAKVVVAFIVAGSPDLVLERHGIPVEAKSQIGAAIAKGDFGALMGGLVTPQMIEAFSICGTPDDCMKRIKDLEAIGVTQIVAGSPIGPAKEKAIKLIGKEIIAK 327
                                    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       


Chain B from PDB  Type:PROTEIN  Length:327
 aligned with MER_METBF | Q46FV4 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:327
                                    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       
            MER_METBF     1 MKFGIEFVPSDPALKIAYYAKLSEQQGFDHVWITDHYNNRDVYSTLTVLALNTNSIKIGPGVTNSYTRNPAITASSIASIAEISGGRAVLGLGPGDKATFDAMGIAWKKPLATTKEAIQAIRDFISGKKVSMDGEMIKFAGAKLAFKAGNIPIYMGAQGPKMLELAGEIADGVLINASHPKDFEVAVEQIKKGAEKAGRDPSEVDVTAYACFSIDKDPVKAVNAAKVVVAFIVAGSPDLVLERHGIPVEAKSQIGAAIAKGDFGALMGGLVTPQMIEAFSICGTPDDCMKRIKDLEAIGVTQIVAGSPIGPAKEKAIKLIGKEIIAK 327
               SCOP domains d1z69b_ B: automated matches                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1z69B00 B:1-327 FMN dependent fluorescent proteins                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh....eeee..ee....hhhhhhhhhhhhhhhhh....eeee..hhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeee....eeeee..........eeee..hhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhh..hhhhheeeeeeeeee..hhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhheeehhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z69 B   1 MKFGIEFVPSDPALKIAYYAKLSEQQGFDHVWITDHYNNRDVYSTLTVLALNTNSIKIGPGVTNSYTRNPAITASSIASIAEISGGRAVLGLGPGDKATFDAMGIAWKKPLATTKEAIQAIRDFISGKKVSMDGEMIKFAGAKLAFKAGNIPIYMGAQGPKMLELAGEIADGVLINASHPKDFEVAVEQIKKGAEKAGRDPSEVDVTAYACFSIDKDPVKAVNAAKVVVAFIVAGSPDLVLERHGIPVEAKSQIGAAIAKGDFGALMGGLVTPQMIEAFSICGTPDDCMKRIKDLEAIGVTQIVAGSPIGPAKEKAIKLIGKEIIAK 327
                                    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       


Chain C from PDB  Type:PROTEIN  Length:327
 aligned with MER_METBF | Q46FV4 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:327
                                    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       
            MER_METBF     1 MKFGIEFVPSDPALKIAYYAKLSEQQGFDHVWITDHYNNRDVYSTLTVLALNTNSIKIGPGVTNSYTRNPAITASSIASIAEISGGRAVLGLGPGDKATFDAMGIAWKKPLATTKEAIQAIRDFISGKKVSMDGEMIKFAGAKLAFKAGNIPIYMGAQGPKMLELAGEIADGVLINASHPKDFEVAVEQIKKGAEKAGRDPSEVDVTAYACFSIDKDPVKAVNAAKVVVAFIVAGSPDLVLERHGIPVEAKSQIGAAIAKGDFGALMGGLVTPQMIEAFSICGTPDDCMKRIKDLEAIGVTQIVAGSPIGPAKEKAIKLIGKEIIAK 327
               SCOP domains d1z69c_ C: automated matches                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1z69C00 C:1-327 FMN dependent fluorescent proteins                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh....eeee..ee....hhhhhhhhhhhhhhhhh....eeee..hhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeee....eeeee..........eeee..hhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhh..hhhhheeeeeeeeee..hhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhh.hhhhhhhh..hhhhhhhhheeehhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z69 C   1 MKFGIEFVPSDPALKIAYYAKLSEQQGFDHVWITDHYNNRDVYSTLTVLALNTNSIKIGPGVTNSYTRNPAITASSIASIAEISGGRAVLGLGPGDKATFDAMGIAWKKPLATTKEAIQAIRDFISGKKVSMDGEMIKFAGAKLAFKAGNIPIYMGAQGPKMLELAGEIADGVLINASHPKDFEVAVEQIKKGAEKAGRDPSEVDVTAYACFSIDKDPVKAVNAAKVVVAFIVAGSPDLVLERHGIPVEAKSQIGAAIAKGDFGALMGGLVTPQMIEAFSICGTPDDCMKRIKDLEAIGVTQIVAGSPIGPAKEKAIKLIGKEIIAK 327
                                    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       


Chain D from PDB  Type:PROTEIN  Length:327
 aligned with MER_METBF | Q46FV4 from UniProtKB/Swiss-Prot  Length:328

    Alignment length:327
                                    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       
            MER_METBF     1 MKFGIEFVPSDPALKIAYYAKLSEQQGFDHVWITDHYNNRDVYSTLTVLALNTNSIKIGPGVTNSYTRNPAITASSIASIAEISGGRAVLGLGPGDKATFDAMGIAWKKPLATTKEAIQAIRDFISGKKVSMDGEMIKFAGAKLAFKAGNIPIYMGAQGPKMLELAGEIADGVLINASHPKDFEVAVEQIKKGAEKAGRDPSEVDVTAYACFSIDKDPVKAVNAAKVVVAFIVAGSPDLVLERHGIPVEAKSQIGAAIAKGDFGALMGGLVTPQMIEAFSICGTPDDCMKRIKDLEAIGVTQIVAGSPIGPAKEKAIKLIGKEIIAK 327
               SCOP domains d1z69d_ D: automated matches                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1z69D00 D:1-327 FMN dependent fluorescent proteins                                                                                                                                                                                                                                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh....eeee..ee....hhhhhhhhhhhhhhhhh....eeee..hhhhhhhhh....hhhhhhhhhhhhhhhhhh...eeee....eeeee..........eeee..hhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhhh.hhhhheeeeeeeeee..hhhhhhhhhhhhhhhhhh..hhhhhhhh....hhhhhhhhhhhh.hhhhhhh...hhhhhhhhheeehhhhhhhhhhhhhhhh..eeeeeeee..hhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1z69 D   1 MKFGIEFVPSDPALKIAYYAKLSEQQGFDHVWITDHYNNRDVYSTLTVLALNTNSIKIGPGVTNSYTRNPAITASSIASIAEISGGRAVLGLGPGDKATFDAMGIAWKKPLATTKEAIQAIRDFISGKKVSMDGEMIKFAGAKLAFKAGNIPIYMGAQGPKMLELAGEIADGVLINASHPKDFEVAVEQIKKGAEKAGRDPSEVDVTAYACFSIDKDPVKAVNAAKVVVAFIVAGSPDLVLERHGIPVEAKSQIGAAIAKGDFGALMGGLVTPQMIEAFSICGTPDDCMKRIKDLEAIGVTQIVAGSPIGPAKEKAIKLIGKEIIAK 327
                                    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
   Legend:   → Mismatch (orange background)
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  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, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1Z69)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (MER_METBF | Q46FV4)
molecular function
    GO:0018537    coenzyme F420-dependent N5,N10-methenyltetrahydromethanopterin reductase activity    Catalysis of the reaction: 5-methyltetrahydromethanopterin + coenzyme F420 + H(+) = 5,10-methylenetetrahydromethanopterin + reduced coenzyme F420.
    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:0016705    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
biological process
    GO:0015948    methanogenesis    The chemical reactions and pathways resulting in the formation of methane, a colorless, odorless, flammable gas with the formula CH4. It is the simplest of the alkanes.
    GO:0019386    methanogenesis, from carbon dioxide    The chemical reactions and pathways resulting in the formation of methane, a colorless, odorless, flammable gas with the formula CH4, from other compounds, including carbon dioxide (CO2).
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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  1z69
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  MER_METBF | Q46FV4
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 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 1Z69)

(-) Related Entries Specified in the PDB File

1ezw THE SAME PROTEIN FROM A DIFFERENT ORGANISM
1f07 THE SAME PROTEIN FROM A DIFFERENT ORGANISM