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Protein

5,10-methenyltetrahydromethanopterin hydrogenase

Gene

hmd

Organism
Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at protein leveli

Functioni

Catalyzes the reversible reduction of methenyl-H4MPT+ to methylene-H4MPT.By similarity

Catalytic activityi

H2 + 5,10-methenyltetrahydromethanopterin = H+ + 5,10-methylenetetrahydromethanopterin.

Pathwayi: methanogenesis from CO(2)

This protein is involved in step 1 of the subpathway that synthesizes 5,10-methylene-5,6,7,8-tetrahydromethanopterin from 5,10-methenyl-5,6,7,8-tetrahydromethanopterin (hydrogen route).
Proteins known to be involved in this subpathway in this organism are:
  1. 5,10-methenyltetrahydromethanopterin hydrogenase (hmd)
This subpathway is part of the pathway methanogenesis from CO(2), which is itself part of One-carbon metabolism.
View all proteins of this organism that are known to be involved in the subpathway that synthesizes 5,10-methylene-5,6,7,8-tetrahydromethanopterin from 5,10-methenyl-5,6,7,8-tetrahydromethanopterin (hydrogen route), the pathway methanogenesis from CO(2) and in One-carbon metabolism.

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Oxidoreductase

Keywords - Biological processi

Methanogenesis, One-carbon metabolism

Enzyme and pathway databases

BRENDAi1.12.98.2. 3260.
UniPathwayiUPA00640; UER00696.

Names & Taxonomyi

Protein namesi
Recommended name:
5,10-methenyltetrahydromethanopterin hydrogenase (EC:1.12.98.2)
Alternative name(s):
H(2)-dependent methylene-H(4)MPT dehydrogenase
H(2)-forming N(5),N(10)-methylenetetrahydromethanopterin dehydrogenase
N(5),N(10)-methenyltetrahydromethanopterin hydrogenase
Gene namesi
Name:hmd
Ordered Locus Names:MJ0784
OrganismiMethanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Methanococcus jannaschii)
Taxonomic identifieri243232 [NCBI]
Taxonomic lineageiArchaeaEuryarchaeotaMethanococciMethanococcalesMethanocaldococcaceaeMethanocaldococcus
Proteomesi
  • UP000000805 Componenti: Chromosome

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00002185081 – 3585,10-methenyltetrahydromethanopterin hydrogenaseAdd BLAST358

Proteomic databases

PRIDEiQ58194.

Interactioni

Protein-protein interaction databases

STRINGi243232.MJ_0784.

Structurei

Secondary structure

1358
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi2 – 6Combined sources5
Helixi12 – 17Combined sources6
Helixi23 – 32Combined sources10
Helixi35 – 39Combined sources5
Helixi42 – 53Combined sources12
Beta strandi59 – 63Combined sources5
Helixi65 – 68Combined sources4
Beta strandi69 – 75Combined sources7
Helixi81 – 89Combined sources9
Helixi93 – 95Combined sources3
Helixi97 – 109Combined sources13
Turni114 – 116Combined sources3
Beta strandi117 – 122Combined sources6
Helixi124 – 127Combined sources4
Beta strandi130 – 133Combined sources4
Helixi135 – 139Combined sources5
Beta strandi143 – 147Combined sources5
Beta strandi151 – 154Combined sources4
Helixi155 – 162Combined sources8
Helixi163 – 165Combined sources3
Beta strandi171 – 174Combined sources4
Beta strandi176 – 178Combined sources3
Helixi180 – 189Combined sources10
Beta strandi195 – 199Combined sources5
Turni206 – 208Combined sources3
Beta strandi212 – 219Combined sources8
Helixi221 – 235Combined sources15
Beta strandi238 – 242Combined sources5
Helixi243 – 245Combined sources3
Helixi246 – 250Combined sources5
Helixi254 – 272Combined sources19
Helixi279 – 300Combined sources22
Helixi302 – 304Combined sources3
Helixi305 – 308Combined sources4
Helixi311 – 316Combined sources6
Helixi318 – 321Combined sources4
Helixi324 – 326Combined sources3
Helixi329 – 339Combined sources11

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2B0JX-ray1.75A1-358[»]
3DAFX-ray1.75A1-358[»]
3DAGX-ray1.75A1-358[»]
3F46X-ray1.95A1-358[»]
3F47X-ray1.75A1-358[»]
3H65X-ray2.15A1-358[»]
ProteinModelPortaliQ58194.
SMRiQ58194.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ58194.

Family & Domainsi

Sequence similaritiesi

Belongs to the HMD family.Curated

Phylogenomic databases

eggNOGiarCOG03196. Archaea.
COG4074. LUCA.
KOiK13942.
OMAiTHACTIP.
PhylomeDBiQ58194.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_01090. HMD. 1 hit.
InterProiIPR008927. 6-PGluconate_DH_C-like.
IPR010062. HMD_.
IPR004889. HMD_C.
IPR024190. METHMP_Hmd.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF03201. HMD. 1 hit.
[Graphical view]
PIRSFiPIRSF016158. HMD. 1 hit.
PIRSF500165. HMDI. 1 hit.
SUPFAMiSSF48179. SSF48179. 1 hit.
SSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR01723. hmd_TIGR. 1 hit.

Sequencei

Sequence statusi: Complete.

Q58194-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MKIAILGAGC YRTHAAAGIT NFMRACEVAK EVGKPEIALT HSSITYGAEL
60 70 80 90 100
LHLVPDVKEV IVSDPCFAEE PGLVVIDEFD PKEVMEAHLS GNPESIMPKI
110 120 130 140 150
REVVKAKAKE LPKPPKACIH LVHPEDVGLK VTSDDREAVE GADIVITWLP
160 170 180 190 200
KGNKQPDIIK KFADAIPEGA IVTHACTIPT TKFAKIFKDL GREDLNITSY
210 220 230 240 250
HPGCVPEMKG QVYIAEGYAS EEAVNKLYEI GKIARGKAFK MPANLIGPVC
260 270 280 290 300
DMCSAVTATV YAGLLAYRDA VTKILGAPAD FAQMMADEAL TQIHNLMKEK
310 320 330 340 350
GIANMEEALD PAALLGTADS MCFGPLAEIL PTALKVLEKH KVVEEEGKTK

CEIMSQKE
Length:358
Mass (Da):38,689
Last modified:November 1, 1996 - v1
Checksum:i9D8E789759BCF43A
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB98781.1.
PIRiH64397.
RefSeqiWP_010870290.1. NC_000909.1.

Genome annotation databases

EnsemblBacteriaiAAB98781; AAB98781; MJ_0784.
GeneIDi1451662.
KEGGimja:MJ_0784.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
L77117 Genomic DNA. Translation: AAB98781.1.
PIRiH64397.
RefSeqiWP_010870290.1. NC_000909.1.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
2B0JX-ray1.75A1-358[»]
3DAFX-ray1.75A1-358[»]
3DAGX-ray1.75A1-358[»]
3F46X-ray1.95A1-358[»]
3F47X-ray1.75A1-358[»]
3H65X-ray2.15A1-358[»]
ProteinModelPortaliQ58194.
SMRiQ58194.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi243232.MJ_0784.

Proteomic databases

PRIDEiQ58194.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsemblBacteriaiAAB98781; AAB98781; MJ_0784.
GeneIDi1451662.
KEGGimja:MJ_0784.

Phylogenomic databases

eggNOGiarCOG03196. Archaea.
COG4074. LUCA.
KOiK13942.
OMAiTHACTIP.
PhylomeDBiQ58194.

Enzyme and pathway databases

UniPathwayiUPA00640; UER00696.
BRENDAi1.12.98.2. 3260.

Miscellaneous databases

EvolutionaryTraceiQ58194.

Family and domain databases

Gene3Di3.40.50.720. 1 hit.
HAMAPiMF_01090. HMD. 1 hit.
InterProiIPR008927. 6-PGluconate_DH_C-like.
IPR010062. HMD_.
IPR004889. HMD_C.
IPR024190. METHMP_Hmd.
IPR016040. NAD(P)-bd_dom.
[Graphical view]
PfamiPF03201. HMD. 1 hit.
[Graphical view]
PIRSFiPIRSF016158. HMD. 1 hit.
PIRSF500165. HMDI. 1 hit.
SUPFAMiSSF48179. SSF48179. 1 hit.
SSF51735. SSF51735. 1 hit.
TIGRFAMsiTIGR01723. hmd_TIGR. 1 hit.
ProtoNetiSearch...

Entry informationi

Entry nameiHMD_METJA
AccessioniPrimary (citable) accession number: Q58194
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 1, 1997
Last sequence update: November 1, 1996
Last modified: November 2, 2016
This is version 109 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programProkaryotic Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Methanococcus jannaschii
    Methanococcus jannaschii: entries and gene names
  2. PATHWAY comments
    Index of metabolic and biosynthesis pathways
  3. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  4. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.