The Crystal Structure of Pyruvoyl-dependent Arginine Decarboxylase from Methanococcus jannaschii


Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

ChainsDomain InfoClassFoldSuperfamilyFamilyDomainSpeciesProvenance Source (Version)
Ld1mt1.6 Alpha and beta proteins (a+b) Pyruvoyl-dependent histidine and arginine decarboxylases Pyruvoyl-dependent histidine and arginine decarboxylases Arginine decarboxylase Arginine decarboxylase (Methanocaldococcus jannaschii ) [TaxId: 2190 ], SCOPe (2.08)
Jd1mt1.5 Alpha and beta proteins (a+b) Pyruvoyl-dependent histidine and arginine decarboxylases Pyruvoyl-dependent histidine and arginine decarboxylases Arginine decarboxylase Arginine decarboxylase (Methanocaldococcus jannaschii ) [TaxId: 2190 ], SCOPe (2.08)
Hd1mt1.4 Alpha and beta proteins (a+b) Pyruvoyl-dependent histidine and arginine decarboxylases Pyruvoyl-dependent histidine and arginine decarboxylases Arginine decarboxylase Arginine decarboxylase (Methanocaldococcus jannaschii ) [TaxId: 2190 ], SCOPe (2.08)
Fd1mt1.3 Alpha and beta proteins (a+b) Pyruvoyl-dependent histidine and arginine decarboxylases Pyruvoyl-dependent histidine and arginine decarboxylases Arginine decarboxylase Arginine decarboxylase (Methanocaldococcus jannaschii ) [TaxId: 2190 ], SCOPe (2.08)
Dd1mt1.2 Alpha and beta proteins (a+b) Pyruvoyl-dependent histidine and arginine decarboxylases Pyruvoyl-dependent histidine and arginine decarboxylases Arginine decarboxylase Arginine decarboxylase (Methanocaldococcus jannaschii ) [TaxId: 2190 ], SCOPe (2.08)
Bd1mt1.1 Alpha and beta proteins (a+b) Pyruvoyl-dependent histidine and arginine decarboxylases Pyruvoyl-dependent histidine and arginine decarboxylases Arginine decarboxylase Arginine decarboxylase (Methanocaldococcus jannaschii ) [TaxId: 2190 ], SCOPe (2.08)
Kd1mt1.6 Alpha and beta proteins (a+b) Pyruvoyl-dependent histidine and arginine decarboxylases Pyruvoyl-dependent histidine and arginine decarboxylases Arginine decarboxylase Arginine decarboxylase (Methanocaldococcus jannaschii ) [TaxId: 2190 ], SCOPe (2.08)
Id1mt1.5 Alpha and beta proteins (a+b) Pyruvoyl-dependent histidine and arginine decarboxylases Pyruvoyl-dependent histidine and arginine decarboxylases Arginine decarboxylase Arginine decarboxylase (Methanocaldococcus jannaschii ) [TaxId: 2190 ], SCOPe (2.08)
Gd1mt1.4 Alpha and beta proteins (a+b) Pyruvoyl-dependent histidine and arginine decarboxylases Pyruvoyl-dependent histidine and arginine decarboxylases Arginine decarboxylase Arginine decarboxylase (Methanocaldococcus jannaschii ) [TaxId: 2190 ], SCOPe (2.08)
Ed1mt1.3 Alpha and beta proteins (a+b) Pyruvoyl-dependent histidine and arginine decarboxylases Pyruvoyl-dependent histidine and arginine decarboxylases Arginine decarboxylase Arginine decarboxylase (Methanocaldococcus jannaschii ) [TaxId: 2190 ], SCOPe (2.08)
Cd1mt1.2 Alpha and beta proteins (a+b) Pyruvoyl-dependent histidine and arginine decarboxylases Pyruvoyl-dependent histidine and arginine decarboxylases Arginine decarboxylase Arginine decarboxylase (Methanocaldococcus jannaschii ) [TaxId: 2190 ], SCOPe (2.08)
Ad1mt1.1 Alpha and beta proteins (a+b) Pyruvoyl-dependent histidine and arginine decarboxylases Pyruvoyl-dependent histidine and arginine decarboxylases Arginine decarboxylase Arginine decarboxylase (Methanocaldococcus jannaschii ) [TaxId: 2190 ], SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

ChainsFamily NameDomain Identifier ArchitecturePossible HomologyHomologyTopologyFamilyProvenance Source (Version)
Be1mt1B01 A: beta barrelsX: RNase A-likeH: RNase A-likeT: RNase A-likeF:ECOD (v294.2)
KMIF4Ge1mt1K1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: MIF4GECOD (v294.2)
IMIF4Ge1mt1I1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: MIF4GECOD (v294.2)
GMIF4Ge1mt1G1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: MIF4GECOD (v294.2)
EMIF4Ge1mt1E1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: MIF4GECOD (v294.2)
CMIF4Ge1mt1C1 A: beta barrelsX: cradle loop barrelH: RIFT-relatedT: acid proteaseF: MIF4GECOD (v294.2)
Ae1mt1A01 A: beta barrelsX: RNase A-likeH: RNase A-likeT: RNase A-likeF:ECOD (v294.2)

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

ChainsAccessionNameDescriptionCommentsSource
B, D, F, H, J
PF01862Pyruvoyl-dependent arginine decarboxylase (PvlArgDC) (PvlArgDC)Pyruvoyl-dependent arginine decarboxylase (PvlArgDC)Methanococcus jannaschii contains homologues of most genes required for spermidine polyamine biosynthesis. Yet genomes from neither this organism nor any other euryarchaeon have orthologues of the pyridoxal 5'-phosphate- dependent ornithine or argini ...Methanococcus jannaschii contains homologues of most genes required for spermidine polyamine biosynthesis. Yet genomes from neither this organism nor any other euryarchaeon have orthologues of the pyridoxal 5'-phosphate- dependent ornithine or arginine decarboxylase genes, required to produce putrescine. Instead,these organisms have a new class of arginine decarboxylase (PvlArgDC) formed by the self-cleavage of a proenzyme into a 5-kDa subunit and a 12-kDa subunit that contains a reactive pyruvoyl group. Although this extremely thermostable enzyme has no significant sequence similarity to previously characterised proteins, conserved active site residues are similar to those of the pyruvoyl-dependent histidine decarboxylase enzyme, and its subunits form a similar (alpha-beta)(3) complex. Homologues of PvlArgDC are found in several bacterial genomes, including those of Chlamydia spp., which have no agmatine ureohydrolase enzyme to convert agmatine (decarboxylated arginine) into putrescine. In these intracellular pathogens, PvlArgDC may function analogously to pyruvoyl-dependent histidine decarboxylase; the cells are proposed to import arginine and export agmatine, increasing the pH and affecting the host cell's metabolism. Phylogenetic analysis of Pvl- ArgDC proteins suggests that this gene has been recruited from the euryarchaeal polyamine biosynthetic pathway to function as a degradative enzyme in bacteria [1].
Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

ChainsPolymerMolecular FunctionBiological ProcessCellular Component
B, D, F, H, J
PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE ALPHA CHAIN -
A, C, E, G, I
PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE BETA CHAIN -

Protein Modification Annotation

Modified Residue(s)
ChainResidue(s)Description
B, D, F, H, J
MSE Parent Component: MET

B, D, F, H, J
PYR AA0127

:  pyruvic acid (Cys) MOD:00136 , pyruvic acid (Ser) MOD:00807 , pyruvic acid MOD:01154 , pyruvic acid (Tyr) MOD:01661
A, C, E, G, I
MSE Parent Component: MET

AA0127

Structure Motif Annotation: Mechanism and Catalytic Site Atlas M-CSA Database Homepage

ChainsEnzyme NameDescriptionCatalytic Residues
A, E, F
arginine decarboxylase  M-CSA #707

Three classes of arginine decarboxylase exist, of which two use the cofactor pyridoxal 5'-phosphate and a third uses a pyruvoyl group. Methanococcus jannaschii uses pyruvoyl-dependent arginine decarboxylase (PvlArgDC) to convert L-arginine into agmatine, which can be converted to putrescine by agmatine ureohydrolase. Putrescine can be used to biosynthesize polyamines. These are essential for cell growth and proliferation and are found in all organisms. Some pathogenic microorganisms, such as Chlamydia sp., are thought to import L-Arg from the host, decarboxylate it, and export the agmatine product, depleting the host's L-Arg supply and increasing the extracellular pH. Agmatine is also an inhibitor of nitric-oxide synthase and a suppressor of apoptosis. PvlArgDC is translated as a proenzyme (pi-chain), which cleaves itself between Ser52 and Ser53 by autocatalytic serinolysis to form two polypeptide (alpha and beta) chains. The alpha chain begins with the newly created pyruvoyl group, which is the cofactor in the decarboxylation reaction, and the smaller beta fragment terminates with a new carboxyl group at Ser52.

Defined by 3 residues: ASN:A-47SER:E-52GLU:F-57 [auth F-109]
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