HMD_METTM
ID HMD_METTM Reviewed; 344 AA.
AC P32440; D9PY07;
DT 01-OCT-1993, integrated into UniProtKB/Swiss-Prot.
DT 30-NOV-2010, sequence version 3.
DT 25-MAY-2022, entry version 123.
DE RecName: Full=5,10-methenyltetrahydromethanopterin hydrogenase;
DE EC=1.12.98.2 {ECO:0000269|PubMed:1765081};
DE AltName: Full=H(2)-dependent methylene-H(4)MPT dehydrogenase;
DE AltName: Full=H(2)-forming N(5),N(10)-methylenetetrahydromethanopterin dehydrogenase {ECO:0000303|PubMed:1521540};
DE AltName: Full=N(5),N(10)-methenyltetrahydromethanopterin hydrogenase;
GN Name=hmd {ECO:0000303|PubMed:1765081}; OrderedLocusNames=MTBMA_c15260;
OS Methanothermobacter marburgensis (strain ATCC BAA-927 / DSM 2133 / JCM
OS 14651 / NBRC 100331 / OCM 82 / Marburg) (Methanobacterium
OS thermoautotrophicum).
OC Archaea; Euryarchaeota; Methanomada group; Methanobacteria;
OC Methanobacteriales; Methanobacteriaceae; Methanothermobacter.
OX NCBI_TaxID=79929;
RN [1]
RP NUCLEOTIDE SEQUENCE [GENOMIC DNA], FUNCTION, CATALYTIC ACTIVITY, ACTIVITY
RP REGULATION, BIOPHYSICOCHEMICAL PROPERTIES, AND PATHWAY.
RC STRAIN=ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 /
RC Marburg;
RX PubMed=1765081; DOI=10.1111/j.1432-1033.1991.tb16491.x;
RA Von Buenau R., Zirngibl C., Thauer R.K., Klein A.;
RT "Hydrogen-forming and coenzyme-F420-reducing methylene
RT tetrahydromethanopterin dehydrogenase are genetically distinct enzymes in
RT Methanobacterium thermoautotrophicum (Marburg).";
RL Eur. J. Biochem. 202:1205-1208(1991).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 /
RC Marburg;
RX PubMed=20802048; DOI=10.1128/jb.00844-10;
RA Liesegang H., Kaster A.K., Wiezer A., Goenrich M., Wollherr A., Seedorf H.,
RA Gottschalk G., Thauer R.K.;
RT "Complete genome sequence of Methanothermobacter marburgensis, a
RT methanoarchaeon model organism.";
RL J. Bacteriol. 192:5850-5851(2010).
RN [3]
RP FUNCTION, CATALYTIC ACTIVITY, ACTIVITY REGULATION, AND BIOPHYSICOCHEMICAL
RP PROPERTIES.
RC STRAIN=ATCC BAA-927 / DSM 2133 / JCM 14651 / NBRC 100331 / OCM 82 /
RC Marburg;
RX PubMed=1521540; DOI=10.1111/j.1432-1033.1992.tb17215.x;
RA Zirngibl C., van Dongen W., Schwoerer B., von Buenau R., Richter M.,
RA Klein A., Thauer R.K.;
RT "H2-forming methylenetetrahydromethanopterin dehydrogenase, a novel type of
RT hydrogenase without iron-sulfur clusters in methanogenic archaea.";
RL Eur. J. Biochem. 208:511-520(1992).
CC -!- FUNCTION: Catalyzes the reversible reduction of methenyl-H(4)MPT(+) to
CC methylene-H(4)MPT. {ECO:0000269|PubMed:1765081}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=5,10-methenyl-5,6,7,8-tetrahydromethanopterin + H2 = 5,10-
CC methylenetetrahydromethanopterin + H(+); Xref=Rhea:RHEA:20017,
CC ChEBI:CHEBI:15378, ChEBI:CHEBI:18276, ChEBI:CHEBI:57818,
CC ChEBI:CHEBI:58337; EC=1.12.98.2;
CC Evidence={ECO:0000269|PubMed:1521540, ECO:0000269|PubMed:1765081};
CC PhysiologicalDirection=left-to-right; Xref=Rhea:RHEA:20018;
CC Evidence={ECO:0000269|PubMed:1521540};
CC PhysiologicalDirection=right-to-left; Xref=Rhea:RHEA:20019;
CC Evidence={ECO:0000269|PubMed:1521540};
CC -!- ACTIVITY REGULATION: Activity requires salt; 100 mM sodium or potassium
CC salts of chloride, phosphate or sulfate are equally effective.
CC Inactivated by O(2). {ECO:0000269|PubMed:1521540,
CC ECO:0000269|PubMed:1765081}.
CC -!- BIOPHYSICOCHEMICAL PROPERTIES:
CC Kinetic parameters:
CC KM=20 uM for 5,10-methylenetetrahydromethanopterin
CC {ECO:0000269|PubMed:1765081};
CC KM=40 uM for 5,10-methylenetetrahydromethanopterin
CC {ECO:0000269|PubMed:1521540};
CC KM=50 uM for 5,10-methenyl-5,6,7,8-tetrahydromethanopterin
CC {ECO:0000269|PubMed:1521540};
CC pH dependence:
CC Optimum pH is 6.0-6.5 when making H(2) and 7.5 in the other
CC direction. {ECO:0000269|PubMed:1521540, ECO:0000269|PubMed:1765081};
CC Temperature dependence:
CC Optimum temperature is 60 degrees Celsius.
CC {ECO:0000269|PubMed:1521540, ECO:0000269|PubMed:1765081};
CC -!- PATHWAY: One-carbon metabolism; methanogenesis from CO(2); 5,10-
CC methylene-5,6,7,8-tetrahydromethanopterin from 5,10-methenyl-5,6,7,8-
CC tetrahydromethanopterin (hydrogen route): step 1/1.
CC {ECO:0000269|PubMed:1521540, ECO:0000269|PubMed:1765081}.
CC -!- SUBUNIT: Homotetramer. {ECO:0000250|UniProtKB:Q02394}.
CC -!- SIMILARITY: Belongs to the HMD family. {ECO:0000305}.
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DR EMBL; X59547; CAA42121.1; -; Genomic_DNA.
DR EMBL; CP001710; ADL59105.1; -; Genomic_DNA.
DR PIR; S19705; S19705.
DR RefSeq; WP_013296316.1; NC_014408.1.
DR PDB; 4JJF; X-ray; 2.20 A; A/B=1-344.
DR PDB; 4JJG; X-ray; 2.50 A; A/B=1-344.
DR PDB; 5OK4; X-ray; 1.29 A; A=1-344.
DR PDB; 6GGU; X-ray; 2.60 A; A=1-344.
DR PDBsum; 4JJF; -.
DR PDBsum; 4JJG; -.
DR PDBsum; 5OK4; -.
DR PDBsum; 6GGU; -.
DR AlphaFoldDB; P32440; -.
DR SMR; P32440; -.
DR STRING; 79929.MTBMA_c15260; -.
DR EnsemblBacteria; ADL59105; ADL59105; MTBMA_c15260.
DR GeneID; 9705235; -.
DR KEGG; mmg:MTBMA_c15260; -.
DR PATRIC; fig|79929.8.peg.1479; -.
DR HOGENOM; CLU_772960_0_0_2; -.
DR OMA; HACTIPT; -.
DR OrthoDB; 31540at2157; -.
DR BRENDA; 1.12.98.2; 7427.
DR UniPathway; UPA00640; UER00696.
DR Proteomes; UP000000345; Chromosome.
DR GO; GO:0047068; F:N5,N10-methenyltetrahydromethanopterin hydrogenase activity; IDA:MENGO.
DR GO; GO:0019386; P:methanogenesis, from carbon dioxide; IEA:UniProtKB-UniPathway.
DR GO; GO:0006730; P:one-carbon metabolic process; IEA:UniProtKB-UniRule.
DR Gene3D; 1.20.120.1300; -; 1.
DR HAMAP; MF_01090; HMD; 1.
DR InterPro; IPR008927; 6-PGluconate_DH-like_C_sf.
DR InterPro; IPR010062; HMD.
DR InterPro; IPR004889; HMD_C.
DR InterPro; IPR038182; HMD_C_sf.
DR InterPro; IPR024190; METHMP_Hmd.
DR InterPro; IPR036291; NAD(P)-bd_dom_sf.
DR Pfam; PF03201; HMD; 1.
DR PIRSF; PIRSF016158; HMD; 1.
DR PIRSF; PIRSF500165; HMDI; 1.
DR SUPFAM; SSF48179; SSF48179; 1.
DR SUPFAM; SSF51735; SSF51735; 1.
DR TIGRFAMs; TIGR01723; hmd_TIGR; 1.
PE 1: Evidence at protein level;
KW 3D-structure; Methanogenesis; One-carbon metabolism; Oxidoreductase.
FT CHAIN 1..344
FT /note="5,10-methenyltetrahydromethanopterin hydrogenase"
FT /id="PRO_0000218512"
FT CONFLICT 74..75
FT /note="DD -> EH (in Ref. 1; CAA42121)"
FT /evidence="ECO:0000305"
FT CONFLICT 91
FT /note="K -> N (in Ref. 1; CAA42121)"
FT /evidence="ECO:0000305"
FT CONFLICT 261
FT /note="I -> M (in Ref. 1; CAA42121)"
FT /evidence="ECO:0000305"
FT CONFLICT 265
FT /note="G -> C (in Ref. 1; CAA42121)"
FT /evidence="ECO:0000305"
FT CONFLICT 304..305
FT /note="ID -> RY (in Ref. 1; CAA42121)"
FT /evidence="ECO:0000305"
FT STRAND 2..6
FT /evidence="ECO:0007829|PDB:5OK4"
FT HELIX 12..17
FT /evidence="ECO:0007829|PDB:5OK4"
FT HELIX 23..32
FT /evidence="ECO:0007829|PDB:5OK4"
FT HELIX 35..39
FT /evidence="ECO:0007829|PDB:5OK4"
FT HELIX 42..53
FT /evidence="ECO:0007829|PDB:5OK4"
FT STRAND 58..62
FT /evidence="ECO:0007829|PDB:5OK4"
FT HELIX 64..67
FT /evidence="ECO:0007829|PDB:5OK4"
FT STRAND 69..72
FT /evidence="ECO:0007829|PDB:5OK4"
FT HELIX 78..87
FT /evidence="ECO:0007829|PDB:5OK4"
FT HELIX 89..91
FT /evidence="ECO:0007829|PDB:5OK4"
FT HELIX 93..106
FT /evidence="ECO:0007829|PDB:5OK4"
FT TURN 110..112
FT /evidence="ECO:0007829|PDB:5OK4"
FT STRAND 113..118
FT /evidence="ECO:0007829|PDB:5OK4"
FT HELIX 120..123
FT /evidence="ECO:0007829|PDB:5OK4"
FT STRAND 126..129
FT /evidence="ECO:0007829|PDB:5OK4"
FT HELIX 131..135
FT /evidence="ECO:0007829|PDB:5OK4"
FT STRAND 139..143
FT /evidence="ECO:0007829|PDB:5OK4"
FT HELIX 148..150
FT /evidence="ECO:0007829|PDB:5OK4"
FT HELIX 151..155
FT /evidence="ECO:0007829|PDB:5OK4"
FT TURN 156..158
FT /evidence="ECO:0007829|PDB:5OK4"
FT HELIX 159..161
FT /evidence="ECO:0007829|PDB:5OK4"
FT STRAND 167..169
FT /evidence="ECO:0007829|PDB:5OK4"
FT HELIX 176..183
FT /evidence="ECO:0007829|PDB:5OK4"
FT TURN 186..188
FT /evidence="ECO:0007829|PDB:4JJF"
FT TURN 190..192
FT /evidence="ECO:0007829|PDB:4JJF"
FT HELIX 194..196
FT /evidence="ECO:0007829|PDB:4JJF"
FT STRAND 198..200
FT /evidence="ECO:0007829|PDB:5OK4"
FT TURN 208..210
FT /evidence="ECO:0007829|PDB:5OK4"
FT STRAND 215..221
FT /evidence="ECO:0007829|PDB:5OK4"
FT HELIX 223..237
FT /evidence="ECO:0007829|PDB:5OK4"
FT STRAND 241..244
FT /evidence="ECO:0007829|PDB:5OK4"
FT HELIX 245..247
FT /evidence="ECO:0007829|PDB:5OK4"
FT HELIX 249..251
FT /evidence="ECO:0007829|PDB:5OK4"
FT TURN 253..255
FT /evidence="ECO:0007829|PDB:5OK4"
FT HELIX 256..275
FT /evidence="ECO:0007829|PDB:5OK4"
FT HELIX 281..302
FT /evidence="ECO:0007829|PDB:5OK4"
FT HELIX 304..309
FT /evidence="ECO:0007829|PDB:5OK4"
FT HELIX 313..316
FT /evidence="ECO:0007829|PDB:5OK4"
FT HELIX 317..320
FT /evidence="ECO:0007829|PDB:5OK4"
FT HELIX 321..323
FT /evidence="ECO:0007829|PDB:5OK4"
FT HELIX 328..342
FT /evidence="ECO:0007829|PDB:5OK4"
SQ SEQUENCE 344 AA; 37654 MW; A34EFC260D324025 CRC64;
MKLAILGAGC YRTHAASGIT NFSRACEVAE MVGKPEIAMT HSTITMGAEL KELAGVDEVV
VADPVFDNQF TVIDDFAYED VIEAHKEDPE KIMPQIREKV NEVAKELPKP PEGAIHFTHP
EDLGFEITTD DREAVADADF IMTWFPKGDM QPDIINKFID DIKPGAIVTH ACTIPTTKFY
KIFEQKHGDL VTKPETLNVT SYHPGAVPEM KGQVYIAEGY ASEDAIETLF ELGQKARGNA
YRLPAELLGP VCDMCSALTA ITYAGILSYR DSVTQVLGAP ASFAQMMAKE SLEQITALME
KVGIDKMEEN LDPGALLGTA DSMNFGASAE ILPTVFEILE KRKK
