CAZyme Information: MGYG000002310_00626

Basic Information

• Species: Microvirga massiliensis
• Lineage: Bacteria; Proteobacteria; Alphaproteobacteria; Rhizobiales; Beijerinckiaceae; Microvirga; Microvirga massiliensis
• CAZyme ID: MGYG000002310_00626
• CAZy Family: GH1
• CAZyme Description: hypothetical protein

CAZyme Property

Protein Length	CGC	Molecular Weight	Isoelectric Point
722	MGYG000002310_1|CGC3	81042.47	6.563

Genome Property

Genome Assembly ID	Genome Size	Genome Type	Country	Continent
MGYG000002310	8892798	Isolate	not provided	not provided

• Gene Location: Start: 640506; End: 642674 Strand: +

Full Sequence      

MQDLKLWGGIECTVARIGSEVRDQSRKTGHHARLDDLNRIAELGIRTLRYPVLWETVSPA
SPDLADFSWHDERLTRLRELGIRPIVTLCHHGSGPSYTSLTDPDFADLFAAHARRVAERY
PEVTHYTPVNEPLTTARFSGLYGHWYPHGTSYRSFLRALVNECTATVLAMRAIREVRPDA
QLVQTEDFGKTFSTPLLDYQARHENERRWLTFDLLCGQVRRDQPWWRILLDHGISEFELE
LFRAGDAAPDIIGINHYLTSERYLDQRLSRYPEHHWGGNGQHRYADAEAVRVPLPREQIG
PAPRLREVWERYRRPIAVTEVHHGCTREEQLRWLVEVWNAARQVRSEGADIRAVTVWSLF
GTVDWNSLLTRADGCYEPGPFDIRGPAPRRTALARAAQALAEHGHFDHPVLDRAGWWRRD
VRFYRPPLVASNKCQLAGSPRRLLITGATGTLGQAFSCICALRGLDHVLVSRKEMDIADP
ASVAAALACHRPWAVINTAGYVRVADAERDPETCFRENAAGAEVLAKTCAEAGLPLLTFS
SDLVFDGRAERAYIETDEVAPSCVYGASKAEAERRVLSVHPDALIIRTSAFFGPWDRYNF
AFDVLRKLSIGEHVIAGIDKVSPTYVPDLVHGALDLLIDEETGIRHLANEGEISWHDFAV
AVAERASFNKARVAAAADTPVLNTALSTAHGAILPVFESALDRFFADSKLDWTVDTSRVA
AE

Enzyme Prediction     

No EC number prediction in MGYG000002310_00626.

CAZyme Signature Domains

Family	Start	End	Evalue	family coverage
GH1	30	374	1.6e-42	0.7995337995337995

CDD Domains     

Cdd ID	Domain	E-Value	qStart	qEnd	sStart	sEnd	Domain Description
COG1091	RfbD	1.36e-64	442	707	2	279	dTDP-4-dehydrorhamnose reductase [Cell wall/membrane/envelope biogenesis].
cd05254	dTDP_HR_like_SDR_e	3.80e-61	442	664	1	230	dTDP-6-deoxy-L-lyxo-4-hexulose reductase and related proteins, extended (e) SDRs. dTDP-6-deoxy-L-lyxo-4-hexulose reductase, an extended SDR, synthesizes dTDP-L-rhamnose from alpha-D-glucose-1-phosphate, providing the precursor of L-rhamnose, an essential cell wall component of many pathogenic bacteria. This subgroup has the characteristic active site tetrad and NADP-binding motif. This subgroup also contains human MAT2B, the regulatory subunit of methionine adenosyltransferase (MAT); MAT catalyzes S-adenosylmethionine synthesis. The human gene encoding MAT2B encodes two major splicing variants which are induced in human cell liver cancer and regulate HuR, an mRNA-binding protein which stabilizes the mRNA of several cyclins, to affect cell proliferation. Both MAT2B variants include this extended SDR domain. Extended SDRs are distinct from classical SDRs. In addition to the Rossmann fold (alpha/beta folding pattern with a central beta-sheet) core region typical of all SDRs, extended SDRs have a less conserved C-terminal extension of approximately 100 amino acids. Extended SDRs are a diverse collection of proteins, and include isomerases, epimerases, oxidoreductases, and lyases; they typically have a TGXXGXXG cofactor binding motif. SDRs are a functionally diverse family of oxidoreductases that have a single domain with a structurally conserved Rossmann fold, an NAD(P)(H)-binding region, and a structurally diverse C-terminal region. Sequence identity between different SDR enzymes is typically in the 15-30% range; they catalyze a wide range of activities including the metabolism of steroids, cofactors, carbohydrates, lipids, aromatic compounds, and amino acids, and act in redox sensing. Classical SDRs have an TGXXX[AG]XG cofactor binding motif and a YXXXK active site motif, with the Tyr residue of the active site motif serving as a critical catalytic residue (Tyr-151, human 15-hydroxyprostaglandin dehydrogenase numbering). In addition to the Tyr and Lys, there is often an upstream Ser and/or an Asn, contributing to the active site; while substrate binding is in the C-terminal region, which determines specificity. The standard reaction mechanism is a 4-pro-S hydride transfer and proton relay involving the conserved Tyr and Lys, a water molecule stabilized by Asn, and nicotinamide. Atypical SDRs generally lack the catalytic residues characteristic of the SDRs, and their glycine-rich NAD(P)-binding motif is often different from the forms normally seen in classical or extended SDRs. Complex (multidomain) SDRs such as ketoreductase domains of fatty acid synthase have a GGXGXXG NAD(P)-binding motif and an altered active site motif (YXXXN). Fungal type ketoacyl reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
pfam04321	RmlD_sub_bind	8.09e-56	443	707	1	282	RmlD substrate binding domain. L-rhamnose is a saccharide required for the virulence of some bacteria. Its precursor, dTDP-L-rhamnose, is synthesized by four different enzymes the final one of which is RmlD. The RmlD substrate binding domain is responsible for binding a sugar nucleotide.
TIGR01214	rmlD	8.53e-56	442	707	1	286	dTDP-4-dehydrorhamnose reductase. This enzyme catalyzes the last of 4 steps in making dTDP-rhamnose, a precursor of LPS core antigen, O-antigen, etc. [Cell envelope, Biosynthesis and degradation of surface polysaccharides and lipopolysaccharides]
PRK09987	PRK09987	5.06e-20	476	722	39	292	dTDP-4-dehydrorhamnose reductase; Provisional

CAZyme Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End
QFU17850.1	0.0	2	713	3	715
QRM34426.1	0.0	4	722	7	723
QGM97233.1	2.71e-301	4	709	9	712
QPQ56369.1	4.88e-291	4	709	5	707
QIL01910.1	4.16e-287	4	704	12	712

PDB Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
3SC6_A	1.57e-24	442	709	7	285	2.65Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose reductase (rfbD) from Bacillus anthracis str. Ames in complex with NADP [Bacillus anthracis str. Ames],3SC6_B 2.65 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose reductase (rfbD) from Bacillus anthracis str. Ames in complex with NADP [Bacillus anthracis str. Ames],3SC6_C 2.65 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose reductase (rfbD) from Bacillus anthracis str. Ames in complex with NADP [Bacillus anthracis str. Ames],3SC6_D 2.65 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose reductase (rfbD) from Bacillus anthracis str. Ames in complex with NADP [Bacillus anthracis str. Ames],3SC6_E 2.65 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose reductase (rfbD) from Bacillus anthracis str. Ames in complex with NADP [Bacillus anthracis str. Ames],3SC6_F 2.65 Angstrom resolution crystal structure of dTDP-4-dehydrorhamnose reductase (rfbD) from Bacillus anthracis str. Ames in complex with NADP [Bacillus anthracis str. Ames]
1KBZ_A	6.73e-18	443	666	3	234	ChainA, dTDP-glucose oxidoreductase [Salmonella enterica subsp. enterica serovar Typhimurium],1KC1_A Chain A, dTDP-glucose oxidoreductase [Salmonella enterica subsp. enterica serovar Typhimurium],1KC3_A Chain A, dTDP-glucose oxidoreductase [Salmonella enterica subsp. enterica serovar Typhimurium],1N2S_A Chain A, dTDP-glucose oxidoreductase [Salmonella enterica subsp. enterica serovar Typhimurium]
6Z1H_A	2.65e-11	30	365	63	412	ChainA, ANCESTRAL RECONSTRUCTED GLYCOSIDASE [synthetic construct],6Z1H_B Chain B, ANCESTRAL RECONSTRUCTED GLYCOSIDASE [synthetic construct],6Z1M_A Chain A, Ancestral reconstructed glycosidase [synthetic construct],6Z1M_B Chain B, Ancestral reconstructed glycosidase [synthetic construct],6Z1M_C Chain C, Ancestral reconstructed glycosidase [synthetic construct]
2YDX_A	2.83e-11	441	682	3	259	Crystalstructure of human S-adenosylmethionine synthetase 2, beta subunit [Homo sapiens],2YDX_B Crystal structure of human S-adenosylmethionine synthetase 2, beta subunit [Homo sapiens],2YDX_C Crystal structure of human S-adenosylmethionine synthetase 2, beta subunit [Homo sapiens],2YDX_D Crystal structure of human S-adenosylmethionine synthetase 2, beta subunit [Homo sapiens],2YDX_E Crystal structure of human S-adenosylmethionine synthetase 2, beta subunit [Homo sapiens]
4NDN_E	3.03e-11	441	682	18	274	Structuralinsights of MAT enzymes: MATa2b complexed with SAM and PPNP [Homo sapiens],4NDN_F Structural insights of MAT enzymes: MATa2b complexed with SAM and PPNP [Homo sapiens]

Swiss-Prot Hits     

Hit ID	E-Value	Query Start	Query End	Hit Start	Hit End	Description
O66251	8.17e-30	442	670	3	238	dTDP-4-dehydrorhamnose reductase OS=Aggregatibacter actinomycetemcomitans OX=714 GN=rmlD PE=1 SV=1
P29781	7.28e-28	442	703	8	267	dTDP-4-dehydrorhamnose reductase OS=Streptomyces griseus OX=1911 GN=strL PE=1 SV=1
Q9L9E9	1.76e-27	442	659	4	222	dTDP-4-keto-6-deoxy-D-glucose reductase OS=Streptomyces niveus OX=193462 GN=novS PE=3 SV=1
A0QTF8	1.46e-25	415	673	12	267	dTDP-4-dehydrorhamnose reductase OS=Mycolicibacterium smegmatis (strain ATCC 700084 / mc(2)155) OX=246196 GN=rmlD PE=1 SV=1
P39631	2.07e-25	442	671	3	231	Spore coat polysaccharide biosynthesis protein SpsK OS=Bacillus subtilis (strain 168) OX=224308 GN=spsK PE=3 SV=3

SignalP and Lipop Annotations

This protein is predicted as OTHER

Other	SP_Sec_SPI	LIPO_Sec_SPII	TAT_Tat_SPI	TATLIP_Sec_SPII	PILIN_Sec_SPIII
1.000046	0.000000	0.000000	0.000000	0.000000	0.000000

TMHMM  Annotations     

There is no transmembrane helices in MGYG000002310_00626.