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Conserved domains on  [gi|949144709|gb|KRP20271|]
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polyketide cyclase/dehydrase and lipid transport [SAR92 bacterium BACL16 MAG-120619-bin48]

Protein Classification

SRPBCC family protein( domain architecture ID 10167503)

SRPBCC (START/RHOalphaC/PITP/Bet v1/CoxG/CalC) family protein may have a deep hydrophobic ligand-binding pocket

CATH:  3.30.530.20
PubMed:  18922149
SCOP:  3000738

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
PYR_PYL_RCAR_like cd07821
Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid ...
 4-127 6.17e-25

Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins; The PYR/PYL/RCAR-like family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. PYR/PYL/RCAR plant proteins are receptors involved in signal transduction. They bind abscisic acid (ABA) and mediate its signaling. ABA is a vital plant hormone, which regulates plant growth, development, and response to environmental stresses. Upon binding ABA, these plant proteins interact with a type 2C protein phosphatase (PP2C), such as ABI1 and ABI2, and inhibit their activity. When ABA is bound, a loop (designated the gate/CL2 loop) closes over the ligand binding pocket, resulting in the weakening of the inactive PYL dimer and facilitating type 2C protein phosphatase binding. In the ABA:PYL1:ABI1 complex, the gate blocks substrate access to the phosphatase active site. A conserved Trp from PP2C inserts into PYL to lock the receptor in a closed formation. This group also contains Methylobacterium extorquens AM1 MxaD. The mxaD gene is located within the mxaFJGIR(S)ACKLDEHB cluster which encodes proteins involved in methanol oxidation. MxaD may participate in the periplasmic electron transport chain for oxidation of methanol. Mutants lacking MxaD exhibit a reduced growth on methanol, and a lower rate of respiration with methanol.


:

Pssm-ID: 176863 [Multi-domain]  Cd Length: 140  Bit Score: 92.00  E-value: 6.17e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949144709   4 IKETVVLACSAEHLWAILSDVTR-CDWVPTVDAIRLE------GSCRVFEMEGMGQVKERILLLDNDAKTLQYSAVETRT 76
Cdd:cd07821    3 VTVSVTIDAPADKVWALLSDFGGlHKWHPAVASCELEgggpgvGAVRTVTLKDGGTVRERLLALDDAERRYSYRIVEGPL 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 949144709  77 PIKHHLATMQVSAVDDDRCRLDWTTEIDP------DLFADAVHHGMRVSIAGIVRVV 127
Cdd:cd07821   83 PVKNYVATIRVTPEGDGGTRVTWTAEFDPpegltdELARAFLTGVYRAGLAALKAAL 139
 
Name Accession Description Interval E-value
PYR_PYL_RCAR_like cd07821
Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid ...
 4-127 6.17e-25

Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins; The PYR/PYL/RCAR-like family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. PYR/PYL/RCAR plant proteins are receptors involved in signal transduction. They bind abscisic acid (ABA) and mediate its signaling. ABA is a vital plant hormone, which regulates plant growth, development, and response to environmental stresses. Upon binding ABA, these plant proteins interact with a type 2C protein phosphatase (PP2C), such as ABI1 and ABI2, and inhibit their activity. When ABA is bound, a loop (designated the gate/CL2 loop) closes over the ligand binding pocket, resulting in the weakening of the inactive PYL dimer and facilitating type 2C protein phosphatase binding. In the ABA:PYL1:ABI1 complex, the gate blocks substrate access to the phosphatase active site. A conserved Trp from PP2C inserts into PYL to lock the receptor in a closed formation. This group also contains Methylobacterium extorquens AM1 MxaD. The mxaD gene is located within the mxaFJGIR(S)ACKLDEHB cluster which encodes proteins involved in methanol oxidation. MxaD may participate in the periplasmic electron transport chain for oxidation of methanol. Mutants lacking MxaD exhibit a reduced growth on methanol, and a lower rate of respiration with methanol.


Pssm-ID: 176863 [Multi-domain]  Cd Length: 140  Bit Score: 92.00  E-value: 6.17e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949144709   4 IKETVVLACSAEHLWAILSDVTR-CDWVPTVDAIRLE------GSCRVFEMEGMGQVKERILLLDNDAKTLQYSAVETRT 76
Cdd:cd07821    3 VTVSVTIDAPADKVWALLSDFGGlHKWHPAVASCELEgggpgvGAVRTVTLKDGGTVRERLLALDDAERRYSYRIVEGPL 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 949144709  77 PIKHHLATMQVSAVDDDRCRLDWTTEIDP------DLFADAVHHGMRVSIAGIVRVV 127
Cdd:cd07821   83 PVKNYVATIRVTPEGDGGTRVTWTAEFDPpegltdELARAFLTGVYRAGLAALKAAL 139
Polyketide_cyc2 pfam10604
Polyketide cyclase / dehydrase and lipid transport; This family contains polyketide cylcases ...
 6-112 3.75e-07

Polyketide cyclase / dehydrase and lipid transport; This family contains polyketide cylcases/dehydrases which are enzymes involved in polyketide synthesis. It also includes other proteins of the START superfamily.


Pssm-ID: 431388  Cd Length: 139  Bit Score: 45.94  E-value: 3.75e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949144709    6 ETVVLACSAEHLWAILSDVT-RCDWVPTVDAIRLEG-------SCRVFEMEGM-GQVKERILLLDNDAKTLQYSAVETRt 76
Cdd:pfam10604   1 VSIEIAAPPEQVWALLSDFEnWPRWHPGVLRVELEGgggplrgVVGTLRVGGRrGTVREELVEYDPAPRLLAYRIVEPL- 79

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 949144709   77 PIKHHLATMQVSAvDDDRCRLDWTTEIDPDLFADAV 112
Cdd:pfam10604  80 GVANYVGTWTVTP-AGGGTRVTWTGEFDGPPLGGPF 114
PasT COG2867
Ribosome association toxin PasT (RatA) of the RatAB toxin-antitoxin module [Translation, ...
 1-105 1.37e-03

Ribosome association toxin PasT (RatA) of the RatAB toxin-antitoxin module [Translation, ribosomal structure and biogenesis];


Pssm-ID: 442114  Cd Length: 137  Bit Score: 36.38  E-value: 1.37e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949144709   1 MKIIKETVVLACSAEHLWAILSDVTRC-DWVPTVDAIRL---EGSCRVFEME-GMGQVKE----RILLldNDAKTLQYSA 71
Cdd:COG2867    1 MPTISRSVLVPYSAEQMFDLVADVERYpEFLPWCKAARVlerDGDEVVAELTvSFKGLREsfttRNTL--DPPERIDFEL 78

                         90       100       110
                 ....*....|....*....|....*....|....
gi 949144709  72 VEtrTPIKHHLATMQVSAVDDDRCRLDWTTEIDP 105
Cdd:COG2867   79 VD--GPFKHLEGRWRFEPLGEGGTKVTFDLDFEF 110
 
Name Accession Description Interval E-value
PYR_PYL_RCAR_like cd07821
Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid ...
 4-127 6.17e-25

Pyrabactin resistance 1 (PYR1), PYR1-like (PYL), regulatory component of abscisic acid receptors (RCARs), and related proteins; The PYR/PYL/RCAR-like family belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. PYR/PYL/RCAR plant proteins are receptors involved in signal transduction. They bind abscisic acid (ABA) and mediate its signaling. ABA is a vital plant hormone, which regulates plant growth, development, and response to environmental stresses. Upon binding ABA, these plant proteins interact with a type 2C protein phosphatase (PP2C), such as ABI1 and ABI2, and inhibit their activity. When ABA is bound, a loop (designated the gate/CL2 loop) closes over the ligand binding pocket, resulting in the weakening of the inactive PYL dimer and facilitating type 2C protein phosphatase binding. In the ABA:PYL1:ABI1 complex, the gate blocks substrate access to the phosphatase active site. A conserved Trp from PP2C inserts into PYL to lock the receptor in a closed formation. This group also contains Methylobacterium extorquens AM1 MxaD. The mxaD gene is located within the mxaFJGIR(S)ACKLDEHB cluster which encodes proteins involved in methanol oxidation. MxaD may participate in the periplasmic electron transport chain for oxidation of methanol. Mutants lacking MxaD exhibit a reduced growth on methanol, and a lower rate of respiration with methanol.


Pssm-ID: 176863 [Multi-domain]  Cd Length: 140  Bit Score: 92.00  E-value: 6.17e-25
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949144709   4 IKETVVLACSAEHLWAILSDVTR-CDWVPTVDAIRLE------GSCRVFEMEGMGQVKERILLLDNDAKTLQYSAVETRT 76
Cdd:cd07821    3 VTVSVTIDAPADKVWALLSDFGGlHKWHPAVASCELEgggpgvGAVRTVTLKDGGTVRERLLALDDAERRYSYRIVEGPL 82

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 949144709  77 PIKHHLATMQVSAVDDDRCRLDWTTEIDP------DLFADAVHHGMRVSIAGIVRVV 127
Cdd:cd07821   83 PVKNYVATIRVTPEGDGGTRVTWTAEFDPpegltdELARAFLTGVYRAGLAALKAAL 139
Polyketide_cyc2 pfam10604
Polyketide cyclase / dehydrase and lipid transport; This family contains polyketide cylcases ...
 6-112 3.75e-07

Polyketide cyclase / dehydrase and lipid transport; This family contains polyketide cylcases/dehydrases which are enzymes involved in polyketide synthesis. It also includes other proteins of the START superfamily.


Pssm-ID: 431388  Cd Length: 139  Bit Score: 45.94  E-value: 3.75e-07
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949144709    6 ETVVLACSAEHLWAILSDVT-RCDWVPTVDAIRLEG-------SCRVFEMEGM-GQVKERILLLDNDAKTLQYSAVETRt 76
Cdd:pfam10604   1 VSIEIAAPPEQVWALLSDFEnWPRWHPGVLRVELEGgggplrgVVGTLRVGGRrGTVREELVEYDPAPRLLAYRIVEPL- 79

                          90       100       110
                  ....*....|....*....|....*....|....*.
gi 949144709   77 PIKHHLATMQVSAvDDDRCRLDWTTEIDPDLFADAV 112
Cdd:pfam10604  80 GVANYVGTWTVTP-AGGGTRVTWTGEFDGPPLGGPF 114
Bet_v1-like cd07816
Ligand-binding bet_v_1 domain of major pollen allergen of white birch (Betula verrucosa), Bet ...
 4-105 1.16e-05

Ligand-binding bet_v_1 domain of major pollen allergen of white birch (Betula verrucosa), Bet v 1, and related proteins; This family includes the ligand binding domain of Bet v 1 (the major pollen allergen of white birch, Betula verrucosa) and related proteins. In addition to birch Bet v 1, this family includes other plant intracellular pathogenesis-related class 10 (PR-10) proteins, norcoclaurine synthases (NCSs), cytokinin binding proteins (CSBPs), major latex proteins (MLPs), and ripening-related proteins. It belongs to the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. Members of this family binds a diverse range of ligands. Bet v 1 can bind brassinosteroids, cytokinins, flavonoids and fatty acids. Hyp-1, a PR-10 from Hypericum perforatum/St. John's wort, catalyzes the condensation of two molecules of emodin to the bioactive naphthodianthrone hypericin. NCSs catalyze the condensation of dopamine and 4-hydroxyphenylacetaldehyde to (S)-norcoclaurine, the first committed step in the biosynthesis of benzylisoquinoline alkaloids such as morphine. The role of MLPs is unclear; however, they are associated with fruit and flower development and in pathogen defense responses. A number of PR-10 proteins in this subgroup, including Bet v 1, have in vitro RNase activity, the biological significance of which is unclear. Bet v 1 family proteins have a conserved glycine-rich P (phosphate-binding)-loop proximal to the entrance of the ligand-binding pocket. However, its conformation differs from that of the canonical P-loop structure found in nucleotide-binding proteins. Several PR-10 members including Bet v1 are allergenic. Cross-reactivity of Bet v 1 with homologs from plant foods results in birch-fruit syndrome.


Pssm-ID: 176858  Cd Length: 148  Bit Score: 42.18  E-value: 1.16e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949144709   4 IKETVVLACSAEHLWAILS--DVTRCDWVPTV--DAIRLEG-----SCRVFEM-EGMG--QVKERILLLDNDAKTLQYSA 71
Cdd:cd07816    3 LEHEVELKVPAEKLWKAFVldSHLLPPKLPPVikSVELLEGdggpgSIKLITFgPGGKvkYVKERIDAVDEENKTYKYTV 82

                         90       100       110
                 ....*....|....*....|....*....|....*..
gi 949144709  72 VE---TRTPIKHHLATMQVSAVDDDRCRLDWTTEIDP 105
Cdd:cd07816   83 IEgdvLKDGYKSYKVEIKFVPKGDGGCVVKWTIEYEK 119
SRPBCC_Smu440-like cd08862
Ligand-binding SRPBCC domain of Streptococcus mutans Smu.440 and related proteins; This family ...
 3-111 2.85e-05

Ligand-binding SRPBCC domain of Streptococcus mutans Smu.440 and related proteins; This family includes the SRPBCC (START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain of Streptococcus mutans Smu.440 and related proteins. This domain belongs to the SRPBCC domain superfamily of proteins that bind hydrophobic ligands. SRPBCC domains have a deep hydrophobic ligand-binding pocket. Streptococcus mutans is a dental pathogen, and the leading cause of dental caries. In this pathogen, the gene encoding Smu.440 is in the same operon as the gene encoding SMU.441, a member of the MarR protein family of transcriptional regulators involved in multiple antibiotic resistance. It has been suggested that SMU.440 is involved in polyketide-like antibiotic resistance.


Pssm-ID: 176871  Cd Length: 138  Bit Score: 40.80  E-value: 2.85e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949144709   3 IIKETVVLACSAEHLWAILSDVTRC-DWVPTVDAIRLEGS----CRVFEMEGMGQVKERILLLdnDAKTLQYSAVETRTP 77
Cdd:cd08862    2 KFEATIVIDAPPERVWAVLTDVENWpAWTPSVETVRLEGPppavGSSFKMKPPGLVRSTFTVT--ELRPGHSFTWTGPAP 79

                         90       100       110
                 ....*....|....*....|....*....|....*...
gi 949144709  78 IKHHLATMQVSAVDDD----RCRLDWTteiDPDLFADA 111
Cdd:cd08862   80 GISAVHRHEFEAKPDGgvrvTTSESLS---GPLAFLFG 114
PasT COG2867
Ribosome association toxin PasT (RatA) of the RatAB toxin-antitoxin module [Translation, ...
 1-105 1.37e-03

Ribosome association toxin PasT (RatA) of the RatAB toxin-antitoxin module [Translation, ribosomal structure and biogenesis];


Pssm-ID: 442114  Cd Length: 137  Bit Score: 36.38  E-value: 1.37e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949144709   1 MKIIKETVVLACSAEHLWAILSDVTRC-DWVPTVDAIRL---EGSCRVFEME-GMGQVKE----RILLldNDAKTLQYSA 71
Cdd:COG2867    1 MPTISRSVLVPYSAEQMFDLVADVERYpEFLPWCKAARVlerDGDEVVAELTvSFKGLREsfttRNTL--DPPERIDFEL 78

                         90       100       110
                 ....*....|....*....|....*....|....
gi 949144709  72 VEtrTPIKHHLATMQVSAVDDDRCRLDWTTEIDP 105
Cdd:COG2867   79 VD--GPFKHLEGRWRFEPLGEGGTKVTFDLDFEF 110
SRPBCC cd07812
START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; SRPBCC ...
 4-120 1.82e-03

START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC (SRPBCC) ligand-binding domain superfamily; SRPBCC domains have a deep hydrophobic ligand-binding pocket; they bind diverse ligands. Included in this superfamily are the steroidogenic acute regulatory protein (StAR)-related lipid transfer (START) domains of mammalian STARD1-STARD15, and the C-terminal catalytic domains of the alpha oxygenase subunit of Rieske-type non-heme iron aromatic ring-hydroxylating oxygenases (RHOs_alpha_C), as well as the SRPBCC domains of phosphatidylinositol transfer proteins (PITPs), Bet v 1 (the major pollen allergen of white birch, Betula verrucosa), CoxG, CalC, and related proteins. Other members of this superfamily include PYR/PYL/RCAR plant proteins, the aromatase/cyclase (ARO/CYC) domains of proteins such as Streptomyces glaucescens tetracenomycin, and the SRPBCC domains of Streptococcus mutans Smu.440 and related proteins.


Pssm-ID: 176854  Cd Length: 141  Bit Score: 36.15  E-value: 1.82e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 949144709   4 IKETVVLACSAEHLWAILSDVTR-CDWVPTVDAIRLE-------GSCRVFEMEGMGQVKERILLLDNDAKTLQYSAVETR 75
Cdd:cd07812    1 VEASIEIPAPPEAVWDLLSDPERwPEWSPGLERVEVLgggeggvGARFVGGRKGGRRLTLTSEVTEVDPPRPGRFRVTGG 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|....*
gi 949144709  76 TPIKHHLATMQVSAVDDDRCRLDWTTEIDPDLFADAVHHGMRVSI 120
Cdd:cd07812   81 GGGVDGTGEWRLEPEGDGGTRVTYTVEYDPPGPLLKVFALLLAGA 125
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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