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(-) Description

Title :  STRUCTURE OF COENZYME F420 DEPENDENT TETRAHYDROMETHANOPTERIN REDUCTASE FROM METHANOBACTERIUM THERMOAUTOTROPHICUM
 
Authors :  S. Shima, E. Warkentin, W. Grabarse, R. K. Thauer, U. Ermler
Date :  15 May 00  (Deposition) - 06 Sep 00  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  A,B  (1x)
Biol. Unit 3:  C,D  (1x)
Keywords :  (Beta, Alpha)8 Barrel, Tim Barrel, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Shima, E. Warkentin, W. Grabarse, M. Sordel, M. Wicke, R. K. Thauer, U. Ermler
Structure Of Coenzyme F(420) Dependent Methylenetetrahydromethanopterin Reductase From Two Methanogenic Archaea.
J. Mol. Biol. V. 300 935 2000
PubMed-ID: 10891279  |  Reference-DOI: 10.1006/JMBI.2000.3909

(-) Compounds

Molecule 1 - COENZYME F420-DEPENDENT N5,N10- METHYLENETETRAHYDROMETHANOPTERIN REDUCTASE
    Chains: A, B, C, D
    Organism Scientific: METHANOTHERMOBACTER THERMAUTOTROPHICUS
    Organism Taxid: 145262

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): ABCD
Biological Unit 2 (1x): AB  
Biological Unit 3 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric Unit (3, 10)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MPO4Ligand/Ion3[N-MORPHOLINO]PROPANE SULFONIC ACID
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MPO4Ligand/Ion3[N-MORPHOLINO]PROPANE SULFONIC ACID
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MPO2Ligand/Ion3[N-MORPHOLINO]PROPANE SULFONIC ACID
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
3MPO2Ligand/Ion3[N-MORPHOLINO]PROPANE SULFONIC ACID

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASN C:2041 , ARG C:2068 , ASN D:3041 , ARG D:3068BINDING SITE FOR RESIDUE CL C 323
02AC2SOFTWAREASN A:41 , ARG A:68 , ASN B:1041 , ARG B:1068BINDING SITE FOR RESIDUE CL B 324
03AC3SOFTWAREGLU A:6 , THR A:34 , HIS A:36 , GLY A:61 , VAL A:62 , ASN A:171 , TYR A:204 , THR A:205 , ILE A:227 , SER A:301 , HOH A:456 , HOH A:475 , HOH A:785BINDING SITE FOR RESIDUE MPO A 331
04AC4SOFTWAREHOH B:449 , HOH B:461 , HOH B:882 , GLU B:1006 , THR B:1034 , HIS B:1036 , GLY B:1061 , VAL B:1062 , ASN B:1171 , TYR B:1204 , THR B:1205BINDING SITE FOR RESIDUE MPO B 332
05AC5SOFTWAREHOH C:361 , HOH C:384 , HOH C:587 , HOH C:729 , HOH C:826 , GLU C:2006 , HIS C:2036 , GLY C:2061 , VAL C:2062 , ASN C:2171 , TYR C:2204 , THR C:2205 , ILE C:2227BINDING SITE FOR RESIDUE MPO C 333
06AC6SOFTWAREHOH D:403 , HOH D:405 , HOH D:883 , GLU D:3006 , THR D:3034 , HIS D:3036 , GLY D:3061 , VAL D:3062 , ASN D:3171 , TYR D:3204 , THR D:3205 , ILE D:3227BINDING SITE FOR RESIDUE MPO D 334
07AC7SOFTWAREPRO A:155 , ILE A:170 , ALA A:180 , ARG A:238 , HOH A:584 , HOH A:798BINDING SITE FOR RESIDUE MPD A 335
08AC8SOFTWAREGLN B:1153 , GLY B:1154 , PRO B:1155 , ILE B:1170 , LEU B:1184 , ARG B:1238BINDING SITE FOR RESIDUE MPD B 336
09AC9SOFTWAREHOH C:482 , HOH C:800 , GLN C:2153 , PRO C:2155 , ILE C:2170 , ALA C:2180 , VAL C:2235 , ARG C:2238BINDING SITE FOR RESIDUE MPD C 337
10BC1SOFTWARELEU D:3158 , ALA D:3181 , LEU D:3184 , ARG D:3238BINDING SITE FOR RESIDUE MPD D 338

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1F07)

(-) Cis Peptide Bonds  (8, 8)

Asymmetric Unit
No.Residues
1Gly A:61 -Val A:62
2Ser A:301 -Pro A:302
3Gly B:1061 -Val B:1062
4Ser B:1301 -Pro B:1302
5Gly C:2061 -Val C:2062
6Ser C:2301 -Pro C:2302
7Gly D:3061 -Val D:3062
8Ser D:3301 -Pro D:3302

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1F07)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1F07)

(-) Exons   (0, 0)

(no "Exon" information available for 1F07)

(-) 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:321
 aligned with MER_METTM | Q50744 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:321
                                    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_METTM      1 MKFGIEFVPNEPIEKIVKLVKLAEDVGFEYAWITDHYNNKNVYETLALIAEGTETIKLGPGVTNPYVRSPAITASAIATLDELSNGRATLGIGPGDKATFDALGIEWVKPVSTIRDAIAMMRTLLAGEKTESGAQLMGVKAVQEKIPIYMGAQGPMMLKTAGEISDGALINASNPKDFEAAVPLIKEGAEAAGKSIADIDVAAYTCCSIDEDAAAAANAAKIVVAFIAAGSPPPVFERHGLPADTGKKFGELLGKGDFGGAIGAVDDALMEAFSVVGTPDEFIPKIEALGEMGVTQYVAGSPIGPDKEKSIKLLGEVIASF  321
               SCOP domains d1f07a_ A: Coenzyme F420 dependent tetrahydromethanopterin reductase                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1f07A00 A:1-321 FMN dependent fluorescent proteins                                                                                                                                                                                                                                                                                CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhh.....eee...hhhhhhhh.....hhhhhhhhhhhhhhhhhh.....................eeee..hhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhh..hhhhheeeeeeeeee..hhhhhhhhhhhhhhhhhhh.hhhhhhhh....hhhhhhhhhhh..hhhhhhhh.hhhhhhhhheeehhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1f07 A    1 MKFGIEFVPNEPIEKIVKLVKLAEDVGFEYAWITDHYNNKNVYETLALIAEGTETIKLGPGVTNPYVRSPAITASAIATLDELSNGRATLGIGPGDKATFDALGIEWVKPVSTIRDAIAMMRTLLAGEKTESGAQLMGVKAVQEKIPIYMGAQGPMMLKTAGEISDGALINASNPKDFEAAVPLIKEGAEAAGKSIADIDVAAYTCCSIDEDAAAAANAAKIVVAFIAAGSPPPVFERHGLPADTGKKFGELLGKGDFGGAIGAVDDALMEAFSVVGTPDEFIPKIEALGEMGVTQYVAGSPIGPDKEKSIKLLGEVIASF  321
                                    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:321
 aligned with MER_METTM | Q50744 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:321
                                    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_METTM      1 MKFGIEFVPNEPIEKIVKLVKLAEDVGFEYAWITDHYNNKNVYETLALIAEGTETIKLGPGVTNPYVRSPAITASAIATLDELSNGRATLGIGPGDKATFDALGIEWVKPVSTIRDAIAMMRTLLAGEKTESGAQLMGVKAVQEKIPIYMGAQGPMMLKTAGEISDGALINASNPKDFEAAVPLIKEGAEAAGKSIADIDVAAYTCCSIDEDAAAAANAAKIVVAFIAAGSPPPVFERHGLPADTGKKFGELLGKGDFGGAIGAVDDALMEAFSVVGTPDEFIPKIEALGEMGVTQYVAGSPIGPDKEKSIKLLGEVIASF  321
               SCOP domains d1f07b_ B: Coenzyme F420 dependent tetrahydromethanopterin reductase                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1f07B00 B:1001-1321 FMN dependent fluorescent proteins                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhhh....eee...hhhhhhhh.....hhhhhhhhhhhhhhhhhh.....................eeee..hhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhh..hhhhheeeeeeeeee..hhhhhhhhhhhhhhhhhhh.hhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1f07 B 1001 MKFGIEFVPNEPIEKIVKLVKLAEDVGFEYAWITDHYNNKNVYETLALIAEGTETIKLGPGVTNPYVRSPAITASAIATLDELSNGRATLGIGPGDKATFDALGIEWVKPVSTIRDAIAMMRTLLAGEKTESGAQLMGVKAVQEKIPIYMGAQGPMMLKTAGEISDGALINASNPKDFEAAVPLIKEGAEAAGKSIADIDVAAYTCCSIDEDAAAAANAAKIVVAFIAAGSPPPVFERHGLPADTGKKFGELLGKGDFGGAIGAVDDALMEAFSVVGTPDEFIPKIEALGEMGVTQYVAGSPIGPDKEKSIKLLGEVIASF 1321
                                  1010      1020      1030      1040      1050      1060      1070      1080      1090      1100      1110      1120      1130      1140      1150      1160      1170      1180      1190      1200      1210      1220      1230      1240      1250      1260      1270      1280      1290      1300      1310      1320 


Chain C from PDB  Type:PROTEIN  Length:321
 aligned with MER_METTM | Q50744 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:321
                                    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_METTM      1 MKFGIEFVPNEPIEKIVKLVKLAEDVGFEYAWITDHYNNKNVYETLALIAEGTETIKLGPGVTNPYVRSPAITASAIATLDELSNGRATLGIGPGDKATFDALGIEWVKPVSTIRDAIAMMRTLLAGEKTESGAQLMGVKAVQEKIPIYMGAQGPMMLKTAGEISDGALINASNPKDFEAAVPLIKEGAEAAGKSIADIDVAAYTCCSIDEDAAAAANAAKIVVAFIAAGSPPPVFERHGLPADTGKKFGELLGKGDFGGAIGAVDDALMEAFSVVGTPDEFIPKIEALGEMGVTQYVAGSPIGPDKEKSIKLLGEVIASF  321
               SCOP domains d1f07c_ C: Coenzyme F420 dependent tetrahydromethanopterin reductase                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1f07C00 C:2001-2321 FMN dependent fluorescent proteins                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhh.....eee...hhhhhhhh.....hhhhhhhhhhhhhhhhhh.....................eeee..hhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhh..hhhhheeeeeeeeee..hhhhhhhhhhhhhhhhhhh.hhhhhhhh....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhh....eeeeeeee..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1f07 C 2001 MKFGIEFVPNEPIEKIVKLVKLAEDVGFEYAWITDHYNNKNVYETLALIAEGTETIKLGPGVTNPYVRSPAITASAIATLDELSNGRATLGIGPGDKATFDALGIEWVKPVSTIRDAIAMMRTLLAGEKTESGAQLMGVKAVQEKIPIYMGAQGPMMLKTAGEISDGALINASNPKDFEAAVPLIKEGAEAAGKSIADIDVAAYTCCSIDEDAAAAANAAKIVVAFIAAGSPPPVFERHGLPADTGKKFGELLGKGDFGGAIGAVDDALMEAFSVVGTPDEFIPKIEALGEMGVTQYVAGSPIGPDKEKSIKLLGEVIASF 2321
                                  2010      2020      2030      2040      2050      2060      2070      2080      2090      2100      2110      2120      2130      2140      2150      2160      2170      2180      2190      2200      2210      2220      2230      2240      2250      2260      2270      2280      2290      2300      2310      2320 


Chain D from PDB  Type:PROTEIN  Length:321
 aligned with MER_METTM | Q50744 from UniProtKB/Swiss-Prot  Length:321

    Alignment length:321
                                    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_METTM      1 MKFGIEFVPNEPIEKIVKLVKLAEDVGFEYAWITDHYNNKNVYETLALIAEGTETIKLGPGVTNPYVRSPAITASAIATLDELSNGRATLGIGPGDKATFDALGIEWVKPVSTIRDAIAMMRTLLAGEKTESGAQLMGVKAVQEKIPIYMGAQGPMMLKTAGEISDGALINASNPKDFEAAVPLIKEGAEAAGKSIADIDVAAYTCCSIDEDAAAAANAAKIVVAFIAAGSPPPVFERHGLPADTGKKFGELLGKGDFGGAIGAVDDALMEAFSVVGTPDEFIPKIEALGEMGVTQYVAGSPIGPDKEKSIKLLGEVIASF  321
               SCOP domains d1f07d_ D: Coenzyme F420 dependent tetrahydromethanopterin reductase                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1f07D00 D:3001-3321 FMN dependent fluorescent proteins                                                                                                                                                                                                                                                                            CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee....hhhhhhhhhhhhhhh...eeee.......hhhhhhhhhhhh....eeee........hhhhhhhhhhhhhhhh.....eee...hhhhhhhhh....hhhhhhhhhhhhhhhhhh.....................eeee..hhhhhhhhhhhh.eeee...hhhhhhhhhhhhhhhhhhh..hhhhheeeeeeeeee..hhhhhhhhhhhhhhhhhhh.hhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheeehhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1f07 D 3001 MKFGIEFVPNEPIEKIVKLVKLAEDVGFEYAWITDHYNNKNVYETLALIAEGTETIKLGPGVTNPYVRSPAITASAIATLDELSNGRATLGIGPGDKATFDALGIEWVKPVSTIRDAIAMMRTLLAGEKTESGAQLMGVKAVQEKIPIYMGAQGPMMLKTAGEISDGALINASNPKDFEAAVPLIKEGAEAAGKSIADIDVAAYTCCSIDEDAAAAANAAKIVVAFIAAGSPPPVFERHGLPADTGKKFGELLGKGDFGGAIGAVDDALMEAFSVVGTPDEFIPKIEALGEMGVTQYVAGSPIGPDKEKSIKLLGEVIASF 3321
                                  3010      3020      3030      3040      3050      3060      3070      3080      3090      3100      3110      3120      3130      3140      3150      3160      3170      3180      3190      3200      3210      3220      3230      3240      3250      3260      3270      3280      3290      3300      3310      3320
   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, 4)

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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1F07)

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (MER_METTM | Q50744)
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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  1f07
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 Related Entries

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(no "Entries Sharing at Least One Protein Chain" available for 1F07)

(-) Related Entries Specified in the PDB File

1ezw STRUCTURE OF COENZYME F420 DEPENDENT TETRAHYDROMETHANOPTERIN REDUCTASE FROM METHANOPYRUS KANDLERI