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(-) Description

Title :  STRUCTURE OF METHYLENE-TETRAHYDROMETHANOPTERIN DEHYDROGENASE FROM METHYLOBACTERIUM EXTORQUENS AM1
 
Authors :  U. Ermler, C. H. Hagemeier, A. Roth, U. Demmer, W. Grabarse, E. Warkenti J. A. Vorholt
Date :  22 May 02  (Deposition) - 11 Sep 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Alpha/Beta Twisted Open Sheet Structure, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  U. Ermler, C. H. Hagemeier, A. Roth, U. Demmer, W. Grabarse, E. Warkentin, J. A. Vorholt
Structure Of Methylene-Tetrahydromethanopterin Dehydrogenas From Methylobacterium Extorquens Am1.
Structure V. 10 1127 2002
PubMed-ID: 12176390  |  Reference-DOI: 10.1016/S0969-2126(02)00802-X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - METHYLENE TETRAHYDROMETHANOPTERIN DEHYDROGENASE
    Chains: A, B, C
    EC Number: 1.5.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET 17B CH1
    Expression System Strain: BL21(DE3) PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: MTDA
    Organism Scientific: METHYLOBACTERIUM EXTORQUENS
    Organism Taxid: 272630
    Strain: AM1
    Synonym: METHYLENETETRAHYDROFOLATE DEHYDROGENASE

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1LU9)

(-) Sites  (0, 0)

(no "Site" information available for 1LU9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1LU9)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Pro A:225 -Pro A:226
2Pro B:225 -Pro B:226
3Pro C:225 -Pro C:226

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LU9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1LU9)

(-) Exons   (0, 0)

(no "Exon" information available for 1LU9)

(-) 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:287
 aligned with MTDA_METEA | P55818 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:287
                                    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       
           MTDA_METEA     2 SKKLLFQFDTDATPSVFDVVVGYDGGADHITGYGNVTPDNVGAYVDGTIYTRGGKEKQSTAIFVGGGDMAAGERVFEAVKKRFFGPFRVSCMLDSNGSNTTAAAGVALVVKAAGGSVKGKKAVVLAGTGPVGMRSAALLAGEGAEVVLCGRKLDKAQAAADSVNKRFKVNVTAAETADDASRAEAVKGAHFVFTAGAIGLELLPQAAWQNESSIEIVADYNAQPPLGIGGIDATDKGKEYGGKRAFGALGIGGLKLKLHRACIAKLFESSEGVFDAEEIYKLAKEMA 288
               SCOP domains d1lu9a2 A:2-97 Methylene-tetrahydromethanopterin dehydrogenase                                  d1lu9a1 A:98-288 Methylene-tetrahydromethanopterin dehydrogenase                                                                                                                                SCOP domains
               CATH domains 1lu9A01 A:2-105,A:257-288 Methylene tetrahydromethanopterin dehydrogenase; domain 1                     1lu9A02 A:106-256 NAD(P)-binding Rossmann-like Domain                                                                                                  1lu9A01 A:2-105,A:257-288        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhh...eeeee......hhhhhhhhhhh..hhhhhh.eeeeee..hhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh...eeee..hhhhhhhhh....eeee.........hhhhhh......eeee................eeeee..eeeehhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lu9 A   2 SKKLLFQFDTDATPSVFDVVVGYDGGADHITGYGNVTPDNVGAYVDGTIYTRGGKEKQSTAIFVGGGDMAAGERVFEAVKKRFFGPFRVSCMLDSNGSNTTAAAGVALVVKAAGGSVKGKKAVVLAGTGPVGMRSAALLAGEGAEVVLCGRKLDKAQAAADSVNKRFKVNVTAAETADDASRAEAVKGAHFVFTAGAIGLELLPQAAWQNESSIEIVADYNAQPPLGIGGIDATDKGKEYGGKRAFGALGIGGLKLKLHRACIAKLFESSEGVFDAEEIYKLAKEMA 288
                                    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       


Chain B from PDB  Type:PROTEIN  Length:287
 aligned with MTDA_METEA | P55818 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:287
                                    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       
           MTDA_METEA     2 SKKLLFQFDTDATPSVFDVVVGYDGGADHITGYGNVTPDNVGAYVDGTIYTRGGKEKQSTAIFVGGGDMAAGERVFEAVKKRFFGPFRVSCMLDSNGSNTTAAAGVALVVKAAGGSVKGKKAVVLAGTGPVGMRSAALLAGEGAEVVLCGRKLDKAQAAADSVNKRFKVNVTAAETADDASRAEAVKGAHFVFTAGAIGLELLPQAAWQNESSIEIVADYNAQPPLGIGGIDATDKGKEYGGKRAFGALGIGGLKLKLHRACIAKLFESSEGVFDAEEIYKLAKEMA 288
               SCOP domains d1lu9b2 B:2-97 Methylene-tetrahydromethanopterin dehydrogenase                                  d1lu9b1 B:98-288 Methylene-tetrahydromethanopterin dehydrogenase                                                                                                                                SCOP domains
               CATH domains 1lu9B01 B:2-105,B:257-288 Methylene tetrahydromethanopterin dehydrogenase; domain 1                     1lu9B02 B:106-256 NAD(P)-binding Rossmann-like Domain                                                                                                  1lu9B01 B:2-105,B:257-288        CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.....hhhhhhhhhhh...eeeee......hhhhhhhhhhh..hhhhhh.eeeeee..hhhhhhhhhhhhhhhh......eeee.....hhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh...eeee..hhhhhhhhh....eeee.........hhhhh.......eeee................eeee....eeehhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lu9 B   2 SKKLLFQFDTDATPSVFDVVVGYDGGADHITGYGNVTPDNVGAYVDGTIYTRGGKEKQSTAIFVGGGDMAAGERVFEAVKKRFFGPFRVSCMLDSNGSNTTAAAGVALVVKAAGGSVKGKKAVVLAGTGPVGMRSAALLAGEGAEVVLCGRKLDKAQAAADSVNKRFKVNVTAAETADDASRAEAVKGAHFVFTAGAIGLELLPQAAWQNESSIEIVADYNAQPPLGIGGIDATDKGKEYGGKRAFGALGIGGLKLKLHRACIAKLFESSEGVFDAEEIYKLAKEMA 288
                                    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       


Chain C from PDB  Type:PROTEIN  Length:287
 aligned with MTDA_METEA | P55818 from UniProtKB/Swiss-Prot  Length:288

    Alignment length:287
                                    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       
           MTDA_METEA     2 SKKLLFQFDTDATPSVFDVVVGYDGGADHITGYGNVTPDNVGAYVDGTIYTRGGKEKQSTAIFVGGGDMAAGERVFEAVKKRFFGPFRVSCMLDSNGSNTTAAAGVALVVKAAGGSVKGKKAVVLAGTGPVGMRSAALLAGEGAEVVLCGRKLDKAQAAADSVNKRFKVNVTAAETADDASRAEAVKGAHFVFTAGAIGLELLPQAAWQNESSIEIVADYNAQPPLGIGGIDATDKGKEYGGKRAFGALGIGGLKLKLHRACIAKLFESSEGVFDAEEIYKLAKEMA 288
               SCOP domains d1lu9c2 C:2-97 Methylene-tetrahydromethanopterin dehydrogenase                                  d1lu9c1 C:98-288 Methylene-tetrahydromethanopterin dehydrogenase                                                                                                                                SCOP domains
               CATH domains 1lu9C01 C:2-105,C:257-288 Methylene tetrahydromethanopterin dehydrogenase; domain 1                     1lu9C02 C:106-256 NAD(P)-binding Rossmann-like Domain                                                                                                  1lu9C01 C:2-105,C:257-288        CATH domains
           Pfam domains (1) ---------------Mpt_N-1lu9C01 C:17-97                                                            ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------------Mpt_N-1lu9C02 C:17-97                                                            ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) ---------------Mpt_N-1lu9C03 C:17-97                                                            ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains (3)
         Sec.struct. author ...eeeeee.....hhhhhhhhhhh...eeeee......hhhhhhhhhhh..hhhhhh.eeeeee..hhhhhhhhhhhhhhhh......eeee...hhhhhhhhhhhhhhhhh.......eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh...eeee..hhhhhhhhh....eeee.........hhhhh.......eeee................eeeee..eeeehhhhhhhhhhhhhhhhhhhhh.....eehhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lu9 C   2 SKKLLFQFDTDATPSVFDVVVGYDGGADHITGYGNVTPDNVGAYVDGTIYTRGGKEKQSTAIFVGGGDMAAGERVFEAVKKRFFGPFRVSCMLDSNGSNTTAAAGVALVVKAAGGSVKGKKAVVLAGTGPVGMRSAALLAGEGAEVVLCGRKLDKAQAAADSVNKRFKVNVTAAETADDASRAEAVKGAHFVFTAGAIGLELLPQAAWQNESSIEIVADYNAQPPLGIGGIDATDKGKEYGGKRAFGALGIGGLKLKLHRACIAKLFESSEGVFDAEEIYKLAKEMA 288
                                    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
   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  (2, 6)

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

(-) CATH Domains  (2, 6)

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

(-) Pfam Domains  (1, 3)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Mpt_N] (2)

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C   (MTDA_METEA | P55818)
molecular function
    GO:0004488    methylenetetrahydrofolate dehydrogenase (NADP+) activity    Catalysis of the reaction: 5,10-methylenetetrahydrofolate + NADP(+) = 5,10-methenyltetrahydrofolate + NADPH.
    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:0046294    formaldehyde catabolic process    The chemical reactions and pathways resulting in the breakdown of formaldehyde (methanal, H2C=O), the simplest aldehyde.
    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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  Cis Peptide Bonds
    Pro A:225 - Pro A:226   [ RasMol ]  
    Pro B:225 - Pro B:226   [ RasMol ]  
    Pro C:225 - Pro C:226   [ RasMol ]  
 

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  1lu9
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  1.5.1.5
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 Related Entries

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

UniProtKB/Swiss-Prot
        MTDA_METEA | P55818: 1lua

(-) Related Entries Specified in the PDB File

1lua 1LUA CONTAINS THE SAME PROTEIN COMPLEXED WITH NADP