1N2M - JenaLib

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Title :   THE S53A PROENZYME STRUCTURE OF METHANOCOCCUS JANNASCHII.

Authors :   W. D. Tolbert, D. E. Graham, R. H. White, S. E. Ealick

Date :   23 Oct 02 (Deposition) - 25 Mar 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: D,E,F  (1x)

Keywords :   Pyruvoyl Group, Pyruvate, Agmatine, Arginine Decarboxylase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   W. D. Tolbert, D. E. Graham, R. H. White, S. E. Ealick
Pyruvoyl-Dependent Arginine Decarboxylase From Methanococcus Jannaschii: Crystal Structures Of The Self-Cleaved And S53A Proenzyme Forms
Structure V. 11 285 2003
PubMed-ID: 12623016 | Reference-DOI: 10.1016/S0969-2126(03)00026-1
(for further references see the PDB file header)

Molecule 1 - PYRUVOYL-DEPENDENT ARGININE DECARBOXYLASE
	Chains	:	A, B, C, D, E, F
	EC Number	:	4.1.1.19
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET19B (NOVAGEN)
	Expression System Strain	:	BL21-CODON-PLUS(DE3)-RIL (STRATAGENE)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MJ0316
	Mutation	:	YES
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190
	Other Details	:	PROENZYME FORM
	Synonym	:	PVLARGDC

		1	2	3	4	5	6
Asymmetric Unit	:	A	B	C	D	E	F
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (1x)	:				D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 8)

No.	Name	Count	Type	Full Name
1	MRD	8	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	MRD	4	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL

Biological Unit 2 (1, 4)

No.	Name	Count	Type	Full Name
1	MRD	4	Ligand/Ion	(4R)-2-METHYLPENTANE-2,4-DIOL

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU A:109 , PHE B:34 , TYR B:77 , TYR B:79 , ILE B:81	BINDING SITE FOR RESIDUE MRD B 7001
2	AC2	SOFTWARE	GLU D:109 , HOH D:6487 , LEU F:31 , TYR F:77 , TYR F:79 , ILE F:81	BINDING SITE FOR RESIDUE MRD F 7002
3	AC3	SOFTWARE	LEU D:31 , PHE D:34 , TYR D:79 , ILE D:81 , GLU E:109	BINDING SITE FOR RESIDUE MRD D 7003
4	AC4	SOFTWARE	LEU E:31 , TYR E:77 , TYR E:79 , ILE E:81 , GLU F:109	BINDING SITE FOR RESIDUE MRD E 7004
5	AC5	SOFTWARE	GLU B:109 , LEU C:31 , PHE C:34 , TYR C:77 , TYR C:79 , ILE C:81	BINDING SITE FOR RESIDUE MRD C 7005
6	AC6	SOFTWARE	TYR A:79	BINDING SITE FOR RESIDUE MRD A 7006
7	AC7	SOFTWARE	PHE D:131 , GLU D:132 , GLY D:135 , TRP D:136 , GLY F:135 , TRP F:136 , GLU F:137	BINDING SITE FOR RESIDUE MRD D 7007
8	AC8	SOFTWARE	GLU B:132 , GLY B:135 , TRP B:136 , GLY C:135 , TRP C:136 , GLU C:137	BINDING SITE FOR RESIDUE MRD B 7008

(no "SS Bond" information available for 1N2M)

(no "Cis Peptide Bond" information available for 1N2M)

(no "SAP(SNP)/Variant" information available for 1N2M)

(no "PROSITE Motif" information available for 1N2M)

(no "Exon" information available for 1N2M)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
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	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:159
 aligned with PDAD_METJA | Q57764 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:159
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156         
           PDAD_METJA     7 PLHAYFKLPNTVSLVAGSSEGETPLNAFDGALLNAGIGNVNLIRISSIMPPEAEIVPLPKLPMGALVPTAYGYIISDVPGETISAAISVAIPKDKSLCGLIMEYEGKCSKKEAEKTVREMAKIGFEMRGWELDRIESIAVEHTVEKLGCAFAAAALWYK 165
               SCOP domains d1n2ma_ A: Arginine decarboxylase                                                                                                                               SCOP domains
               CATH domains 1n2mA00 A:7-165 Pyruvoyl-Dependent Histidine Decarboxylase, subunit B                                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeeeee..hhhhhhhhhhhhhh....eeee...ee....ee..........eeeeeeeeeee.....eeeeeeeeeee......eeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeee....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n2m A   7 PLHAYFKLPNTVSLVAGSSEGETPLNAFDGALLNAGIGNVNLIRISAIMPPEAEIVPLPKLPMGALVPTAYGYIISDVPGETISAAISVAIPKDKSLCGLIMEYEGKCSKKEAEKTVREMAKIGFEMRGWELDRIESIAVEHTVEKLGCAFAAAALWYK 165
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156

Chain B from PDB  Type:PROTEIN  Length:160
 aligned with PDAD_METJA | Q57764 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:160
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165
           PDAD_METJA     6 NPLHAYFKLPNTVSLVAGSSEGETPLNAFDGALLNAGIGNVNLIRISSIMPPEAEIVPLPKLPMGALVPTAYGYIISDVPGETISAAISVAIPKDKSLCGLIMEYEGKCSKKEAEKTVREMAKIGFEMRGWELDRIESIAVEHTVEKLGCAFAAAALWYK 165
               SCOP domains d1n2mb_ B: Arginine decarboxylase                                                                                                                                SCOP domains
               CATH domains 1n2mB00 B:6-165 Pyruvoyl-Dependent Histidine Decarboxylase, subunit B                                                                                            CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh...eeeeeeeeee..hhhhhhhhhhhhhh....eeee...ee....ee..........eeeeeeeeeee.....eeeeeeeeeee......eeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeee....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n2m B   6 NPLHAYFKLPNTVSLVAGSSEGETPLNAFDGALLNAGIGNVNLIRISAIMPPEAEIVPLPKLPMGALVPTAYGYIISDVPGETISAAISVAIPKDKSLCGLIMEYEGKCSKKEAEKTVREMAKIGFEMRGWELDRIESIAVEHTVEKLGCAFAAAALWYK 165
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165

Chain C from PDB  Type:PROTEIN  Length:163
 aligned with PDAD_METJA | Q57764 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:163
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162   
           PDAD_METJA     3 AEINPLHAYFKLPNTVSLVAGSSEGETPLNAFDGALLNAGIGNVNLIRISSIMPPEAEIVPLPKLPMGALVPTAYGYIISDVPGETISAAISVAIPKDKSLCGLIMEYEGKCSKKEAEKTVREMAKIGFEMRGWELDRIESIAVEHTVEKLGCAFAAAALWYK 165
               SCOP domains d1n2mc_ C: Arginine decarboxylase                                                                                                                                   SCOP domains
               CATH domains 1n2mC00 C:3-165 Pyruvoyl-Dependent Histidine Decarboxylase, subunit B                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeeeeee..hhhhhhhhhhhhhh....eeee...ee....ee..........eeeeeeeeeee.....eeeeeeeeeee......eeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeee....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n2m C   3 AEINPLHAYFKLPNTVSLVAGSSEGETPLNAFDGALLNAGIGNVNLIRISAIMPPEAEIVPLPKLPMGALVPTAYGYIISDVPGETISAAISVAIPKDKSLCGLIMEYEGKCSKKEAEKTVREMAKIGFEMRGWELDRIESIAVEHTVEKLGCAFAAAALWYK 165
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162

Chain D from PDB  Type:PROTEIN  Length:154
 aligned with PDAD_METJA | Q57764 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:154
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
           PDAD_METJA    12 FKLPNTVSLVAGSSEGETPLNAFDGALLNAGIGNVNLIRISSIMPPEAEIVPLPKLPMGALVPTAYGYIISDVPGETISAAISVAIPKDKSLCGLIMEYEGKCSKKEAEKTVREMAKIGFEMRGWELDRIESIAVEHTVEKLGCAFAAAALWYK 165
               SCOP domains d1n2md_ D: Arginine decarboxylase                                                                                                                          SCOP domains
               CATH domains 1n2mD00 D:12-165 Pyruvoyl-Dependent Histidine Decarboxylase, subunit B                                                                                     CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeeeeee..hhhhhhhhhhhhhh....eeee...ee....ee..........eeeeeeeeeee.....eeeeeeeeeee......eeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeee....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n2m D  12 FKLPNTVSLVAGSSEGETPLNAFDGALLNAGIGNVNLIRISAIMPPEAEIVPLPKLPMGALVPTAYGYIISDVPGETISAAISVAIPKDKSLCGLIMEYEGKCSKKEAEKTVREMAKIGFEMRGWELDRIESIAVEHTVEKLGCAFAAAALWYK 165
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161

Chain E from PDB  Type:PROTEIN  Length:162
 aligned with PDAD_METJA | Q57764 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:162
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163  
           PDAD_METJA     4 EINPLHAYFKLPNTVSLVAGSSEGETPLNAFDGALLNAGIGNVNLIRISSIMPPEAEIVPLPKLPMGALVPTAYGYIISDVPGETISAAISVAIPKDKSLCGLIMEYEGKCSKKEAEKTVREMAKIGFEMRGWELDRIESIAVEHTVEKLGCAFAAAALWYK 165
               SCOP domains d1n2me_ E: Arginine decarboxylase                                                                                                                                  SCOP domains
               CATH domains 1n2mE00 E:4-165 Pyruvoyl-Dependent Histidine Decarboxylase, subunit B                                                                                              CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .............eeeeeeeeee..hhhhhhhhhhhhhh....eeee...ee....ee..........eeeeeeeeeee.....eeeeeeeeeee......eeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeee....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1n2m E   4 EINPLHAYFKLPNTVSLVAGSSEGETPLNAFDGALLNAGIGNVNLIRISAIMPPEAEIVPLPKLPMGALVPTAYGYIISDVPGETISAAISVAIPKDKSLCGLIMEYEGKCSKKEAEKTVREMAKIGFEMRGWELDRIESIAVEHTVEKLGCAFAAAALWYK 165
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163

Chain F from PDB  Type:PROTEIN  Length:153
 aligned with PDAD_METJA | Q57764 from UniProtKB/Swiss-Prot  Length:165

    Alignment length:153
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162   
           PDAD_METJA    13 KLPNTVSLVAGSSEGETPLNAFDGALLNAGIGNVNLIRISSIMPPEAEIVPLPKLPMGALVPTAYGYIISDVPGETISAAISVAIPKDKSLCGLIMEYEGKCSKKEAEKTVREMAKIGFEMRGWELDRIESIAVEHTVEKLGCAFAAAALWYK 165
               SCOP domains d1n2mf_ F: Arginine decarboxylase                                                                                                                         SCOP domains
               CATH domains 1n2mF00 F:13-165 Pyruvoyl-Dependent Histidine Decarboxylase, subunit B                                                                                    CATH domains
           Pfam domains (1) PvlArgDC-1n2mF01 F:13-164                                                                                                                               - Pfam domains (1)
           Pfam domains (2) PvlArgDC-1n2mF02 F:13-164                                                                                                                               - Pfam domains (2)
           Pfam domains (3) PvlArgDC-1n2mF03 F:13-164                                                                                                                               - Pfam domains (3)
           Pfam domains (4) PvlArgDC-1n2mF04 F:13-164                                                                                                                               - Pfam domains (4)
           Pfam domains (5) PvlArgDC-1n2mF05 F:13-164                                                                                                                               - Pfam domains (5)
           Pfam domains (6) PvlArgDC-1n2mF06 F:13-164                                                                                                                               - Pfam domains (6)
         Sec.struct. author ....eeeeeeeeee..hhhhhhhhhhhhhh....eeee...ee....ee..........eeeeeeeeeee.....eeeeeeeeeee......eeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeee....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1n2m F  13 KLPNTVSLVAGSSEGETPLNAFDGALLNAGIGNVNLIRISAIMPPEAEIVPLPKLPMGALVPTAYGYIISDVPGETISAAISVAIPKDKSLCGLIMEYEGKCSKKEAEKTVREMAKIGFEMRGWELDRIESIAVEHTVEKLGCAFAAAALWYK 165
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162

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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric Unit

Classes(

)

Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Pyruvoyl-dependent histidine and arginine decarboxylases (10)

Superfamily: Pyruvoyl-dependent histidine and arginine decarboxylases (10)

Family: Arginine decarboxylase (4)

Protein domain: Arginine decarboxylase (3)

Methanococcus jannaschii [TaxId: 2190] (3)

1a	d1n2ma_	A:
1b	d1n2mb_	B:
1c	d1n2mc_	C:
1d	d1n2md_	D:
1e	d1n2me_	E:
1f	d1n2mf_	F:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(bba) Sandwich (528)

Topology: Pyruvoyl-Dependent Histidine Decarboxylase; Chain B (11)

Homologous Superfamily: Pyruvoyl-Dependent Histidine Decarboxylase, subunit B (11)

Methanocaldococcus jannaschii. Organism_taxid: 2190. (5)

1a	1n2mC00	C:3-165
1b	1n2mE00	E:4-165
1c	1n2mB00	B:6-165
1d	1n2mA00	A:7-165
1e	1n2mD00	D:12-165
1f	1n2mF00	F:13-165

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E,F (PDAD_METJA | Q57764)

molecular function
	GO:0008792	arginine decarboxylase activity	Catalysis of the reaction: L-arginine + H(+) = agmatine + CO(2).
	GO:0016831	carboxy-lyase activity	Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
	GO:0006527	arginine catabolic process	The chemical reactions and pathways resulting in the breakdown of arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
	GO:0006520	cellular amino acid metabolic process	The chemical reactions and pathways involving amino acids, carboxylic acids containing one or more amino groups, as carried out by individual cells.

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	PDAD_METJA \| Q57764	:	1mt1 1n13 2qqc 2qqd

1mt1	ORIGINAL STRUCTURE (SELENOMETHIONINE LABELED ENZYME)
1n13	NATIVE STRUCTURE/AGMATINE COMPLEX

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