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(-) Description

Title :  STRUCTURE OF D280A ARGININE DEIMINASE WITH L-ARGININE FORMING A S-ALKYLTHIOURONIUM REACTION INTERMEDIATE
 
Authors :  A. Galkin, X. Lu, D. Dunaway-Mariano, O. Herzberg
Date :  15 Jul 05  (Deposition) - 09 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Arginine Degradation Pathway, L-Arginine Deiminase, X-Ray Structure, Catalytic Mechanism, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Galkin, X. Lu, D. Dunaway-Mariano, O. Herzberg
Crystal Structures Representing The Michaelis Complex And The Thiouronium Reaction Intermediate Of Pseudomonas Aeruginosa Arginine Deiminase.
J. Biol. Chem. V. 280 34080 2005
PubMed-ID: 16091358  |  Reference-DOI: 10.1074/JBC.M505471200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ARGININE DEIMINASE
    Chains: A, B, C, D
    EC Number: 3.5.3.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET100/ADIN
    Expression System Strain: BL21(DE3)STAR
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ARCA
    Mutation: YES
    Organism Scientific: PSEUDOMONAS AERUGINOSA
    Organism Taxid: 287
    Synonym: ADI, ARGININE DIHYDROLASE, AD

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1CYR4Mod. Amino AcidN~5~-[{[(2R)-2-AMINO-2-CARBOXYETHYL]SULFANYL}(IMINIO)METHYL]-L-ORNITHINATE

(-) Sites  (0, 0)

(no "Site" information available for 2ABR)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2ABR)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2ABR)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2ABR)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2ABR)

(-) Exons   (0, 0)

(no "Exon" information available for 2ABR)

(-) Sequences/Alignments

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:402
 aligned with ARCA_PSEAE | P13981 from UniProtKB/Swiss-Prot  Length:418

    Alignment length:412
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415  
           ARCA_PSEAE     6 TKLGVHSEAGKLRKVMVCSPGLAHQRLTPSNCDELLFDDVIWVNQAKRDHFDFVTKMRERGIDVLEMHNLLTETIQNPEALKWILDRKITADSVGLGLTSELRSWLESLEPRKLAEYLIGGVAADDLPASEGANILKMYREYLGHSSFLLPPLPNTQFTRDTTCWIYGGVTLNPMYWPARRQETLLTTAIYKFHPEFANAEFEIWYGDPDKDHGSSTLEGGDVMPIGNGVVLIGMGERSSRQAIGQVAQSLFAKGAAERVIVAGLPKSRAAMHLDTVFSFCDRDLVTVFPEVVKEIVPFSLRPDPSSPYGMNIRREEKTFLEVVAESLGLKKLRVVETGGNSFAAEREQWDDGNNVVCLEPGVVVGYDRNTYTNTLLRKAGVEVITISASELGRGRGGGHCMTCPIVRDPID 417
               SCOP domains d2abra1 A:6-417 Arginine deiminase                                                                                                                                                                                                                                                                                                                                                                                           SCOP domains
               CATH domains 2abrA01 A:6-71,A:157-417                                          -------------------------------------------------------------------------------------2abrA01 A:6-71,A:157-417 L-arginine/glycine Amidinotransferase; Chain A                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee......eeeeee...hhhhhh....hhhhhh.....hhhhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhee.hhh..hhhhhhhhhhhhhhh...eee.......hhhhheeee..eeee....hhhhhhhhhhhhhhhhhh........................hhh.eee....eeeeee....hhhhhhhhhhhhhhh....eeeeee....---.hhhh.eeeee..eeeehhhhhh..eeeeeee.......eeeee...hhhhhhhhhh.....eeee..-------..........eeee..eeeee..hhhhhhhhhhh..eeeee...hhhhhh........eeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2abr A   6 TKLGVHSEAGKLRKVMVCSPGLAHQRLTPSNCDELLFDDVIWVNQAKRDHFDFVTKMRERGIDVLEMHNLLTETIQNPEALKWILDRKITADSVGLGLTSELRSWLESLEPRKLAEYLIGGVAADDLPASEGANILKMYREYLGHSSFLLPPLPNTQFTRDTTCWIYGGVTLNPMYWPARRQETLLTTAIYKFHPEFANAEFEIWYGDPDKDHGSSTLEGGDVMPIGNGVVLIGMGERSSRQAIGQVAQSLFAKGAAERVIVAGLPKS---MHLATVFSFCDRDLVTVFPEVVKEIVPFSLRPDPSSPYGMNIRREEKTFLEVVAESLGLKKLRVVETG-------REQWDDGNNVVCLEPGVVVGYDRNTYTNTLLRKAGVEVITISASELGRGRGGGHcMTCPIVRDPID 417
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       | - |     285       295       305       315       325       335        |-      |355       365       375       385       395       405|      415  
                                                                                                                                                                                                                                                                                                     273 277                                                                344     352                                                   406-CYR       


Chain B from PDB  Type:PROTEIN  Length:406
 aligned with ARCA_PSEAE | P13981 from UniProtKB/Swiss-Prot  Length:418

    Alignment length:412
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415  
           ARCA_PSEAE     6 TKLGVHSEAGKLRKVMVCSPGLAHQRLTPSNCDELLFDDVIWVNQAKRDHFDFVTKMRERGIDVLEMHNLLTETIQNPEALKWILDRKITADSVGLGLTSELRSWLESLEPRKLAEYLIGGVAADDLPASEGANILKMYREYLGHSSFLLPPLPNTQFTRDTTCWIYGGVTLNPMYWPARRQETLLTTAIYKFHPEFANAEFEIWYGDPDKDHGSSTLEGGDVMPIGNGVVLIGMGERSSRQAIGQVAQSLFAKGAAERVIVAGLPKSRAAMHLDTVFSFCDRDLVTVFPEVVKEIVPFSLRPDPSSPYGMNIRREEKTFLEVVAESLGLKKLRVVETGGNSFAAEREQWDDGNNVVCLEPGVVVGYDRNTYTNTLLRKAGVEVITISASELGRGRGGGHCMTCPIVRDPID 417
               SCOP domains d2abrb_ B: Arginine deiminase                                                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2abrB01 B:6-71,B:157-417                                          -------------------------------------------------------------------------------------2abrB01 B:6-71,B:157-417 L-arginine/glycine Amidinotransferase; Chain A                                                                                                                                                                                               CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee......eeeeee...hhhhhh...............hhhhhhhhhhhhhhhhhh...eeeehhhhhhhhh.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhee.hhh..hhhhhhhhhhhhhhh...eee.......hhhhheeee..eeee.......hhhhhhhhhhhhhhhhhhhh...eeee............hhh.eee....eeeeee....hhhhhhhhhhhhhh.....eeeeee...--...hhhh.eeeee..eeeehhhhhh..eeeeeee.......eeeee...hhhhhhhhhh.....eeee..----.............eeee..eeeee..hhhhhhhhhhh..eeeeehhhhhhhhh.......eeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2abr B   6 TKLGVHSEAGKLRKVMVCSPGLAHQRLTPSNCDELLFDDVIWVNQAKRDHFDFVTKMRERGIDVLEMHNLLTETIQNPEALKWILDRKITADSVGLGLTSELRSWLESLEPRKLAEYLIGGVAADDLPASEGANILKMYREYLGHSSFLLPPLPNTQFTRDTTCWIYGGVTLNPMYWPARRQETLLTTAIYKFHPEFANAEFEIWYGDPDKDHGSSTLEGGDVMPIGNGVVLIGMGERSSRQAIGQVAQSLFAKGAAERVIVAGLPK--AAMHLATVFSFCDRDLVTVFPEVVKEIVPFSLRPDPSSPYGMNIRREEKTFLEVVAESLGLKKLRVVETG----AAEREQWDDGNNVVCLEPGVVVGYDRNTYTNTLLRKAGVEVITISASELGRGRGGGHcMTCPIVRDPID 417
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265      |275       285       295       305       315       325       335        |-   |   355       365       375       385       395       405|      415  
                                                                                                                                                                                                                                                                                                    272  |                                                                  344  349                                                      406-CYR       
                                                                                                                                                                                                                                                                                                       275                                                                                                                                              


Chain C from PDB  Type:PROTEIN  Length:403
 aligned with ARCA_PSEAE | P13981 from UniProtKB/Swiss-Prot  Length:418

    Alignment length:411
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416 
           ARCA_PSEAE     7 KLGVHSEAGKLRKVMVCSPGLAHQRLTPSNCDELLFDDVIWVNQAKRDHFDFVTKMRERGIDVLEMHNLLTETIQNPEALKWILDRKITADSVGLGLTSELRSWLESLEPRKLAEYLIGGVAADDLPASEGANILKMYREYLGHSSFLLPPLPNTQFTRDTTCWIYGGVTLNPMYWPARRQETLLTTAIYKFHPEFANAEFEIWYGDPDKDHGSSTLEGGDVMPIGNGVVLIGMGERSSRQAIGQVAQSLFAKGAAERVIVAGLPKSRAAMHLDTVFSFCDRDLVTVFPEVVKEIVPFSLRPDPSSPYGMNIRREEKTFLEVVAESLGLKKLRVVETGGNSFAAEREQWDDGNNVVCLEPGVVVGYDRNTYTNTLLRKAGVEVITISASELGRGRGGGHCMTCPIVRDPID 417
               SCOP domains d2abrc_ C: Arginine deiminase                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2abrC01 C:7-71,C:157-417                                         -------------------------------------------------------------------------------------2abrC01 C:7-71,C:157-417 L-arginine/glycine Amidinotransferase; Chain A                                                                                                                                                                                               CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee......eeeeee...hhhhhh...............hhhhhhhhhhhhhhhhhh...eeeehhhhhhhhh.hhhhhhhhhhhhh........hhhhhhhhhhh.hhhhhhhhhhhhee.hhh.......hhhhhhhhh....eee..hhhhhh....eee...eeee.....hhhhhhhhhhhhhhhhhhhhhh...eeeee...........hhh.eee....eeeeee....hhhhhhhhhhhhhh.....eeeeee....--..hhhh.eeeee..eeeehhhhhh..eeeeeee.......eeeee...hhhhhhhhhh.....eeee..------...........eeee..eeeee..hhhhhhhhh....eeeee................eeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2abr C   7 KLGVHSEAGKLRKVMVCSPGLAHQRLTPSNCDELLFDDVIWVNQAKRDHFDFVTKMRERGIDVLEMHNLLTETIQNPEALKWILDRKITADSVGLGLTSELRSWLESLEPRKLAEYLIGGVAADDLPASEGANILKMYREYLGHSSFLLPPLPNTQFTRDTTCWIYGGVTLNPMYWPARRQETLLTTAIYKFHPEFANAEFEIWYGDPDKDHGSSTLEGGDVMPIGNGVVLIGMGERSSRQAIGQVAQSLFAKGAAERVIVAGLPKS--AMHLATVFSFCDRDLVTVFPEVVKEIVPFSLRPDPSSPYGMNIRREEKTFLEVVAESLGLKKLRVVETG------EREQWDDGNNVVCLEPGVVVGYDRNTYTNTLLRKAGVEVITISASELGRGRGGGHcMTCPIVRDPID 417
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266      |276       286       296       306       316       326       336       | -    |  356       366       376       386       396       406       416 
                                                                                                                                                                                                                                                                                                    273  |                                                                 344    351                                                    406-CYR       
                                                                                                                                                                                                                                                                                                       276                                                                                                                                             


Chain D from PDB  Type:PROTEIN  Length:402
 aligned with ARCA_PSEAE | P13981 from UniProtKB/Swiss-Prot  Length:418

    Alignment length:411
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415 
           ARCA_PSEAE     6 TKLGVHSEAGKLRKVMVCSPGLAHQRLTPSNCDELLFDDVIWVNQAKRDHFDFVTKMRERGIDVLEMHNLLTETIQNPEALKWILDRKITADSVGLGLTSELRSWLESLEPRKLAEYLIGGVAADDLPASEGANILKMYREYLGHSSFLLPPLPNTQFTRDTTCWIYGGVTLNPMYWPARRQETLLTTAIYKFHPEFANAEFEIWYGDPDKDHGSSTLEGGDVMPIGNGVVLIGMGERSSRQAIGQVAQSLFAKGAAERVIVAGLPKSRAAMHLDTVFSFCDRDLVTVFPEVVKEIVPFSLRPDPSSPYGMNIRREEKTFLEVVAESLGLKKLRVVETGGNSFAAEREQWDDGNNVVCLEPGVVVGYDRNTYTNTLLRKAGVEVITISASELGRGRGGGHCMTCPIVRDPI 416
               SCOP domains d2abrd_ D: Arginine deiminase                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2abrD01 D:6-71,D:157-416                                          -------------------------------------------------------------------------------------2abrD01 D:6-71,D:157-416 L-arginine/glycine Amidinotransferase; Chain A                                                                                                                                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee......eeeeee...hhhhhh...............hhhhhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh.hhhhhhhhhhhh........hhhhhhhhhhhhhh.........hhhhhhhhhheee....eee....hhhhhhhhhhhhhhhhhhhhhhh....eee............hhh.eeeee..eeee......hhhhhhhhhhhhhhh....eeeeee.....--.hhhh.eeeee..eeeehhhhhh..eeeee............ee...hhhhhhhhhhh....eeee..-------..........eeee..eeeee..hhhhhhhhhhh..eeeeehhhhhh..........eeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2abr D   6 TKLGVHSEAGKLRKVMVCSPGLAHQRLTPSNCDELLFDDVIWVNQAKRDHFDFVTKMRERGIDVLEMHNLLTETIQNPEALKWILDRKITADSVGLGLTSELRSWLESLEPRKLAEYLIGGVAADDLPASEGANILKMYREYLGHSSFLLPPLPNTQFTRDTTCWIYGGVTLNPMYWPARRQETLLTTAIYKFHPEFANAEFEIWYGDPDKDHGSSTLEGGDVMPIGNGVVLIGMGERSSRQAIGQVAQSLFAKGAAERVIVAGLPKSR--MHLATVFSFCDRDLVTVFPEVVKEIVPFSLRPDPSSPYGMNIRREEKTFLEVVAESLGLKKLRVVETG-------REQWDDGNNVVCLEPGVVVGYDRNTYTNTLLRKAGVEVITISASELGRGRGGGHcMTCPIVRDPI 416
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265        |- |     285       295       305       315       325       335        |-      |355       365       375       385       395       405|      415 
                                                                                                                                                                                                                                                                                                      274  |                                                                344     352                                                   406-CYR      
                                                                                                                                                                                                                                                                                                         277
   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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2ABR)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D   (ARCA_PSEAE | P13981)
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:0019546    arginine deiminase pathway    The chemical reactions and pathways resulting in the breakdown of arginine into other compounds, including ornithine and CO2, using the enzyme arginine deiminase.
    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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        ARCA_PSEAE | P13981: 1rxx 2a9g 2aaf 2aci

(-) Related Entries Specified in the PDB File

1rxx 2a9g 2aaf 2aci