1YGY,1PSD,1YBA,1SC6,1YBA


Conserved Protein Domain Family
ACT_3PGDH-like

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cd04879: ACT_3PGDH-like 
Click on image for an interactive view with Cn3D
ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH)
ACT_3PGDH-like: The ACT_3PGDH-like CD includes the C-terminal ACT (regulatory) domain of D-3-phosphoglycerate dehydrogenase (3PGDH), with or without an extended C-terminal (xct) region found in various bacteria, archaea, fungi, and plants. 3PGDH is an enzyme that belongs to the D-isomer specific, 2-hydroxyacid dehydrogenase family and catalyzes the oxidation of D-3-phosphoglycerate to 3- phosphohydroxypyruvate, which is the first step in the biosynthesis of L-serine, using NAD+ as the oxidizing agent. In bacteria, 3PGDH is feedback controlled by the end product L-serine in an allosteric manner. In the Escherichia coli homotetrameric enzyme, the interface at adjacent ACT (regulatory) domains couples to create an extended beta-sheet. Each regulatory interface forms two serine-binding sites. The mechanism by which serine transmits inhibition to the active site is postulated to involve the tethering of the regulatory domains together to create a rigid quaternary structure with a solvent-exposed active site cleft. This CD also includes the C-terminal ACT domain of the L-serine dehydratase (LSD), iron-sulfur-dependent, beta subunit, found in various bacterial anaerobes such as Clostridium, Bacillus, and Treponema species. LSD enzymes catalyze the deamination of L-serine, producing pyruvate and ammonia. Unlike the eukaryotic L-serine dehydratase, which requires the pyridoxal-5'-phosphate (PLP) cofactor, the prokaryotic L-serine dehydratase contains an [4Fe-4S] cluster instead of a PLP active site. The LSD alpha and beta subunits of the 'clostridial' enzyme are encoded by the sdhA and sdhB genes. The single subunit bacterial homologs of L-serine dehydratase (LSD1, LSD2, TdcG) present in E. coli, and other Enterobacteriales, lack the ACT domain described here. Members of this CD belong to the superfamily of ACT regulatory domains.
Statistics
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PSSM-Id: 153151
View PSSM: cd04879
Aligned: 169 rows
Threshold Bit Score: 53.2381
Threshold Setting Gi: 6458183
Created: 18-Aug-2005
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
 
L-serine
Conserved site includes 3 residues -Click on image for an interactive view with Cn3D
Feature 1:L-serine binding site [chemical binding site]
Evidence:
  • Structure:1YBA; active conformation of E. coli 3PGDH homotetramer in the absence of serine; the four L-serine binding sites are highlighted.
    View structure with Cn3D
  • Structure:1PSD_A; E. coli 3PGDH homodimer, contacts of one monomer with a single L-serine at 3.5 A.
    View structure with Cn3D
  • Citation:PMID 7719856
  • Comment:The bound serine inhibitor spans the ACT-ACT interface forming hydrogen bond with conserved residues (generally His and Asn) of one subunit with a second Asn of the adjacent subunit.

Sequence Alignment
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Format: Row Display: Color Bits: Type Selection:
Feature 1            # #                 #                                                 
1YGY_B      456 NLIIHYVDrPGALGKIGTLLGtaGVNIQAAQLSEdaegpgATILLRLDQdv----pDDVRTAIAAavdAYKLEVV 526 Mycobacterium tubercu...
1YBA_D      339 RLXHIHENrPGVLTALNKIFAeqGVNIAAQYLQTsa--qxGYVVIDIEAded--vaEKALQAXKAipgTIRARLL 409 Escherichia coli
AAY82681    325 RLTIANKNvSGMIGKITAIIAeeGLNIIDMKNRSrd--diAYNVIDLDSep----sTKSIEAIKGeenIINVRQI 393 uncultured bacterium ...
NP_266760   321 RVTLINKNvPNVVAQISLAVAaeNINIANIVNRGqg--dyAYTLLDLDEkde-gklAALVSRFEAadnIIRVRLI 392 Lactococcus lactis su...
ZP_00538167 316 RLTIAHQNiPNMVGQIASVLAteQINIANMINGSkd--giAYTIIDIDNhl---deTISLEQLNAipgVLKTRLL 385 Exiguobacterium sp. 2...
ZP_00233239 325 RIGICHKNiPNMVGQITTELGkySLNILDMINRSkn--eyAYTLIDIDKetq-anlEQLKQDLLAvqgVLRVRVI 396 Listeria monocytogene...
YP_037345   317 RITIMHQNvPNMVGQITGCLAehHINIADMINRSkh--swAYTMIDIDNgiddiikENIVENISKitgVVAVRMI 389 Bacillus thuringiensi...
AAO91226    320 RIAITNKNvPNMVAQVSTVLSqaDINIIDMINKSrd--eiAYTLIDVNKki----dQNILHQLQSidgIIRVRLL 388 Coxiella burnetii RSA...
ZP_00531765 319 RIAISNSNvPKMVGQITSVLAdsGINIVDMLNKSrg--diAYNLLDLGTev----gKDIADKIKKiegVLAVRIM 387 Chlorobium phaeobacte...
ZP_01354897 318 RVTICHRNkPNMLAQFTTVFSskNLNIENLANKSkg--dyAYTVLDLCTvv----tEEFVKELEEiegVLKVRVI 386 Clostridium phytoferm...

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