1HO4,1HO4


Conserved Protein Domain Family
PNPsynthase
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cd00003: PNPsynthase 
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Pyridoxine 5'-phosphate (PNP) synthase domain; pyridoxal 5'-phosphate is the active form of vitamin B6 that acts as an essential, ubiquitous coenzyme in amino acid metabolism. In bacteria, formation of pyridoxine 5'-phosphate is a step in the biosynthesis of vitamin B6. PNP synthase, a homooctameric enzyme, catalyzes the final step in PNP biosynthesis, the condensation of 1-amino-acetone 3-phosphate and 1-deoxy-D-xylulose 5-phosphate. PNP synthase adopts a TIM barrel topology, intersubunit contacts are mediated by three ''extra'' helices, generating a tetramer of symmetric dimers with shared active sites; the open state has been proposed to accept substrates and to release products, while most of the catalytic events are likely to occur in the closed state; a hydrophilic channel running through the center of the barrel was identified as the essential structural feature that enables PNP synthase to release water molecules produced during the reaction from the closed, solvent-shielded active site.
Links
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Statistics
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PSSM-Id: 237977
Aligned: 52 rows
Threshold Bit Score: 295.179
Created: 4-Sep-2001
Updated: 2-Oct-2020
Structure
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Program:
Drawing:
Aligned Rows:
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Conserved site includes 18 residues -Click on image for an interactive view with Cn3D
Feature 1:active site [active site]
Evidence:
  • Structure:P1 site (phosphate binding site) is the main anchor for PNP binding
  • Comment:P1 site is sandwiched between two loops, main chain amide nitrogens and the guanidino group of an arginine from a neighboring chain bind the phosphate
  • Structure:P2 site binds inorganic phosphate
  • Comment:an arginine from a neighboring chain participates as well
  • Structure:specificity pocket
  • Comment:residues that line the pyridine moiety
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Sequence Alignment
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Format: Row Display: Color Bits: Type Selection: 
Feature 1           # ##       #                        # #   ##                            #   
1HO4_A        4 LLGVNIDHIATLRNARGTaYPDPVQAAFIAEQAGAdGITVHLREDRRHITDRDVRILRQTLD---------TRMNLEMAv 74  Escherichia coli
Q8YI24        4 KLSVNLNAIAMLRNRRDLpWPSVTGLGRAALAAGAaGLTVHPRPDQRHIRFSDLGDIRALIDdey----pqAEFNIEGFp 79  Brucella melitensis
Q92NT6        4 KLSVNLNAIAMLRNRRDLpWPSVTGLGRTALQAGAsGLTVHPRPDQRHIRFSDLQPIRDLIDdef----paAEFNMEGFp 79  Sinorhizobium me...
Q98KL6        4 KLSVNLNAIAMLRNRRDLpWPSVTGIGRLALAAGAhGLTVHPRPDERHTRHSDLPEIRALIDdef----pqAEFNIEGYp 79  Mesorhizobium loti
NP_711695     4 KLSVNINKIATLRNSRGGnIPDLSYFANLVLKAGAhGITVHPREDERHIRKEDVFVLKEFIDsynrknntnIEYNLEGEp 83  Leptospira inter...
YP_431475     4 VLSVNLNKIALIRNSRGRdYPSVKAFGRRALQAGAgGVTIHPRPDQRHARYSDIADLSELVKef-----adAELNIEGYp 78  Hahella chejuens...
ZP_01075097   3 HLSVNLNKIGLLRNSRGRdYPNMVEVAKKTLELGAfGITIHPRPDQRHATYQDARDLKALLAny-----pgKELNIEGFp 77  Marinomonas sp. ...
ZP_01116220   3 KLSVNVNKIALLRNSRGHdAPNVVEFARRFIELGVtGITIHPRQDERHITRQDARDLGDLIRpl-----ndIELNIEGYp 77  Reinekea sp. MED297
YP_527185     4 DLSVNLNKIALIRNSREGnYPDVTAFGRLSLDAGAaGLTVHPRPDQRHITPDDVRNLAALRTey-----prTEFNIEGNp 78  Saccharophagus d...
ZP_01224462   3 DLSINLNKIALIRNSREGnYPDVVEFAKVCIDQGAnGITVHPRPDQRHIRPDDVRRLAALVKpl-----tnVEFNVEGNp 77  marine gamma pro...

Feature 1                                        ##  #                          #               
1HO4_A       75 -------TEEMLAIAVETKPHFCCLVPEKRQEVTTEGGLDVagQRDKMRDACKRLADAGIqVSLFID--ADEEQIKAAAE 145 Escherichia coli
Q8YI24       80 -------SEAFLDLVEKHEPEQVTLVPDDPMQATSDHGWDFmsKADFLAPIVARLKGRGMrVSLFAD--PDSLGYERAKA 150 Brucella melitensis
Q92NT6       80 -------NEAFLELVERHEPEQVTLVPDDPAQATSDHGWDFrkSHNLLGNVVGRLKKRGFrVSLFADgiPDPEALKLAKE 152 Sinorhizobium me...
Q98KL6       80 -------SEDFLALVEKHQPEQVTLVPDDPAQATSDHGWNFvaDAALLTPIVRRLKKGGFrVSLFSD--ADPAGMTAARD 150 Mesorhizobium loti
NP_711695    84 -------SPRFLDLVLKTKPDQATLVPVTPGEITSDHGFDFekDMEILSEYSKILKKDKIrVSLFVE--TGLKNLKLASL 154 Leptospira inter...
YP_431475    79 -------EEELIEQVLRYKPHQFTLVPDKPDQITSDHGWDLnqDGEFVTDIVRKVQAAGVrVSLFMD--PDEAQIKLAQE 149 Hahella chejuens...
ZP_01075097  78 -------DQTFIDVVLEVVPEQCTLVPDDPNQLTSDHGWNLgrDSETLVPIIQKMQAAGIrVCLFMD--PDASAMKMAKD 148 Marinomonas sp. ...
ZP_01116220  78 -------SETFLQLIEEVRPDQTTLVPDAPDQLTSDHGFDFhtQAEFLDPILTRLKATGTrVSVFLD--PDVEQVKLAAQ 148 Reinekea sp. MED297
YP_527185    79 fapargtYPGLIELVAETNPEQCTLVPDNDAQKTSDHGFDLktDGERLIPLIEKLHSLGArVSLFMD--PDPEQIALAKQ 156 Saccharophagus d...
ZP_01224462  78 fapaigdYPGFIELVAETMPDQCTLVPDGDDQLTSDHGFDLtsSGEQLQPIIERLHSLGMrVSLFMD--PDLAQIELAKE 155 marine gamma pro...

Feature 1             #                                          ##                     ##      
1HO4_A      146 VGAPFIEIHTGCYADak---tdAEQAQELARIAKAATFAASLGLKVNAGHGLTYHNVKAIAA-IPEMHELNIGHAIIGRA 221 Escherichia coli
Q8YI24      151 IGADRVELYTGPYGAthd--dpAAAARELDRLEKAARAATALGLAVNAGHDLTVDNLPALVKrIPQLAEVSIGHGLTADA 228 Brucella melitensis
Q92NT6      153 TGADRIELYTGPYGGcyd--dpEKAERIAIELGRTAEIAIGLGLAVNAGHDLTVANLPLLVEhIPELAEVSIGHGLTADA 230 Sinorhizobium me...
Q98KL6      151 TGADRIELYTGPYGSyhs--dsAKADKELERLGKTADAAFAAGLQVNAGHDLTVGNLPALAKrIPALAEVSIGHGLTADA 228 Mesorhizobium loti
NP_711695   155 SGADRVEFYTGPFAEafdhspqIGKKRFETEYVPAATEILNQKMGINAGHDLDHENLKIFSK-LPGLQEVSIGHRLISRA 233 Leptospira inter...
YP_431475   150 TGAKRIELYTEEYAHay---gaPQFDAIAAKYLACARYAVSLGLTVNAGHDLNLENLAPLVA-EGTIAEVSIGHALTVEA 225 Hahella chejuens...
ZP_01075097 149 TGADRVELYTEAYANay---gtEEVENVLADYNSAAQAAVDAGLEVNAGHDLDLENVKALCD-SGLITEVSIGHALTVES 224 Marinomonas sp. ...
ZP_01116220 149 SKTDRIELYTEEYASqf---hrPQHTEVHQRFHDAAVEAQKLGLGVNAGHDLNLENLPAFLN-IPGILEVSIGHALIVEC 224 Reinekea sp. MED297
YP_527185   157 IGADRIELYTGPYAWafg-rnkEEGEQQFLLHKAAAEAALLCGLGINAGHDLNLQNLPLYSQ-LPGLQEVSIGHALTVDA 234 Saccharophagus d...
ZP_01224462 156 IGADRIELYTGPYAAaw---gsDQLEPLFQQHLAAAELSTRLGMGVNAGHDLNLHNLAKFAS-IPNLLEVSIGHAFTVDS 231 marine gamma pro...

Feature 1                       
1HO4_A      222 VMTGLKDAVAEMKRLM 237 Escherichia coli
Q8YI24      229 LMYGIPVTVSRYITAL 244 Brucella melitensis
Q92NT6      231 LEYGMAETVRRFRRAC 246 Sinorhizobium meliloti
Q98KL6      229 LEYGMAGTVGRFLRAC 244 Mesorhizobium loti
NP_711695   234 LETGIDQSVKDYLQAL 249 Leptospira interrogans serovar Lai str. 56601
YP_431475   226 LEMGFDQVIQKYVEIL 241 Hahella chejuensis KCTC 2396
ZP_01075097 225 LDLGWNNVVKAYLDRL 240 Marinomonas sp. MED121
ZP_01116220 225 LEYGMPFVARRYLDIC 240 Reinekea sp. MED297
YP_527185   235 LLMGYSEAVAAYRAIC 250 Saccharophagus degradans 2-40
ZP_01224462 232 LSLGMAQTVQRYKALL 247 marine gamma proteobacterium HTCC2207

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