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(-) Description

Title :  TLS REFINEMENT OF THE STRUCTURE OF SE-METHIONINE LABELLED COENZYME F420-DEPENDENT METHYLENETETRAHYDROMETHANOPTERIN DEHYDROGENASE (MTD) FROM METHANOPYRUS KANDLERI
 
Authors :  E. Warkentin, C. H. Hagemeier, S. Shima, R. K. Thauer, U. Ermler
Date :  30 Jul 04  (Deposition) - 01 Feb 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Monomer: Alpha/Beta Domain, Helix Bundle; Trimer Of Dimers, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Warkentin, C. H. Hagemeier, S. Shima, R. K. Thauer, U. Ermler
The Structure Of F420-Dependent Methylenetetrahydromethanopterin Dehydrogenase: A Crystallographic 'Superstructure' Of The Selenomethionine-Labelled Protein Crystal Structure.
Acta Crystallogr. , Sect. D V. 61 198 2005
PubMed-ID: 15681872  |  Reference-DOI: 10.1107/S0907444904030732
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - F420-DEPENDENT METHYLENETETRAHYDROMETHANOPTERIN DEHYDROGENASE
    Chains: A, B, C
    EC Number: 1.5.99.9
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PET17B
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Gene: MTD
    Organism Scientific: METHANOPYRUS KANDLERI
    Organism Taxid: 2320
    Synonym: MTD, COENZYME F420 DEPENDENT N5,N10- METHYLENETETRAHYDROMETHANOPTERIN DEHYDROGENASE

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 52)

Asymmetric Unit (2, 52)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
2MSE48Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 96)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2MSE96Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:4009 , HOH A:4014 , HOH A:4025 , HOH A:4034 , HOH A:4487 , HOH B:4046BINDING SITE FOR RESIDUE MG A 5001
2AC2SOFTWAREHOH A:4036 , HOH A:4089 , HOH A:4190 , HOH A:4488 , HOH B:4057 , HOH B:4081BINDING SITE FOR RESIDUE MG A 5002
3AC3SOFTWAREHOH A:4091 , HOH A:4210 , HOH A:4213 , HOH A:4510 , HOH B:4184 , HOH B:4299BINDING SITE FOR RESIDUE MG A 5003
4AC4SOFTWAREHOH A:4178 , HOH A:4180 , HOH A:4279 , HOH A:4361BINDING SITE FOR RESIDUE MG A 5004

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1U6K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1U6K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1U6K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1U6K)

(-) Exons   (0, 0)

(no "Exon" information available for 1U6K)

(-) 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:282
 aligned with MTD_METKA | P94951 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:282
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281  
            MTD_METKA     2 TVAKAIFIKCGNLGTSMMMDMLLDERADREDVEFRVVGTSVKMDPECVEAAVEMALDIAEDFEPDFIVYGGPNPAAPGPSKAREMLADSEYPAVIIGDAPGLKVKDEMEEQGLGYILVKPDAMLGARREFLDPVEMAIYNADLMKVLAATGVFRVVQEAFDELIEKAKEDEISENDLPKLVIDRNTLLEREEFENPYAMVKAMAALEIAENVADVSVEGCFVEQDKERYVPIVASAHEMMRKAAELADEARELEKSNDAVLRTPHAPDGKVLSKRKFMEDPE 283
               SCOP domains d1u6ka_ A: F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeee...hhhhhhhhhhhh.......eeeeeee.....hhhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhh..eeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.eeeehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1u6k A   2 TVAKAIFIKCGNLGTSmmmDmLLDERADREDVEFRVVGTSVKmDPECVEAAVEmALDIAEDFEPDFIVYGGPNPAAPGPSKAREmLADSEYPAVIIGDAPGLKVKDEmEEQGLGYILVKPDAmLGARREFLDPVEmAIYNADLmKVLAATGVFRVVQEAFDELIEKAKEDEISENDLPKLVIDRNTLLEREEFENPYAmVKAmAALEIAENVADVSVEGCFVEQDKERYVPIVASAHEmmRKAAELADEARELEKSNDAVLRTPHAPDGKVLSKRKFmEDPE 283
                                    11      ||21|       31        41  |     51   |    61        71        81    |   91       101       111       121  |    131     | 141   |   151       161       171       181       191       201  |    211       221       231       241       251       261       271       281  
                                           18-MSE                    44-MSE     55-MSE                         86-MSE                109-MSE        124-MSE      137-MSE 145-MSE                                                200-MSE                                 240-MSE                                279-MSE
                                            19-MSE                                                                                                                                                                                  204-MSE                              241-MSE                                      
                                             20-MSE                                                                                                                                                                                                                                                                   
                                               22-MSE                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:282
 aligned with MTD_METKA | P94951 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:282
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281  
            MTD_METKA     2 TVAKAIFIKCGNLGTSMMMDMLLDERADREDVEFRVVGTSVKMDPECVEAAVEMALDIAEDFEPDFIVYGGPNPAAPGPSKAREMLADSEYPAVIIGDAPGLKVKDEMEEQGLGYILVKPDAMLGARREFLDPVEMAIYNADLMKVLAATGVFRVVQEAFDELIEKAKEDEISENDLPKLVIDRNTLLEREEFENPYAMVKAMAALEIAENVADVSVEGCFVEQDKERYVPIVASAHEMMRKAAELADEARELEKSNDAVLRTPHAPDGKVLSKRKFMEDPE 283
               SCOP domains d1u6kb_ B: F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeeeee..hhhhhhhhhhhh.......eeeeeeeee...hhhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhh..eeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh.eeeehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1u6k B   2 TVAKAIFIKCGNLGTSmmmDmLLDERADREDVEFRVVGTSVKmDPECVEAAVEmALDIAEDFEPDFIVYGGPNPAAPGPSKAREmLADSEYPAVIIGDAPGLKVKDEmEEQGLGYILVKPDAmLGARREFLDPVEmAIYNADLmKVLAATGVFRVVQEAFDELIEKAKEDEISENDLPKLVIDRNTLLEREEFENPYAmVKAmAALEIAENVADVSVEGCFVEQDKERYVPIVASAHEmmRKAAELADEARELEKSNDAVLRTPHAPDGKVLSKRKFmEDPE 283
                                    11      ||21|       31        41  |     51   |    61        71        81    |   91       101       111       121  |    131     | 141   |   151       161       171       181       191       201  |    211       221       231       241       251       261       271       281  
                                           18-MSE                    44-MSE     55-MSE                         86-MSE                109-MSE        124-MSE      137-MSE 145-MSE                                                200-MSE                                 240-MSE                                279-MSE
                                            19-MSE                                                                                                                                                                                  204-MSE                              241-MSE                                      
                                             20-MSE                                                                                                                                                                                                                                                                   
                                               22-MSE                                                                                                                                                                                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:282
 aligned with MTD_METKA | P94951 from UniProtKB/Swiss-Prot  Length:283

    Alignment length:282
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281  
            MTD_METKA     2 TVAKAIFIKCGNLGTSMMMDMLLDERADREDVEFRVVGTSVKMDPECVEAAVEMALDIAEDFEPDFIVYGGPNPAAPGPSKAREMLADSEYPAVIIGDAPGLKVKDEMEEQGLGYILVKPDAMLGARREFLDPVEMAIYNADLMKVLAATGVFRVVQEAFDELIEKAKEDEISENDLPKLVIDRNTLLEREEFENPYAMVKAMAALEIAENVADVSVEGCFVEQDKERYVPIVASAHEMMRKAAELADEARELEKSNDAVLRTPHAPDGKVLSKRKFMEDPE 283
               SCOP domains d1u6kc_ C: F420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD)                                                                                                                                                                                                             SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -MTD-1u6kC01 C:3-282                                                                                                                                                                                                                                                                     - Pfam domains (1)
           Pfam domains (2) -MTD-1u6kC02 C:3-282                                                                                                                                                                                                                                                                     - Pfam domains (2)
           Pfam domains (3) -MTD-1u6kC03 C:3-282                                                                                                                                                                                                                                                                     - Pfam domains (3)
         Sec.struct. author ..eeeeeeee..hhhhhhhhhhhh.......eeeeeeeee...hhhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhh..eeeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.eeeehhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......................... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1u6k C   2 TVAKAIFIKCGNLGTSmmmDmLLDERADREDVEFRVVGTSVKmDPECVEAAVEmALDIAEDFEPDFIVYGGPNPAAPGPSKAREmLADSEYPAVIIGDAPGLKVKDEmEEQGLGYILVKPDAmLGARREFLDPVEmAIYNADLmKVLAATGVFRVVQEAFDELIEKAKEDEISENDLPKLVIDRNTLLEREEFENPYAmVKAmAALEIAENVADVSVEGCFVEQDKERYVPIVASAHEmmRKAAELADEARELEKSNDAVLRTPHAPDGKVLSKRKFmEDPE 283
                                    11      ||21|       31        41  |     51   |    61        71        81    |   91       101       111       121  |    131     | 141   |   151       161       171       181       191       201  |    211       221       231       241       251       261       271       281  
                                           18-MSE                    44-MSE     55-MSE                         86-MSE                109-MSE        124-MSE      137-MSE 145-MSE                                                200-MSE                                 240-MSE                                279-MSE
                                            19-MSE                                                                                                                                                                                  204-MSE                              241-MSE                                      
                                             20-MSE                                                                                                                                                                                                                                                                   
                                               22-MSE
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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, 3)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1U6K)

(-) Pfam Domains  (1, 3)

Asymmetric Unit
(-)
Clan: no clan defined [family: MTD] (4)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (MTD_METKA | P94951)
molecular function
    GO:0008901    ferredoxin hydrogenase activity    Catalysis of the reaction: 2 reduced ferredoxin + 2 H+ = 2 oxidized ferredoxin + H2.
    GO:0030268    methylenetetrahydromethanopterin dehydrogenase activity    Catalysis of the reaction: 5,10-methylenetetrahydromethanopterin + coenzyme F420 + 2 H(+) = 5,10-methenyl-5,6,7,8-tetrahydromethanopterin + 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.
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MTD_METKA | P94951: 1qv9 1u6i 1u6j 3iqe 3iqf 3iqz

(-) Related Entries Specified in the PDB File

1qv9 SE-METHIONINE DERIVATIVE
1u5j
1u6i