1LXY - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ARGININE DEIMINASE COVALENTLY LINKED WITH L-CITRULLINE

Authors :   K. Das, G. H. Buttler, V. Kwiatkowski, P. Yadav, E. Arnold

Date :   06 Jun 02 (Deposition) - 20 Jan 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym./Biol. Unit : A,B

Keywords :   Deiminase; Hydrolase; 5-Fold Pseudo-Symmetric Domain; 5- Helix Bundle Domain (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. Das, G. H. Buttler, V. Kwiatkowski, A. D. Clark Jr. , P. Yadav, E. Arnold
Crystal Structures Of Arginine Deiminase With Covalent Reaction Intermediates; Implications For Catalytic Mechanism
Structure V. 12 657 2004
PubMed-ID: 15062088 | Reference-DOI: 10.1016/J.STR.2004.02.017
(for further references see the PDB file header)

Molecule 1 - ARGININE DEIMINASE
	Chains	:	A, B
	EC Number	:	3.5.3.6
	Organism Scientific	:	MYCOPLASMA ARGININI
	Organism Taxid	:	2094
	Other Details	:	5-FOLD PSEUDOSYMMETRIC GUANIDINO GROUP MODIFYING ENZYME
	Synonym	:	ADI; ARGININE DIHYDROLASE; AD

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CIR	2	Ligand/Ion	CITRULLINE
2	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:44 , ASN A:155 , ASP A:161 , ARG A:180 , GLY A:215 , ARG A:232 , MET A:268 , HIS A:269 , ASP A:271 , THR A:272 , GLY A:392 , MET A:393 , CYS A:398	BINDING SITE FOR RESIDUE CIR A 500
2	AC2	SOFTWARE	LEU B:44 , ASN B:155 , PHE B:158 , ARG B:160 , ASP B:161 , ARG B:180 , GLY B:215 , ARG B:232 , MET B:268 , HIS B:269 , ASP B:271 , THR B:272 , GLY B:392 , MET B:393 , CYS B:398	BINDING SITE FOR RESIDUE CIR B 500
3	AC3	SOFTWARE	ARG A:344 , GLU A:345 , PHE A:348 , ARG A:366 , ASN A:367 , HOH A:667 , HOH A:755 , LEU B:49 , GLU B:50 , HOH B:692	BINDING SITE FOR RESIDUE TRS A 601
4	AC4	SOFTWARE	LEU A:49 , GLU A:50 , HOH A:648 , ARG B:344 , GLU B:345 , PHE B:348 , ARG B:366 , ASN B:367 , HOH B:665 , HOH B:731	BINDING SITE FOR RESIDUE TRS B 602

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

Asymmetric/Biological Unit

No.	Residues
1	Glu A:103	-	Pro A:104
2	Glu B:103	-	Pro B:104

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

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

(no "Exon" information available for 1LXY)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	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:409
 aligned with ARCA_MYCAR | P23793 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:409
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401         
           ARCA_MYCAR     2 SVFDSKFKGIHVYSEIGELESVLVHEPGREIDYITPARLDELLFSAILESHDARKEHKQFVAELKANDINVVELIDLVAETYDLASQEAKDKLIEEFLEDSEPVLSEEHKVVVRNFLKAKKTSRELVEIMMAGITKYDLGIEADHELIVDPMPNLYFTRDPFASVGNGVTIHYMRYKVRQRETLFSRFVFSNHPKLINTPWYYDPSLKLSIEGGDVFIYNNDTLVVGVSERTDLQTVTLLAKNIVANKECEFKRIVAINVPKWTNLMHLDTWLTMLDKDKFLYSPIANDVFKFWDYDLVNGGAEPQPVENGLPLEGLLQSIINKKPVLIPIAGEGASQMEIERETHFDGTNYLAIRPGVVIGYSRNEKTNAALEAAGIKVLPFHGNQLSLGMGNARCMSMPLSRKDVKW 410
               SCOP domains d1lxya_ A: Arginine deiminase                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains --------1lxyA01 A:10-74,A:153-406                                        ------------------------------------------------------------------------------1lxyA01 A:10-74,A:153-406 L-arginine/glycine Amidinotransferase; Chain A                                                                                                                                                                                      ---- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeeee...hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhh.hhhhhhhhhhhheehhhhh......eee..hhhhhh....eeee..eeee....hhhhhhhhhhhhhhhhhh.......eeehhhhh...hhh.eee....eeeeee....hhhhhhhhhhhhhhh......eeeeee........hhhh.eeeee..eeee.hhhh...eeeeee..........eee..hhhhhhhhhhh...eeee......hhhhhhhhhhh.....eeee..eeeee..hhhhhhhhhhh..eeeee.hhhhhh.........eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lxy A   2 SVFDSKFKGIHVYSEIGELESVLVHEPGREIDYITPARLDELLFSAILESHDARKEHKQFVAELKANDINVVELIDLVAETYDLASQEAKDKLIEEFLEDSEPVLSEEHKVVVRNFLKAKKTSRELVEIMMAGITKYDLGIEADHELIVDPMPNLYFTRDPFASVGNGVTIHYMRYKVRQRETLFSRFVFSNHPKLINTPWYYDPSLKLSIEGGDVFIYNNDTLVVGVSERTDLQTVTLLAKNIVANKECEFKRIVAINVPKWTNLMHLDTWLTMLDKDKFLYSPIANDVFKFWDYDLVNGGAEPQPVENGLPLEGLLQSIINKKPVLIPIAGEGASQMEIERETHFDGTNYLAIRPGVVIGYSRNEKTNAALEAAGIKVLPFHGNQLSLGMGNARCMSMPLSRKDVKW 410
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401

Chain B from PDB  Type:PROTEIN  Length:409
 aligned with ARCA_MYCAR | P23793 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:409
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401         
           ARCA_MYCAR     2 SVFDSKFKGIHVYSEIGELESVLVHEPGREIDYITPARLDELLFSAILESHDARKEHKQFVAELKANDINVVELIDLVAETYDLASQEAKDKLIEEFLEDSEPVLSEEHKVVVRNFLKAKKTSRELVEIMMAGITKYDLGIEADHELIVDPMPNLYFTRDPFASVGNGVTIHYMRYKVRQRETLFSRFVFSNHPKLINTPWYYDPSLKLSIEGGDVFIYNNDTLVVGVSERTDLQTVTLLAKNIVANKECEFKRIVAINVPKWTNLMHLDTWLTMLDKDKFLYSPIANDVFKFWDYDLVNGGAEPQPVENGLPLEGLLQSIINKKPVLIPIAGEGASQMEIERETHFDGTNYLAIRPGVVIGYSRNEKTNAALEAAGIKVLPFHGNQLSLGMGNARCMSMPLSRKDVKW 410
               SCOP domains d1lxyb_ B: Arginine deiminase                                                                                                                                                                                                                                                                                                                                                                                             SCOP domains
               CATH domains --------1lxyB01 B:10-74,B:153-406                                        ------------------------------------------------------------------------------1lxyB01 B:10-74,B:153-406 L-arginine/glycine Amidinotransferase; Chain A                                                                                                                                                                                      ---- CATH domains
           Pfam domains (1) -----------------------Amidinotransf-1lxyB01 B:25-405                                                                                                                                                                                                                                                                                                                                                               ----- Pfam domains (1)
           Pfam domains (2) -----------------------Amidinotransf-1lxyB02 B:25-405                                                                                                                                                                                                                                                                                                                                                               ----- Pfam domains (2)
         Sec.struct. author ..................eeeeee...hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhh.hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..hhhhhhhhhhhheehhhhh......eee..hhhhhh....eeee..eeee....hhhhhhhhhhhhhhhhhh.......eeehhhhh...hhh.eee....eeeeee....hhhhhhhhhhhhhhh......eeeeee........hhhh.eeeee..eeee.hhhh...eeeeee..........ee...hhhhhhhhhhh...eeee......hhhhhhhhhhh.....eeee..eeeee..hhhhhhhhhhh..eeeee.hhhhhh.........eeeee..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lxy B   2 SVFDSKFKGIHVYSEIGELESVLVHEPGREIDYITPARLDELLFSAILESHDARKEHKQFVAELKANDINVVELIDLVAETYDLASQEAKDKLIEEFLEDSEPVLSEEHKVVVRNFLKAKKTSRELVEIMMAGITKYDLGIEADHELIVDPMPNLYFTRDPFASVGNGVTIHYMRYKVRQRETLFSRFVFSNHPKLINTPWYYDPSLKLSIEGGDVFIYNNDTLVVGVSERTDLQTVTLLAKNIVANKECEFKRIVAINVPKWTNLMHLDTWLTMLDKDKFLYSPIANDVFKFWDYDLVNGGAEPQPVENGLPLEGLLQSIINKKPVLIPIAGEGASQMEIERETHFDGTNYLAIRPGVVIGYSRNEKTNAALEAAGIKVLPFHGNQLSLGMGNARCMSMPLSRKDVKW 410
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: Pentein, beta/alpha-propeller (68)

Superfamily: Pentein (68)

Family: Arginine deiminase (7)

Protein domain: Arginine deiminase (7)

Mycoplasma arginini [TaxId: 2094] (2)

1a	d1lxya_	A:
1b	d1lxyb_	B:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 5-stranded Propeller (36)

Topology: L-arginine/glycine Amidinotransferase; Chain A (36)

Homologous Superfamily: L-arginine/glycine Amidinotransferase; Chain A (33)

Mycoplasma arginini. Organism_taxid: 2094 (2)

1a	1lxyA01	A:10-74,A:153-406
1b	1lxyB01	B:10-74,B:153-406

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GME (20)

Family: Amidinotransf (10)

Mycoplasma arginini (2)

1a	Amidinotransf-1lxyB01	B:25-405
1b	Amidinotransf-1lxyB02	B:25-405

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ARCA_MYCAR | P23793)

molecular function
	GO:0016990	arginine deiminase activity	Catalysis of the reaction: L-arginine + H2O = L-citrulline + NH3.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
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:0019547	arginine catabolic process to ornithine	The chemical reactions and pathways resulting in the breakdown of arginine into other compounds, including ornithine.
	GO:0006525	arginine metabolic process	The chemical reactions and pathways involving arginine, 2-amino-5-(carbamimidamido)pentanoic acid.
	GO:0018101	protein citrullination	The hydrolysis of peptidyl-arginine to form peptidyl-citrulline.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Glu A:103 - Pro A:104	[ RasMol ]
		Glu B:103 - Pro B:104	[ RasMol ]

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Description

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Ligands, Modified Residues, Ions (2, 4)

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SS Bonds (0, 0)

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