About DExH/D Proteins

DExH/D proteins are essential in all aspects of RNA metabolism and processing.
They play important roles in

transcription
pre-mRNA splicing
RNA export
RNA degradation
ribosome biogenesis
translation
mitochondrial RNA splicing
RNA editing
development
replication of many viruses

Wherever there is RNA in living organisms - DExH/D proteins are likely to be involved.
DExH/D proteins comprise DEAD-box, DEAH-box, and DExH-box proteins, which are closely related to each other. DExH/D proteins are a subgroup of the Superfamily 2 (SF2) helicases (Gorbalenya & Koonin, Curr. Opin. Struct, Biol. 3, 419-429; 1993):

Conserved "helicase domains". Capital letters indicate highly conserved aminoacids, small letters more frequent conservative substitutions. x represents variable residues but indicates important spacings between conserved positions. The sequence in the Walker II motif provided the name for DEAD, DExH, and DEAH subgroups. The boxes underneath the sequence indicate the functional role of the motifs derived from X-ray structures and mutational analysis.

motifs...................I..............Ia................Ib...............Ic.................II............III................IV...........................V........Va......................VI.......

DEAH_group....LP....GETGSGKTTQxxQ....TQPRRVAA....RVxxE....VGYxIRF....TxxxYxTDGxLL....LxxY....DEAHERxxxTD....SAT....GRxxPV....LVFxxG....QxxxF....RxxVxATNIAETSLTIxGxxYVxDxGxxKxxxY....S....QRxGRxGRxxxxG...

DEAD_group............TGTGKTxxF........PTRELAxQ...........GG...............TPG.............VxDEAD...........SAT..............VIF...........F...............RGL............................HRxGRxGR........

DExH_group............TGxGKTxxxL.......PxxAL...............................T...............VxDExH...........SAT................FxxS...........................T......VID..................QRxGRxGR........

SNF2_group............MGxGKT...........P...................................................IxDExH...........TGT................FxxM...........................T...........................QAxDRxHR........

RAD3_group............SGxGKT...............................................................VxDExH...........SGT................FxxS.......................................................QCxGRxLR........

UL9__group............MGxGKT...............................................................VxDExx...........DAT................FxxT...........................T...........................QSxGRxRT........

Characteristic motifs were identified from alignments of 30 DEAH, ca. 40 DEAD, and ca. 40 DExH proteins. (Alignments of more proteins in each group might slighly alter the ratio between identical and conservative substituted residues as well as the alignments of the conserved motifs for the different groups). The numbering of the motifs is according to Gorbalenya and Koonin, (Curr. Opin. Struct, Biol. 3, 419-429; 1993); motifs Ib, Ic, and Va are named by myself. Red letters represent identical amino acids, blue letters conservative substitutions. The points separating the conserved motifs do not represent spacings between the motifs. However, aligned amino acids from the different groups have comparable distance. The conserved motifs are usually surrounded by a cluster of less, but still significant conserved residues which are not indicated here. Single conserved residues in the sequence should be seen in light of this. Similarity within the DEAH-group continues throughout the C-terminus.
For comparison, I have aligned sequences of other SF2 proteins in order to emphasize differences. While those might seem small, there is work suggesting that these differences matter quite a bit as conserved motifs do not play the same role in all SF2 proteins.

Inspection of the given motifs shows that the sequence of motif II alone does not sufficiently indicate whether a protein is actually a member of the DEAD, DExH, or DEAH group. Many SF2 proteins feature a "misleading" motif II but are clearly missing or significantly different in other motifs. (To further illustrate this fact: Some (viral) DExH proteins have actually a DEAH-motif II. Also, several other SF2 proteins have a DEAH-motif II, but are far from beeing DEAH proteins. And finally, there are some restriction enzymes with a DEAD-motif but with clear divergence in (almost all) other motifs.)
Thus, DExH or DEAH are rather misnomers which, however, are kept for historical reasons (until one comes up with another catchy description). The reason to combine DEAD, DEAH and DExH proteins is their predominant involvement in RNA related processes justifying the discrimination between DExH/D and other SF2 helicases (Staley & Guthrie, Cell 90, 1041-1050, 1998). However, there are exceptions (like in probably every classification), most notably the RecQ-like DExH proteins which are clearly DNA helicases. For consistency, these proteins are included in the database.
DExH/D proteins are often called "putative RNA helicases", based on the observation that some protein family members are actually RNA helicases: they unwind duplex RNA duplexes (more then 26 DExH/D proteins have been shown to be RNA helicases). This activity requires energy provided by binding and/or hydrolysis of NTPs. All DExH/D proteins which have been subject to biochemical analysis were found to hydrolyze NTP. In most cases, this activity is stimulated by nucleic acids.

How DExH/D proteins exactly perform the helicase activity, i.e. how they transform the energy of NTP hydrolysis and/or binding into mechanical (conformational) work on RNA remains to be shown.