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Conserved domains on  [gi|985380390|gb|KXA61775|]
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porphobilinogen synthase [Veillonella atypica]

Protein Classification

porphobilinogen synthase( domain architecture ID 18392256)

porphobilinogen synthase catalyzes the second step in the porphyrin and heme biosynthetic pathway in a zinc-dependent manner

CATH:  3.20.20.70
Gene Ontology:  GO:0004655|GO:0006782|GO:0046872
PubMed:  15381398
SCOP:  4003237

Graphical summary

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List of domain hits

Name Accession Description Interval E-value
HemB COG0113
Delta-aminolevulinic acid dehydratase, porphobilinogen synthase [Coenzyme transport and ...
1-308 0e+00

Delta-aminolevulinic acid dehydratase, porphobilinogen synthase [Coenzyme transport and metabolism]; Delta-aminolevulinic acid dehydratase, porphobilinogen synthase is part of the Pathway/BioSystem: Heme biosynthesis


:

Pssm-ID: 439883  Cd Length: 321  Bit Score: 559.61  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390   1 MRDLVRETTLDTTDLIYPLFIVPGEGIKEEIDTLPGQYHLSVDEAVKVAQEAYDLGIRGVEIFGIPTYKDEQGSSAWDME 80
Cdd:COG0113   13 IRRLVRETRLSPDDLIYPLFVVEGENEREPIPSMPGVYRLSLDLLVEEAEEAVELGIPAVALFGVPELKDEDGSEAYNPD 92
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390  81 QPVQQAIKAIREAVPNLLVIADVCLCQYTSTGHCGMIDHHEILNDETLPLLCKVAVSQAQAGAHMVAPSDMMDGRVGAIR 160
Cdd:COG0113   93 GLVQRAIRAIKAAVPELVVITDVCLDEYTSHGHCGILDDGYVDNDETLEVLAKQALSQAEAGADIVAPSDMMDGRVGAIR 172
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390 161 EALDEAGFTNVSIMsyaakyasayyGPFRGAVNSAPQFGDRKSYQMDPANRLEAMREIELDIAEGTDIIMIKPALCYLDI 240
Cdd:COG0113  173 EALDEAGFTDVPIMsysakyasafyGPFRDAAGSAPQFGDRKTYQMDPANSREALREVALDIEEGADMVMVKPALPYLDI 252
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 985380390 241 VREARDRYELPLAVYNVSGEYAMVKTAAAAGLIDEQRLVMETMLSMKRAGAKIIITYHALDVARWLKQ 308
Cdd:COG0113  253 IRRVKDEFDVPVAAYQVSGEYAMIKAAAQNGWLDEERVVLESLLSIKRAGADGILTYFAKEAARWLKE 320
 
Name Accession Description Interval E-value
HemB COG0113
Delta-aminolevulinic acid dehydratase, porphobilinogen synthase [Coenzyme transport and ...
1-308 0e+00

Delta-aminolevulinic acid dehydratase, porphobilinogen synthase [Coenzyme transport and metabolism]; Delta-aminolevulinic acid dehydratase, porphobilinogen synthase is part of the Pathway/BioSystem: Heme biosynthesis


Pssm-ID: 439883  Cd Length: 321  Bit Score: 559.61  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390   1 MRDLVRETTLDTTDLIYPLFIVPGEGIKEEIDTLPGQYHLSVDEAVKVAQEAYDLGIRGVEIFGIPTYKDEQGSSAWDME 80
Cdd:COG0113   13 IRRLVRETRLSPDDLIYPLFVVEGENEREPIPSMPGVYRLSLDLLVEEAEEAVELGIPAVALFGVPELKDEDGSEAYNPD 92
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390  81 QPVQQAIKAIREAVPNLLVIADVCLCQYTSTGHCGMIDHHEILNDETLPLLCKVAVSQAQAGAHMVAPSDMMDGRVGAIR 160
Cdd:COG0113   93 GLVQRAIRAIKAAVPELVVITDVCLDEYTSHGHCGILDDGYVDNDETLEVLAKQALSQAEAGADIVAPSDMMDGRVGAIR 172
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390 161 EALDEAGFTNVSIMsyaakyasayyGPFRGAVNSAPQFGDRKSYQMDPANRLEAMREIELDIAEGTDIIMIKPALCYLDI 240
Cdd:COG0113  173 EALDEAGFTDVPIMsysakyasafyGPFRDAAGSAPQFGDRKTYQMDPANSREALREVALDIEEGADMVMVKPALPYLDI 252
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 985380390 241 VREARDRYELPLAVYNVSGEYAMVKTAAAAGLIDEQRLVMETMLSMKRAGAKIIITYHALDVARWLKQ 308
Cdd:COG0113  253 IRRVKDEFDVPVAAYQVSGEYAMIKAAAQNGWLDEERVVLESLLSIKRAGADGILTYFAKEAARWLKE 320
ALAD pfam00490
Delta-aminolevulinic acid dehydratase;
1-304 0e+00

Delta-aminolevulinic acid dehydratase;


Pssm-ID: 459829  Cd Length: 315  Bit Score: 555.02  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390    1 MRDLVRETTLDTTDLIYPLFIVPGEGIKEEIDTLPGQYHLSVDEAVKVAQEAYDLGIRGVEIFGIPTYKDEQGSSAWDME 80
Cdd:pfam00490  12 LRRLVRETRLSPSDLIYPLFVVEGENEKEPIPSMPGVYRLSLDRLVKEVEEAVDLGIPAVILFGIPDEKDETGSEAYNPD 91
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390   81 QPVQQAIKAIREAVPNLLVIADVCLCQYTSTGHCGMIDHHEILNDETLPLLCKVAVSQAQAGAHMVAPSDMMDGRVGAIR 160
Cdd:pfam00490  92 GIVQRAIRAIKEAFPDLVVITDVCLCEYTSHGHCGILDGGEVDNDETLELLAKQAVSHAEAGADIVAPSDMMDGRVGAIR 171
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390  161 EALDEAGFTNVSIMsyaakyasayyGPFRGAVNSAPQFGDRKSYQMDPANRLEAMREIELDIAEGTDIIMIKPALCYLDI 240
Cdd:pfam00490 172 EALDEAGFTDVPIMsysakyasafyGPFRDAAGSAPSFGDRKTYQMDPANRREALREVALDIEEGADIVMVKPALPYLDI 251
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 985380390  241 VREARDRYELPLAVYNVSGEYAMVKTAAAAGLIDEQRLVMETMLSMKRAGAKIIITYHALDVAR 304
Cdd:pfam00490 252 IRRVKDRFDLPVAAYQVSGEYAMIKAAAANGWIDEKRVVLESLLSIKRAGADIIITYFAKEAAR 315
PRK09283 PRK09283
porphobilinogen synthase;
1-307 0e+00

porphobilinogen synthase;


Pssm-ID: 236450  Cd Length: 323  Bit Score: 554.65  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390   1 MRDLVRETTLDTTDLIYPLFIVPGEGIKEEIDTLPGQYHLSVDEAVKVAQEAYDLGIRGVEIFGIPTYKDEQGSSAWDME 80
Cdd:PRK09283  17 LRRLVRETRLTPNDLIYPLFVVEGENEREEIPSMPGVYRLSIDLLVKEAEEAVELGIPAVALFGVPELKDEDGSEAYNPD 96
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390  81 QPVQQAIKAIREAVPNLLVIADVCLCQYTSTGHCGMIDHHEILNDETLPLLCKVAVSQAQAGAHMVAPSDMMDGRVGAIR 160
Cdd:PRK09283  97 GLVQRAIRAIKKAFPELGVITDVCLDEYTSHGHCGILEDGYVDNDETLELLAKQALSQAEAGADIVAPSDMMDGRVGAIR 176
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390 161 EALDEAGFTNVSIMSYAAKYASAYYGPFRGAVNSAPQFGDRKSYQMDPANRLEAMREIELDIAEGTDIIMIKPALCYLDI 240
Cdd:PRK09283 177 EALDEAGFTDVPIMSYSAKYASAFYGPFRDAAGSAPQFGDRKTYQMDPANRREALREVALDIEEGADMVMVKPALPYLDI 256
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 985380390 241 VREARDRYELPLAVYNVSGEYAMVKTAAAAGLIDEQRLVMETMLSMKRAGAKIIITYHALDVARWLK 307
Cdd:PRK09283 257 IRRVKDEFNLPVAAYQVSGEYAMIKAAAQNGWIDEERVVLESLLSIKRAGADGILTYFAKDAARWLR 323
ALAD smart01004
Delta-aminolevulinic acid dehydratase; This entry represents porphobilinogen (PBG) synthase ...
1-306 0e+00

Delta-aminolevulinic acid dehydratase; This entry represents porphobilinogen (PBG) synthase (PBGS, or 5-aminoaevulinic acid dehydratase, or ALAD, ), which functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses a Knorr-type condensation reaction between two molecules of ALA to generate porphobilinogen, the pyrrolic building block used in later steps. The structure of the enzyme is based on a TIM barrel topology made up of eight identical subunits, where each subunit binds to a metal ion that is essential for activity, usually zinc (in yeast, mammals and certain bacteria) or magnesium (in plants and other bacteria). A lysine has been implicated in the catalytic mechanism. The lack of PBGS enzyme causes a rare porphyric disorder known as ALAD porphyria, which appears to involve conformational changes in the enzyme.


Pssm-ID: 214968  Cd Length: 321  Bit Score: 541.59  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390     1 MRDLVRETTLDTTDLIYPLFIVPGEGIKEEIDTLPGQYHLSVDEAVKVAQEAYDLGIRGVEIFGIPTYKDEQGSSAWDME 80
Cdd:smart01004  15 LRRLVRETRLSPSDLIYPLFVTEGEDEKEPIPSMPGVYRLSVDLLVEEAEEAVELGIPAVILFGVPEKKDEDGSEAYNPD 94
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390    81 QPVQQAIKAIREAVPNLLVIADVCLCQYTSTGHCGMIDHH-EILNDETLPLLCKVAVSQAQAGAHMVAPSDMMDGRVGAI 159
Cdd:smart01004  95 GLVQRAIRAIKKAFPDLVVITDVCLCEYTSHGHCGILDEDgYVDNDETLEVLAKQALSQAEAGADIVAPSDMMDGRVGAI 174
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390   160 REALDEAGFTNVSIMSYAAKYASAYYGPFRGAVNSAPQFGDRKSYQMDPANRLEAMREIELDIAEGTDIIMIKPALCYLD 239
Cdd:smart01004 175 REALDAAGFTDVPIMSYSAKYASAFYGPFRDAAGSAPQFGDRKTYQMDPANRREALREVALDIAEGADMVMVKPALPYLD 254
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 985380390   240 IVREARDRYELPLAVYNVSGEYAMVKTAAAAGLIDEQRLVMETMLSMKRAGAKIIITYHALDVARWL 306
Cdd:smart01004 255 IIRRVKDEFDLPVAAYQVSGEYAMIKAAAQNGWIDEERVVLESLLSIKRAGADLIITYFAKEAARWL 321
ALAD_PBGS cd00384
Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase ...
1-306 0e+00

Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the biosynthesis of tetrapyrroles, such as heme, vitamin B12 and chlorophyll. This reaction involves the formation of a Schiff base link between the substrate and the enzyme. PBGSs are metalloenzymes, some of which have a second, allosteric metal binding site, beside the metal ion binding site in their active site. Although PBGS is a family of homologous enzymes, its metal ion utilization at catalytic site varies between zinc and magnesium and/or potassium. PBGS can be classified into two groups based on differences in their active site metal binding site. They either contain a cysteine-rich zinc binding site (consensus DXCXCX(Y/F)X3G(H/Q)CG) or an aspartate-rich magnesium binding site (consensus DXALDX(Y/F)X3G(H/Q)DG). The cysteine-rich zinc binding site appears more common. Most members represented by this model also have a second allosteric magnesium binding site (consensus RX~164DX~65EXXXD, missing in a eukaryotic subfamily with cysteine-rich zinc binding site).


Pssm-ID: 238226  Cd Length: 314  Bit Score: 534.77  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390   1 MRDLVRETTLDTTDLIYPLFIVPGEGIKEEIDTLPGQYHLSVDEAVKVAQEAYDLGIRGVEIFGIPTYKDEQGSSAWDME 80
Cdd:cd00384    9 LRDLVRETRLSPDDLIYPLFVVEGIDEKEEISSMPGVYRLSVDSLVEEAEELADLGIRAVILFGIPEHKDEIGSEAYDPD 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390  81 QPVQQAIKAIREAVPNLLVIADVCLCQYTSTGHCGMIDHHEILNDETLPLLCKVAVSQAQAGAHMVAPSDMMDGRVGAIR 160
Cdd:cd00384   89 GIVQRAIRAIKEAVPELVVITDVCLCEYTDHGHCGILKDDYVDNDATLELLAKIAVSHAEAGADIVAPSDMMDGRVAAIR 168
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390 161 EALDEAGFTNVSIMSYAAKYASAYYGPFRGAVNSAPQFGDRKSYQMDPANRLEAMREIELDIAEGTDIIMIKPALCYLDI 240
Cdd:cd00384  169 EALDEAGFSDVPIMSYSAKYASAFYGPFRDAADSAPSFGDRKTYQMDPANRREALREVELDIEEGADILMVKPALAYLDI 248
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 985380390 241 VREARDRYELPLAVYNVSGEYAMVKTAAAAGLIDEQRLVMETMLSMKRAGAKIIITYHALDVARWL 306
Cdd:cd00384  249 IRDVRERFDLPVAAYNVSGEYAMIKAAAKNGWIDEERVVLESLTSIKRAGADLIITYFAKDAARWL 314
 
Name Accession Description Interval E-value
HemB COG0113
Delta-aminolevulinic acid dehydratase, porphobilinogen synthase [Coenzyme transport and ...
1-308 0e+00

Delta-aminolevulinic acid dehydratase, porphobilinogen synthase [Coenzyme transport and metabolism]; Delta-aminolevulinic acid dehydratase, porphobilinogen synthase is part of the Pathway/BioSystem: Heme biosynthesis


Pssm-ID: 439883  Cd Length: 321  Bit Score: 559.61  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390   1 MRDLVRETTLDTTDLIYPLFIVPGEGIKEEIDTLPGQYHLSVDEAVKVAQEAYDLGIRGVEIFGIPTYKDEQGSSAWDME 80
Cdd:COG0113   13 IRRLVRETRLSPDDLIYPLFVVEGENEREPIPSMPGVYRLSLDLLVEEAEEAVELGIPAVALFGVPELKDEDGSEAYNPD 92
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390  81 QPVQQAIKAIREAVPNLLVIADVCLCQYTSTGHCGMIDHHEILNDETLPLLCKVAVSQAQAGAHMVAPSDMMDGRVGAIR 160
Cdd:COG0113   93 GLVQRAIRAIKAAVPELVVITDVCLDEYTSHGHCGILDDGYVDNDETLEVLAKQALSQAEAGADIVAPSDMMDGRVGAIR 172
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390 161 EALDEAGFTNVSIMsyaakyasayyGPFRGAVNSAPQFGDRKSYQMDPANRLEAMREIELDIAEGTDIIMIKPALCYLDI 240
Cdd:COG0113  173 EALDEAGFTDVPIMsysakyasafyGPFRDAAGSAPQFGDRKTYQMDPANSREALREVALDIEEGADMVMVKPALPYLDI 252
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 985380390 241 VREARDRYELPLAVYNVSGEYAMVKTAAAAGLIDEQRLVMETMLSMKRAGAKIIITYHALDVARWLKQ 308
Cdd:COG0113  253 IRRVKDEFDVPVAAYQVSGEYAMIKAAAQNGWLDEERVVLESLLSIKRAGADGILTYFAKEAARWLKE 320
ALAD pfam00490
Delta-aminolevulinic acid dehydratase;
1-304 0e+00

Delta-aminolevulinic acid dehydratase;


Pssm-ID: 459829  Cd Length: 315  Bit Score: 555.02  E-value: 0e+00
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390    1 MRDLVRETTLDTTDLIYPLFIVPGEGIKEEIDTLPGQYHLSVDEAVKVAQEAYDLGIRGVEIFGIPTYKDEQGSSAWDME 80
Cdd:pfam00490  12 LRRLVRETRLSPSDLIYPLFVVEGENEKEPIPSMPGVYRLSLDRLVKEVEEAVDLGIPAVILFGIPDEKDETGSEAYNPD 91
                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390   81 QPVQQAIKAIREAVPNLLVIADVCLCQYTSTGHCGMIDHHEILNDETLPLLCKVAVSQAQAGAHMVAPSDMMDGRVGAIR 160
Cdd:pfam00490  92 GIVQRAIRAIKEAFPDLVVITDVCLCEYTSHGHCGILDGGEVDNDETLELLAKQAVSHAEAGADIVAPSDMMDGRVGAIR 171
                         170       180       190       200       210       220       230       240
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390  161 EALDEAGFTNVSIMsyaakyasayyGPFRGAVNSAPQFGDRKSYQMDPANRLEAMREIELDIAEGTDIIMIKPALCYLDI 240
Cdd:pfam00490 172 EALDEAGFTDVPIMsysakyasafyGPFRDAAGSAPSFGDRKTYQMDPANRREALREVALDIEEGADIVMVKPALPYLDI 251
                         250       260       270       280       290       300
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 985380390  241 VREARDRYELPLAVYNVSGEYAMVKTAAAAGLIDEQRLVMETMLSMKRAGAKIIITYHALDVAR 304
Cdd:pfam00490 252 IRRVKDRFDLPVAAYQVSGEYAMIKAAAANGWIDEKRVVLESLLSIKRAGADIIITYFAKEAAR 315
PRK09283 PRK09283
porphobilinogen synthase;
1-307 0e+00

porphobilinogen synthase;


Pssm-ID: 236450  Cd Length: 323  Bit Score: 554.65  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390   1 MRDLVRETTLDTTDLIYPLFIVPGEGIKEEIDTLPGQYHLSVDEAVKVAQEAYDLGIRGVEIFGIPTYKDEQGSSAWDME 80
Cdd:PRK09283  17 LRRLVRETRLTPNDLIYPLFVVEGENEREEIPSMPGVYRLSIDLLVKEAEEAVELGIPAVALFGVPELKDEDGSEAYNPD 96
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390  81 QPVQQAIKAIREAVPNLLVIADVCLCQYTSTGHCGMIDHHEILNDETLPLLCKVAVSQAQAGAHMVAPSDMMDGRVGAIR 160
Cdd:PRK09283  97 GLVQRAIRAIKKAFPELGVITDVCLDEYTSHGHCGILEDGYVDNDETLELLAKQALSQAEAGADIVAPSDMMDGRVGAIR 176
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390 161 EALDEAGFTNVSIMSYAAKYASAYYGPFRGAVNSAPQFGDRKSYQMDPANRLEAMREIELDIAEGTDIIMIKPALCYLDI 240
Cdd:PRK09283 177 EALDEAGFTDVPIMSYSAKYASAFYGPFRDAAGSAPQFGDRKTYQMDPANRREALREVALDIEEGADMVMVKPALPYLDI 256
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 985380390 241 VREARDRYELPLAVYNVSGEYAMVKTAAAAGLIDEQRLVMETMLSMKRAGAKIIITYHALDVARWLK 307
Cdd:PRK09283 257 IRRVKDEFNLPVAAYQVSGEYAMIKAAAQNGWIDEERVVLESLLSIKRAGADGILTYFAKDAARWLR 323
ALAD smart01004
Delta-aminolevulinic acid dehydratase; This entry represents porphobilinogen (PBG) synthase ...
1-306 0e+00

Delta-aminolevulinic acid dehydratase; This entry represents porphobilinogen (PBG) synthase (PBGS, or 5-aminoaevulinic acid dehydratase, or ALAD, ), which functions during the second stage of tetrapyrrole biosynthesis. This enzyme catalyses a Knorr-type condensation reaction between two molecules of ALA to generate porphobilinogen, the pyrrolic building block used in later steps. The structure of the enzyme is based on a TIM barrel topology made up of eight identical subunits, where each subunit binds to a metal ion that is essential for activity, usually zinc (in yeast, mammals and certain bacteria) or magnesium (in plants and other bacteria). A lysine has been implicated in the catalytic mechanism. The lack of PBGS enzyme causes a rare porphyric disorder known as ALAD porphyria, which appears to involve conformational changes in the enzyme.


Pssm-ID: 214968  Cd Length: 321  Bit Score: 541.59  E-value: 0e+00
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390     1 MRDLVRETTLDTTDLIYPLFIVPGEGIKEEIDTLPGQYHLSVDEAVKVAQEAYDLGIRGVEIFGIPTYKDEQGSSAWDME 80
Cdd:smart01004  15 LRRLVRETRLSPSDLIYPLFVTEGEDEKEPIPSMPGVYRLSVDLLVEEAEEAVELGIPAVILFGVPEKKDEDGSEAYNPD 94
                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390    81 QPVQQAIKAIREAVPNLLVIADVCLCQYTSTGHCGMIDHH-EILNDETLPLLCKVAVSQAQAGAHMVAPSDMMDGRVGAI 159
Cdd:smart01004  95 GLVQRAIRAIKKAFPDLVVITDVCLCEYTSHGHCGILDEDgYVDNDETLEVLAKQALSQAEAGADIVAPSDMMDGRVGAI 174
                          170       180       190       200       210       220       230       240
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390   160 REALDEAGFTNVSIMSYAAKYASAYYGPFRGAVNSAPQFGDRKSYQMDPANRLEAMREIELDIAEGTDIIMIKPALCYLD 239
Cdd:smart01004 175 REALDAAGFTDVPIMSYSAKYASAFYGPFRDAAGSAPQFGDRKTYQMDPANRREALREVALDIAEGADMVMVKPALPYLD 254
                          250       260       270       280       290       300
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 985380390   240 IVREARDRYELPLAVYNVSGEYAMVKTAAAAGLIDEQRLVMETMLSMKRAGAKIIITYHALDVARWL 306
Cdd:smart01004 255 IIRRVKDEFDLPVAAYQVSGEYAMIKAAAQNGWIDEERVVLESLLSIKRAGADLIITYFAKEAARWL 321
ALAD_PBGS cd00384
Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase ...
1-306 0e+00

Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the biosynthesis of tetrapyrroles, such as heme, vitamin B12 and chlorophyll. This reaction involves the formation of a Schiff base link between the substrate and the enzyme. PBGSs are metalloenzymes, some of which have a second, allosteric metal binding site, beside the metal ion binding site in their active site. Although PBGS is a family of homologous enzymes, its metal ion utilization at catalytic site varies between zinc and magnesium and/or potassium. PBGS can be classified into two groups based on differences in their active site metal binding site. They either contain a cysteine-rich zinc binding site (consensus DXCXCX(Y/F)X3G(H/Q)CG) or an aspartate-rich magnesium binding site (consensus DXALDX(Y/F)X3G(H/Q)DG). The cysteine-rich zinc binding site appears more common. Most members represented by this model also have a second allosteric magnesium binding site (consensus RX~164DX~65EXXXD, missing in a eukaryotic subfamily with cysteine-rich zinc binding site).


Pssm-ID: 238226  Cd Length: 314  Bit Score: 534.77  E-value: 0e+00
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390   1 MRDLVRETTLDTTDLIYPLFIVPGEGIKEEIDTLPGQYHLSVDEAVKVAQEAYDLGIRGVEIFGIPTYKDEQGSSAWDME 80
Cdd:cd00384    9 LRDLVRETRLSPDDLIYPLFVVEGIDEKEEISSMPGVYRLSVDSLVEEAEELADLGIRAVILFGIPEHKDEIGSEAYDPD 88
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390  81 QPVQQAIKAIREAVPNLLVIADVCLCQYTSTGHCGMIDHHEILNDETLPLLCKVAVSQAQAGAHMVAPSDMMDGRVGAIR 160
Cdd:cd00384   89 GIVQRAIRAIKEAVPELVVITDVCLCEYTDHGHCGILKDDYVDNDATLELLAKIAVSHAEAGADIVAPSDMMDGRVAAIR 168
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390 161 EALDEAGFTNVSIMSYAAKYASAYYGPFRGAVNSAPQFGDRKSYQMDPANRLEAMREIELDIAEGTDIIMIKPALCYLDI 240
Cdd:cd00384  169 EALDEAGFSDVPIMSYSAKYASAFYGPFRDAADSAPSFGDRKTYQMDPANRREALREVELDIEEGADILMVKPALAYLDI 248
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 985380390 241 VREARDRYELPLAVYNVSGEYAMVKTAAAAGLIDEQRLVMETMLSMKRAGAKIIITYHALDVARWL 306
Cdd:cd00384  249 IRDVRERFDLPVAAYNVSGEYAMIKAAAKNGWIDEERVVLESLTSIKRAGADLIITYFAKDAARWL 314
ALAD_PBGS_aspartate_rich cd04823
Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase ...
1-307 5.07e-159

Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the biosynthesis of tetrapyrroles, such as heme, vitamin B12 and chlorophyll. This reaction involves the formation of a Schiff base link between the substrate and the enzyme. PBGSs are metalloenzymes, some of which have a second, allosteric metal binding site, beside the metal ion binding site in their active site. Although PBGS is a family of homologous enzymes, its metal ion utilization at catalytic site varies between zinc and magnesium and/or potassium. PBGS can be classified into two groups based on differences in their active site metal binding site. All of PBGS_aspartate_rich contain an aspartate rich metal binding site with the general sequence DXALDX(Y/F)X3G(H/Q)DG. They also contain an allosteric magnesium binding sequence RX~164DX~65EXXXD and are activated by magnesium and/or potassium, but not by zinc. PBGSs_aspartate_rich are found in some bacterial species and photosynthetic organisms such as vascular plants, mosses and algae, but not in archaea.


Pssm-ID: 240127  Cd Length: 320  Bit Score: 446.23  E-value: 5.07e-159
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390   1 MRDLVRETTLDTTDLIYPLFIVPGEGIKEEIDTLPGQYHLSVDEAVKVAQEAYDLGIRGVEIFGI--PTYKDEQGSSAWD 78
Cdd:cd04823   12 LRRLVRETTLSPDDLILPLFVHEGENQREPIPSMPGVFRLSIDELLKEAEEAVDLGIPAVALFPVtpPELKSEDGSEAYN 91
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390  79 MEQPVQQAIKAIREAVPNLLVIADVCLCQYTSTGHCGMIDHHEILNDETLPLLCKVAVSQAQAGAHMVAPSDMMDGRVGA 158
Cdd:cd04823   92 PDNLVCRAIRAIKEAFPELGIITDVALDPYTSHGHDGIVRDGGILNDETVEVLCKQALVQAEAGADIVAPSDMMDGRIGA 171
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390 159 IREALDEAGFTNVSIMSYAAKYASAYYGPFRGAVNSAPQFGDRKSYQMDPANRLEAMREIELDIAEGTDIIMIKPALCYL 238
Cdd:cd04823  172 IREALDAEGFTNVSILSYAAKYASAFYGPFRDALGSAPRKGDKKTYQMDPANSREALREVALDIAEGADMVMVKPGMPYL 251
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 985380390 239 DIVREARDRYELPLAVYNVSGEYAMVKTAAAAGLIDEQRLVMETMLSMKRAGAKIIITYHALDVARWLK 307
Cdd:cd04823  252 DIIRRVKDEFGVPTFAYQVSGEYAMLKAAAQNGWLDEDKVMLESLLAFKRAGADGILTYFAKEAAEWLR 320
PRK13384 PRK13384
porphobilinogen synthase;
1-305 4.55e-121

porphobilinogen synthase;


Pssm-ID: 172020  Cd Length: 322  Bit Score: 350.19  E-value: 4.55e-121
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390   1 MRDLVRETTLDTTDLIYPLFIvpGEGIKEE--IDTLPGQYHLSVDEAVKVAQEAYDLGIRGVEIFGIPTYKDEQGSSAWD 78
Cdd:PRK13384  19 MRDLVRETEVSLSDLIYPIFI--EEHITDAvpISTLPGISRLPESALADEIERLYALGIRYVMPFGISHHKDAKGSDTWD 96
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390  79 MEQPVQQAIKAIREAVPNLLVIADVCLCQYTSTGHCGMIDHHEILNDETLPLLCKVAVSQAQAGAHMVAPSDMMDGRVGA 158
Cdd:PRK13384  97 DNGLLARMVRTIKAAVPEMMVIPDICFCEYTDHGHCGVLHNDEVDNDATVENLVKQSVTAAKAGADMLAPSAMMDGQVKA 176
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390 159 IREALDEAGFTNVSIMSYAAKYASAYYGPFRGAVNSAPQfGDRKSYQMDPANRLEAMREIELDIAEGTDIIMIKPALCYL 238
Cdd:PRK13384 177 IRQGLDAAGFEHVAILAHSAKFASSFYGPFRAAVDCELS-GDRKSYQLDYANGRQALLEALLDEAEGADILMVKPGTPYL 255
                        250       260       270       280       290       300
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 985380390 239 DIVREARDRYELPLAVYNVSGEYAMVKTAAAAGLIDEQRLVMETMLSMKRAGAKIIITYHALDVARW 305
Cdd:PRK13384 256 DVLSRLRQETHLPLAAYQVGGEYAMIKFAALAGALDERAVVTETLGGLKRAGADLIVSYYAKQYAQW 322
eu_ALAD_PBGS_cysteine_rich cd04824
Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase ...
2-306 2.04e-116

Porphobilinogen synthase (PBGS), which is also called delta-aminolevulinic acid dehydratase (ALAD), catalyzes the condensation of two 5-aminolevulinic acid (ALA) molecules to form the pyrrole porphobilinogen (PBG), which is the second step in the biosynthesis of tetrapyrroles, such as heme, vitamin B12 and chlorophyll. This reaction involves the formation of a Schiff base link between the substrate and the enzyme. PBGSs are metalloenzymes, some of which have a second, allosteric metal binding site, beside the metal ion binding site in their active site. Although PBGS is a family of homologous enzymes, its metal ion utilization at catalytic site varies between zinc and magnesium and/or potassium. PBGS can be classified into two groups based on differences in their active site metal binding site. The eukaryotic PBGSs represented by this model, which contain a cysteine-rich zinc binding motif (DXCXCX(Y/F)X3G(H/Q)CG), require zinc for their activity, they do not contain an additional allosteric metal binding site and do not bind magnesium.


Pssm-ID: 240128  Cd Length: 320  Bit Score: 338.18  E-value: 2.04e-116
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390   2 RDLVRETTLDTTDLIYPLFIVPGEGIKEEIDTLPGQYHLSVDEAVKVAQEAYDLGIRGVEIFGIPT---YKDEQGSSAWD 78
Cdd:cd04824   10 RQWQSERTLTKSNLIYPIFITDNPDAKQPIDSLPGINRYGVNRLEEFLRPLVAKGLRSVILFGVPLkpgKDDRSGSAADD 89
                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390  79 MEQPVQQAIKAIREAVPNLLVIADVCLCQYTSTGHCGMI-DHHEILNDETLPLLCKVAVSQAQAGAHMVAPSDMMDGRVG 157
Cdd:cd04824   90 EDGPVIQAIKLIREEFPELLIACDVCLCEYTSHGHCGILyEDGTINNEASVKRLAEVALAYAKAGAHIVAPSDMMDGRVR 169
                        170       180       190       200       210       220       230       240
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 985380390 158 AIREALDEAGFTN-VSIMSYAAKYASAYYGPFRGAVNSAPQFGDRKSYQMDPANRLEAMREIELDIAEGTDIIMIKPALC 236
Cdd:cd04824  170 AIKQALIQAGLGNkVSVMSYSAKFASCLYGPFRDAACSAPSFGDRRCYQLPPGARGLALRAVERDVSEGADMIMVKPGTP 249
                        250       260       270       280       290       300       310
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 985380390 237 YLDIVREARDRY-ELPLAVYNVSGEYAMVKTAAAAGLIDEQRLVMETMLSMKRAGAKIIITYHALDVARWL 306
Cdd:cd04824  250 YLDIVREAKDKHpDLPLAVYHVSGEYAMLHAAAEAGAFDLKRAVLEAMTGFRRAGADIIITYFTPELLDWL 320
 
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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