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Conserved domains on  [gi|556278356|ref|WP_023288815|]
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MULTISPECIES: acireductone dioxygenase [Klebsiella]

Protein Classification

1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase( domain architecture ID 10004526)

1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase, also called acireductone dioxygenase, catalyzes the oxidation of 1,2-dihydroxy-3-keto-5-methylthiopentene to yield two different products depending on which active site metal is present (Fe2+ or Ni2+) as part of the methionine salvage pathway

CATH:  2.60.120.10
EC:  1.13.11.53|1.13.11.54
Gene Ontology:  GO:0019509|GO:0010309|GO:0005506|GO:0010308|GO:0016151
PubMed:  9880484|16989860|14697267|19478949
SCOP:  4002777

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
Adi1 COG1791
Acireductone dioxygenase (methionine salvage), cupin superfamily [Amino acid transport and ...
 1-180 3.33e-110

Acireductone dioxygenase (methionine salvage), cupin superfamily [Amino acid transport and metabolism];


:

Pssm-ID: 441396  Cd Length: 180  Bit Score: 311.74  E-value: 3.33e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556278356   1 MSALTLFSVKDPQTPvWHSTDAKAIQEQLNAKGVRFERWQADRDLGAAPSAETVIAAYQHAIDKLVAEKGYQSWDVISLR 80
Cdd:COG1791    1 MATLRIYPDDGPEQP-TTITDLEEIARELAPLGVRFERWDAGQDLLTDAEKEEVLAAYRSEIERLKAERGYQSVDVISLH 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556278356  81 ADNPQKEALREKFLNEHTHGEDEVRFFVEGAGLFCLHIGDEVFQVLCEKNDLISVPAHTPHWFDMGSEPNFTAIRIFDNP 160
Cdd:COG1791   80 PDTPNLDALRAKFLSEHTHTEDEVRFFVAGEGLFGLHLGGKVYEVLCEAGDLISVPAGTEHWFDMGPSPRFKAIRLFTNP 159

                        170       180
                 ....*....|....*....|
gi 556278356 161 EGWIAQFTGDDIASAYPRLA 180
Cdd:COG1791  160 EGWVAHYTGSDIADRFPRLE 179
 
Name Accession Description Interval E-value
Adi1 COG1791
Acireductone dioxygenase (methionine salvage), cupin superfamily [Amino acid transport and ...
 1-180 3.33e-110

Acireductone dioxygenase (methionine salvage), cupin superfamily [Amino acid transport and metabolism];


Pssm-ID: 441396  Cd Length: 180  Bit Score: 311.74  E-value: 3.33e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556278356   1 MSALTLFSVKDPQTPvWHSTDAKAIQEQLNAKGVRFERWQADRDLGAAPSAETVIAAYQHAIDKLVAEKGYQSWDVISLR 80
Cdd:COG1791    1 MATLRIYPDDGPEQP-TTITDLEEIARELAPLGVRFERWDAGQDLLTDAEKEEVLAAYRSEIERLKAERGYQSVDVISLH 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556278356  81 ADNPQKEALREKFLNEHTHGEDEVRFFVEGAGLFCLHIGDEVFQVLCEKNDLISVPAHTPHWFDMGSEPNFTAIRIFDNP 160
Cdd:COG1791   80 PDTPNLDALRAKFLSEHTHTEDEVRFFVAGEGLFGLHLGGKVYEVLCEAGDLISVPAGTEHWFDMGPSPRFKAIRLFTNP 159

                        170       180
                 ....*....|....*....|
gi 556278356 161 EGWIAQFTGDDIASAYPRLA 180
Cdd:COG1791  160 EGWVAHYTGSDIADRFPRLE 179
cupin_ARD cd02232
acireductone dioxygenase (ARD), cupin domain; Acireductone dioxygenase (ARD; also known as 1, ...
 27-165 1.79e-61

acireductone dioxygenase (ARD), cupin domain; Acireductone dioxygenase (ARD; also known as 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase) catalyzes the oxidation of 1,2-dihydroxy-3-keto-5-methylthiopentene to yield two different products depending on which active site metal is present (Fe2+ or Ni2+) as part of the methionine salvage pathway. The ARD apo-enzyme, obtained after the metal is removed, is catalytically inactive. The Fe(II)-ARD reaction yields an alpha-keto acid and formic acid, while Ni(II)-ARD instead catalyzes a shunt out of the methionine salvage pathway, yielding methylthiocarboxylic acid, formic acid, and CO. ARD belongs to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization


Pssm-ID: 380360  Cd Length: 134  Bit Score: 186.59  E-value: 1.79e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556278356  27 EQLNAKGVRFERWQADRDLGAApsaetviAAYQHAIDKLVAEKGYQSWDVISLRADNPQKEALREKFLNEHTHGEDEVRF 106
Cdd:cd02232    2 EELAELGVLYERWDADDLEAAG-------AAYDEELDALKKERGYKSRDVVTLSPETPNYEEKLKKFFEEHLHEDDEVRF 74

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 556278356 107 FVEGAGLFCLHIG-DEVFQVLCEKNDLISVPAHTPHWFDMGSEPNFTAIRIFDNPEGWIA 165
Cdd:cd02232   75 ILDGSGYFDVRDKdDEWIRILVEKGDLIVVPAGIYHRFTLDENPYIKAVRLFKDEPGWVP 134
ARD pfam03079
ARD/ARD' family; The two acireductone dioxygenase enzymes (ARD and ARD', previously known as ...
 11-165 1.29e-39

ARD/ARD' family; The two acireductone dioxygenase enzymes (ARD and ARD', previously known as E-2 and E-2') from Klebsiella pneumoniae share the same amino acid sequence, but bind different metal ions: ARD binds Ni2+, ARD' binds Fe2+. ARD and ARD' can be experimentally interconverted by removal of the bound metal ion and reconstitution with the appropriate metal ion. The two enzymes share the same substrate, 1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield different products. ARD' yields the alpha-keto precursor of methionine (and formate), thus forming part of the ubiquitous methionine salvage pathway that converts 5'-methylthioadenosine (MTA) to methionine. This pathway is responsible for the tight control of the concentration of MTA, which is a powerful inhibitor of polyamine biosynthesis and transmethylation reactions. ARD yields methylthiopropanoate, carbon monoxide and formate, and thus prevents the conversion of MTA to methionine. The role of the ARD catalyzed reaction is unclear: methylthiopropanoate is cytotoxic, and carbon monoxide can activate guanylyl cyclase, leading to increased intracellular cGMP levels. This family also contains other members, whose functions are not well characterized.


Pssm-ID: 281122  Cd Length: 157  Bit Score: 132.09  E-value: 1.29e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556278356   11 DPQTPvwHSTDAKAIQEQLNAKGVRFERWQADRDLGAAPSAETVIAAYQHAIDKLVaekgyqswDVISLRADNPQKEALR 90
Cdd:pfam03079  12 DQRLP--HHTFPKEKAETDELAKLGVLYWKLDADDEETAEDLLRILKYKHYDDVDI--------DVTVCPETTPNFDEKL 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 556278356   91 EKFLNEHTHGEDEVRFFVEGAGLFCLHIGDEVF-QVLCEKNDLISVPAHTPHWFDMGSEPNFTAIRIFDNPEGWIA 165
Cdd:pfam03079  82 EKFFEEHLHTDEEIRYIVEGTGYFDVRDKDDVWiRVFVEKGDLISLPAGIYHRFTTTPDNYVKALRLFVTKPGWTA 157
 
Name Accession Description Interval E-value
Adi1 COG1791
Acireductone dioxygenase (methionine salvage), cupin superfamily [Amino acid transport and ...
 1-180 3.33e-110

Acireductone dioxygenase (methionine salvage), cupin superfamily [Amino acid transport and metabolism];


Pssm-ID: 441396  Cd Length: 180  Bit Score: 311.74  E-value: 3.33e-110
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556278356   1 MSALTLFSVKDPQTPvWHSTDAKAIQEQLNAKGVRFERWQADRDLGAAPSAETVIAAYQHAIDKLVAEKGYQSWDVISLR 80
Cdd:COG1791    1 MATLRIYPDDGPEQP-TTITDLEEIARELAPLGVRFERWDAGQDLLTDAEKEEVLAAYRSEIERLKAERGYQSVDVISLH 79

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556278356  81 ADNPQKEALREKFLNEHTHGEDEVRFFVEGAGLFCLHIGDEVFQVLCEKNDLISVPAHTPHWFDMGSEPNFTAIRIFDNP 160
Cdd:COG1791   80 PDTPNLDALRAKFLSEHTHTEDEVRFFVAGEGLFGLHLGGKVYEVLCEAGDLISVPAGTEHWFDMGPSPRFKAIRLFTNP 159

                        170       180
                 ....*....|....*....|
gi 556278356 161 EGWIAQFTGDDIASAYPRLA 180
Cdd:COG1791  160 EGWVAHYTGSDIADRFPRLE 179
cupin_ARD cd02232
acireductone dioxygenase (ARD), cupin domain; Acireductone dioxygenase (ARD; also known as 1, ...
 27-165 1.79e-61

acireductone dioxygenase (ARD), cupin domain; Acireductone dioxygenase (ARD; also known as 1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase) catalyzes the oxidation of 1,2-dihydroxy-3-keto-5-methylthiopentene to yield two different products depending on which active site metal is present (Fe2+ or Ni2+) as part of the methionine salvage pathway. The ARD apo-enzyme, obtained after the metal is removed, is catalytically inactive. The Fe(II)-ARD reaction yields an alpha-keto acid and formic acid, while Ni(II)-ARD instead catalyzes a shunt out of the methionine salvage pathway, yielding methylthiocarboxylic acid, formic acid, and CO. ARD belongs to the cupin superfamily with a conserved "jelly roll-like" beta-barrel fold capable of homodimerization


Pssm-ID: 380360  Cd Length: 134  Bit Score: 186.59  E-value: 1.79e-61
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556278356  27 EQLNAKGVRFERWQADRDLGAApsaetviAAYQHAIDKLVAEKGYQSWDVISLRADNPQKEALREKFLNEHTHGEDEVRF 106
Cdd:cd02232    2 EELAELGVLYERWDADDLEAAG-------AAYDEELDALKKERGYKSRDVVTLSPETPNYEEKLKKFFEEHLHEDDEVRF 74

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|
gi 556278356 107 FVEGAGLFCLHIG-DEVFQVLCEKNDLISVPAHTPHWFDMGSEPNFTAIRIFDNPEGWIA 165
Cdd:cd02232   75 ILDGSGYFDVRDKdDEWIRILVEKGDLIVVPAGIYHRFTLDENPYIKAVRLFKDEPGWVP 134
ARD pfam03079
ARD/ARD' family; The two acireductone dioxygenase enzymes (ARD and ARD', previously known as ...
 11-165 1.29e-39

ARD/ARD' family; The two acireductone dioxygenase enzymes (ARD and ARD', previously known as E-2 and E-2') from Klebsiella pneumoniae share the same amino acid sequence, but bind different metal ions: ARD binds Ni2+, ARD' binds Fe2+. ARD and ARD' can be experimentally interconverted by removal of the bound metal ion and reconstitution with the appropriate metal ion. The two enzymes share the same substrate, 1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield different products. ARD' yields the alpha-keto precursor of methionine (and formate), thus forming part of the ubiquitous methionine salvage pathway that converts 5'-methylthioadenosine (MTA) to methionine. This pathway is responsible for the tight control of the concentration of MTA, which is a powerful inhibitor of polyamine biosynthesis and transmethylation reactions. ARD yields methylthiopropanoate, carbon monoxide and formate, and thus prevents the conversion of MTA to methionine. The role of the ARD catalyzed reaction is unclear: methylthiopropanoate is cytotoxic, and carbon monoxide can activate guanylyl cyclase, leading to increased intracellular cGMP levels. This family also contains other members, whose functions are not well characterized.


Pssm-ID: 281122  Cd Length: 157  Bit Score: 132.09  E-value: 1.29e-39
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 556278356   11 DPQTPvwHSTDAKAIQEQLNAKGVRFERWQADRDLGAAPSAETVIAAYQHAIDKLVaekgyqswDVISLRADNPQKEALR 90
Cdd:pfam03079  12 DQRLP--HHTFPKEKAETDELAKLGVLYWKLDADDEETAEDLLRILKYKHYDDVDI--------DVTVCPETTPNFDEKL 81

                          90       100       110       120       130       140       150
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 556278356   91 EKFLNEHTHGEDEVRFFVEGAGLFCLHIGDEVF-QVLCEKNDLISVPAHTPHWFDMGSEPNFTAIRIFDNPEGWIA 165
Cdd:pfam03079  82 EKFFEEHLHTDEEIRYIVEGTGYFDVRDKDDVWiRVFVEKGDLISLPAGIYHRFTTTPDNYVKALRLFVTKPGWTA 157
QdoI COG1917
Cupin domain protein related to quercetin dioxygenase [General function prediction only];
94-157 5.05e-06

Cupin domain protein related to quercetin dioxygenase [General function prediction only];


Pssm-ID: 441521 [Multi-domain]  Cd Length: 99  Bit Score: 43.30  E-value: 5.05e-06
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 556278356  94 LNEHTHGEDEVRFFVEGAGLFclHIGDEVFQVlcEKNDLISVPAHTPHWFDMGSEPNFTAIRIF 157
Cdd:COG1917   36 TPWHSHPGEELIYVLEGEGEV--EVGGEEYEL--KPGDVVFIPPGVPHAFRNLGDEPAVLLVVF 95
Cupin_2 pfam07883
Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ( ...
 96-149 1.74e-05

Cupin domain; This family represents the conserved barrel domain of the 'cupin' superfamily ('cupa' is the Latin term for a small barrel).


Pssm-ID: 462300 [Multi-domain]  Cd Length: 71  Bit Score: 41.09  E-value: 1.74e-05
                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|....*.
gi 556278356   96 EHTH-GEDEVRFFVEGAGLfcLHIGDEVFQVlcEKNDLISVPAHTPHWFD-MGSEP 149
Cdd:pfam07883  13 PHRHpGEDEFFYVLEGEGE--LTVDGEEVVL--KAGDSVYFPAGVPHRFRnTGDEP 64
ManC COG0662
Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];
97-143 3.04e-05

Mannose-6-phosphate isomerase, cupin superfamily [Carbohydrate transport and metabolism];


Pssm-ID: 440426 [Multi-domain]  Cd Length: 114  Bit Score: 41.28  E-value: 3.04e-05
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*...
gi 556278356  97 HTH-GEDEVRFFVEGAGLFclHIGDEVFQVlcEKNDLISVPAHTPHWF 143
Cdd:COG0662   43 HVHpHRDEFFYVLEGTGEV--TIGDEEVEL--KAGDSVYIPAGVPHRL 86
cupin_MJ1618 cd02214
Methanocaldococcus jannaschii MJ1618 and related proteins, cupin domain; This family includes ...
 97-142 1.04e-04

Methanocaldococcus jannaschii MJ1618 and related proteins, cupin domain; This family includes bacterial and archaeal proteins homologous to MJ1618, a Methanocaldococcus jannaschii protein of unknown function with a cupin beta barrel domain. The active site of members of the cupin superfamily is generally located at the center of a conserved barrel and usually includes a metal ion.


Pssm-ID: 380344 [Multi-domain]  Cd Length: 100  Bit Score: 39.42  E-value: 1.04e-04
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 556278356  97 HTH-GEDEVRFFVEGAGLfcLHIGDEVFQVlcEKNDLISVPAHTPHW 142
Cdd:cd02214   35 HRLkGSEEVYYILEGEGT--MEIDGEPREV--GPGDAVLIPPGAVQR 77
cupin_RmlC-like cd02208
RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP ...
 96-157 1.88e-03

RmlC-like cupin superfamily; This superfamily contains proteins similar to the RmlC (dTDP (deoxythymidine diphosphates)-4-dehydrorhamnose 3,5-epimerase)-like cupins. RmlC is a dTDP-sugar isomerase involved in the synthesis of L-rhamnose, a saccharide required for the virulence of some pathogenic bacteria. Cupins are a functionally diverse superfamily originally discovered based on the highly conserved motif found in germin and germin-like proteins. This conserved motif forms a beta-barrel fold found in all of the cupins, giving rise to the name cupin ('cupa' is the Latin term for small barrel). The active site of members of this superfamily is generally located at the center of a conserved barrel and usually includes a metal ion. The different functional classes in this superfamily include single domain bacterial isomerases and epimerases involved in the modification of cell wall carbohydrates, two domain bicupins such as the desiccation-tolerant seed storage globulins, and multidomain nuclear transcription factors involved in legume root nodulation.


Pssm-ID: 380338 [Multi-domain]  Cd Length: 73  Bit Score: 35.54  E-value: 1.88e-03
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|...
gi 556278356  96 EHTHGE-DEVRFFVEGAGLfcLHIGDEVfQVLCEKNDLISVPAHTPHWFDMGSEPNFTAIRIF 157
Cdd:cd02208   14 PHWHPEqDEIFYVLSGEGE--LTLDDGE-TVELKAGDIVLIPPGVPHSFVNTSDEPAVFLVVS 73
cupin_TTHA0104 cd06122
Thermus thermophilus TTHA0104 and related proteins, cupin domain; This family contains ...
 97-141 2.18e-03

Thermus thermophilus TTHA0104 and related proteins, cupin domain; This family contains bacterial proteins including TTHA0104 (also called TT1209), a putative antibiotic synthesis protein from Thermus thermophilus. TTHA0104 is a cupin-like protein. The cupins are a functionally diverse superfamily originally discovered based on the highly conserved motif found in germin and germin-like proteins. This conserved motif forms a beta-barrel fold found in all of the cupins, giving rise to the name cupin (cupa is the Latin term for small barrel).


Pssm-ID: 380377 [Multi-domain]  Cd Length: 102  Bit Score: 36.00  E-value: 2.18e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*.
gi 556278356  97 HTH-GEDEVRFFVEGAGLFclHIGDEVFQvlCEKNDLISVPAHTPH 141
Cdd:cd06122   43 HAHaGSDKVYFVLEGEGRF--TVGDEERE--LGAGEAVLAPAGVPH 84
cupin_TM1459-like cd02222
Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial ...
 97-143 4.29e-03

Thermotoga maritima TM1459 and related proteins, cupin domain; This family includes bacterial and archaeal proteins homologous to Thermotoga maritima TM1459, a manganese-containing cupin that has been shown to cleave C=C bonds in the presence of alkylperoxide as oxidant in vitro. Its biological function is still unknown. This family also includes Halorhodospira halophila Hhal_0468. Structures of these proteins show a cupin fold with a conserved "jelly roll-like" beta-barrel fold that form a homodimer.


Pssm-ID: 380351 [Multi-domain]  Cd Length: 91  Bit Score: 34.73  E-value: 4.29e-03
                         10        20        30        40
                 ....*....|....*....|....*....|....*....|....*..
gi 556278356  97 HTHGEDEVRFFVEGAGlfCLHIGDEVFQVlcEKNDLISVPAHTPHWF 143
Cdd:cd02222   33 HTHPWEHEVYVLRGKG--VVVIGGEEYPV--KPGDVVYIPPNEPHQF 75
 
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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