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(-) Description

Title :  CRYSTAL STRUCTURE OF ARGININE DEIMINASE COVALENTLY LINKED WITH A REACTION INTERMEDIATE
 
Authors :  K. Das, G. H. Buttler, V. Kwiatkowski, A. D. Clark Jr. , P. Yadav, E. Arnold
Date :  05 Feb 04  (Deposition) - 13 Apr 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Deiminase, Hydrolase, 5-Fold Pseudo-Symmetric Domain, 5- Helix Bundle Domain, Raction Intermediate (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)

(-) Compounds

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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric/Biological Unit (3, 13)
No.NameCountTypeFull Name
1ARG2Mod. Amino AcidARGININE
2TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3UNX9Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:44 , ASN A:155 , PHE A:158 , ARG A:160 , ASP A:161 , ARG A:180 , GLY A:215 , ARG A:232 , MET A:268 , HIS A:269 , ASP A:271 , GLY A:392 , MET A:393 , CYS A:398 , HOH A:963BINDING SITE FOR RESIDUE ARG A 950
02AC2SOFTWARELEU B:44 , ASN B:155 , ARG B:160 , ASP B:161 , ARG B:180 , GLY B:215 , ARG B:232 , MET B:268 , HIS B:269 , ASP B:271 , GLY B:392 , MET B:393 , CYS B:398 , HOH B:962BINDING SITE FOR RESIDUE ARG B 951
03AC3SOFTWAREARG A:344 , GLU A:345 , PHE A:348 , ARG A:366 , ASN A:367 , HOH A:1035 , HOH A:1067 , HOH A:1111 , ILE B:48 , LEU B:49 , GLU B:50BINDING SITE FOR RESIDUE TRS A 952
04AC4SOFTWARELEU A:49 , GLU A:50 , ARG B:344 , GLU B:345 , PHE B:348 , ARG B:366 , ASN B:367 , HOH B:987 , HOH B:996 , HOH B:1041BINDING SITE FOR RESIDUE TRS B 953
05AC5SOFTWAREUNX A:956 , UNX A:959 , UNX A:962 , GLU B:57 , ASN B:387 , GLN B:388 , UNX B:955 , UNX B:957 , UNX B:961BINDING SITE FOR RESIDUE UNX B 954
06AC6SOFTWAREUNX A:956 , UNX A:959 , UNX A:960 , UNX A:962 , GLN B:388 , UNX B:954 , UNX B:957 , UNX B:958 , UNX B:961BINDING SITE FOR RESIDUE UNX B 955
07AC7SOFTWAREASN A:387 , UNX A:959 , UNX A:960 , UNX A:962 , UNX B:954 , UNX B:955 , UNX B:957 , UNX B:958 , UNX B:961BINDING SITE FOR RESIDUE UNX A 956
08AC8SOFTWAREUNX A:956 , UNX A:959 , UNX A:960 , UNX A:962 , HOH A:1467 , UNX B:954 , UNX B:955 , UNX B:958 , UNX B:961 , HOH B:1386BINDING SITE FOR RESIDUE UNX B 957
09AC9SOFTWAREUNX A:956 , UNX A:959 , UNX A:960 , UNX B:955 , UNX B:957 , UNX B:961 , HOH B:1386BINDING SITE FOR RESIDUE UNX B 958
10BC1SOFTWAREUNX A:956 , UNX A:960 , UNX A:962 , HOH A:1054 , HOH A:1467 , UNX B:954 , UNX B:955 , UNX B:957 , UNX B:958 , UNX B:961 , HOH B:1386BINDING SITE FOR RESIDUE UNX A 959
11BC2SOFTWAREUNX A:956 , UNX A:959 , HOH A:1054 , HOH A:1467 , UNX B:955 , UNX B:957 , UNX B:958 , UNX B:961 , HOH B:1222BINDING SITE FOR RESIDUE UNX A 960
12BC3SOFTWAREUNX A:956 , UNX A:959 , UNX A:960 , UNX A:962 , ASN B:387 , UNX B:954 , UNX B:955 , UNX B:957 , UNX B:958BINDING SITE FOR RESIDUE UNX B 961
13BC4SOFTWAREGLU A:57 , ASN A:387 , GLN A:388 , UNX A:956 , UNX A:959 , GLN B:388 , UNX B:954 , UNX B:955 , UNX B:957 , UNX B:961BINDING SITE FOR RESIDUE UNX A 962

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1S9R)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:103 -Pro A:104
2Glu B:103 -Pro B:104

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S9R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1S9R)

(-) Exons   (0, 0)

(no "Exon" information available for 1S9R)

(-) 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:410
 aligned with ARCA_MYCAR | P23793 from UniProtKB/Swiss-Prot  Length:410

    Alignment length:410
                                                                                                                                                                                                                                                                                                                                                                                                                                                  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        |-
           ARCA_MYCAR     2 SVFDSKFKGIHVYSEIGELESVLVHEPGREIDYITPARLDELLFSAILESHDARKEHKQFVAELKANDINVVELIDLVAETYDLASQEAKDKLIEEFLEDSEPVLSEEHKVVVRNFLKAKKTSRELVEIMMAGITKYDLGIEADHELIVDPMPNLYFTRDPFASVGNGVTIHYMRYKVRQRETLFSRFVFSNHPKLINTPWYYDPSLKLSIEGGDVFIYNNDTLVVGVSERTDLQTVTLLAKNIVANKECEFKRIVAINVPKWTNLMHLDTWLTMLDKDKFLYSPIANDVFKFWDYDLVNGGAEPQPVENGLPLEGLLQSIINKKPVLIPIAGEGASQMEIERETHFDGTNYLAIRPGVVIGYSRNEKTNAALEAAGIKVLPFHGNQLSLGMGNARCMSMPLSRKDVKW-   -
               SCOP domains d1s9ra_ A: Arginine deiminase                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------1s9rA01 A:10-74,A:153-406                                        ------------------------------------------------------------------------------1s9rA01 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.....hhhhhhhhhhhhhh..hhhhhhhhhhhheehhhhh......eee..hhhhhh....eeee..eeee....hhhhhhhhhhhhhhhhhh.......eeehhhhh...hhh.eee....eeeeee....hhhhhhhhhhhhhhh......eeeeee........hhhh.eee....eeee.hhhh...eeeeee..........eee..hhhhhhhhhhh...eeee......hhhhhhhhhhh.....eeee..eeeee..hhhhhhhhhhh..eeeee.hhhhhh.........eeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s9r A   2 SVFDSKFKGIHVYSEIGELESVLVHEPGREIDYITPARLDELLFSAILESHDARKEHKQFVAELKANDINVVELIDLVAETYDLASQEAKDKLIEEFLEDSEPVLSEEHKVVVRNFLKAKKTSRELVEIMMAGITKYDLGIEADHELIVDPMPNLYFTRDPFASVGNGVTIHYMRYKVRQRETLFSRFVFSNHPKLINTPWYYDPSLKLSIEGGDVFIYNNDTLVVGVSERTDLQTVTLLAKNIVANKECEFKRIVAINVPKWTNLMHLDTWLTMLDKDKFLYSPIANDVFKFWDYDLVNGGAEPQPVENGLPLEGLLQSIINKKPVLIPIAGEGASQMEIERETHFDGTNYLAIRPGVVIGYSRNEKTNAALEAAGIKVLPFHGNQLSLGMGNARCMSMPLSRKDVKWR 950
                                    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       950
                                                                                                                                                                                                                                                                                                                                                                                                                                                  410|
                                                                                                                                                                                                                                                                                                                                                                                                                                                   950


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

    Alignment length:410
                                                                                                                                                                                                                                                                                                                                                                                                                                                  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        |-
           ARCA_MYCAR     2 SVFDSKFKGIHVYSEIGELESVLVHEPGREIDYITPARLDELLFSAILESHDARKEHKQFVAELKANDINVVELIDLVAETYDLASQEAKDKLIEEFLEDSEPVLSEEHKVVVRNFLKAKKTSRELVEIMMAGITKYDLGIEADHELIVDPMPNLYFTRDPFASVGNGVTIHYMRYKVRQRETLFSRFVFSNHPKLINTPWYYDPSLKLSIEGGDVFIYNNDTLVVGVSERTDLQTVTLLAKNIVANKECEFKRIVAINVPKWTNLMHLDTWLTMLDKDKFLYSPIANDVFKFWDYDLVNGGAEPQPVENGLPLEGLLQSIINKKPVLIPIAGEGASQMEIERETHFDGTNYLAIRPGVVIGYSRNEKTNAALEAAGIKVLPFHGNQLSLGMGNARCMSMPLSRKDVKW-   -
               SCOP domains d1s9rb_ B: Arginine deiminase                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains --------1s9rB01 B:10-74,B:153-406                                        ------------------------------------------------------------------------------1s9rB01 B:10-74,B:153-406 L-arginine/glycine Amidinotransferase; Chain A                                                                                                                                                                                      ----- CATH domains
           Pfam domains (1) -----------------------Amidinotransf-1s9rB01 B:25-405                                                                                                                                                                                                                                                                                                                                                               ------ Pfam domains (1)
           Pfam domains (2) -----------------------Amidinotransf-1s9rB02 B:25-405                                                                                                                                                                                                                                                                                                                                                               ------ Pfam domains (2)
         Sec.struct. author ..................eeeeee...hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh..hhhhhhhhhhhheehhhhh......eee..hhhhhh....eeee..eeee....hhhhhhhhhhhhhhhhhh.......eeehhhhh...hhh.eee....eeeeee....hhhhhhhhhhhhhhh......eeeeee........hhhh.eee....eeee.hhhh...eeeeee..........eee..hhhhhhhhhhh...eeee......hhhhhhhhhhh.....eeee..eeeee..hhhhhhhhhhh..eeeee.hhhhhh.........eeeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s9r B   2 SVFDSKFKGIHVYSEIGELESVLVHEPGREIDYITPARLDELLFSAILESHDARKEHKQFVAELKANDINVVELIDLVAETYDLASQEAKDKLIEEFLEDSEPVLSEEHKVVVRNFLKAKKTSRELVEIMMAGITKYDLGIEADHELIVDPMPNLYFTRDPFASVGNGVTIHYMRYKVRQRETLFSRFVFSNHPKLINTPWYYDPSLKLSIEGGDVFIYNNDTLVVGVSERTDLQTVTLLAKNIVANKECEFKRIVAINVPKWTNLMHLDTWLTMLDKDKFLYSPIANDVFKFWDYDLVNGGAEPQPVENGLPLEGLLQSIINKKPVLIPIAGEGASQMEIERETHFDGTNYLAIRPGVVIGYSRNEKTNAALEAAGIKVLPFHGNQLSLGMGNARCMSMPLSRKDVKWR 951
                                    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       951
                                                                                                                                                                                                                                                                                                                                                                                                                                                  410|
                                                                                                                                                                                                                                                                                                                                                                                                                                                   951
   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, 2)

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

(-) CATH Domains  (1, 2)

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

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: GME (20)

(-) Gene Ontology  (7, 7)

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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ARCA_MYCAR | P23793: 1lxy

(-) Related Entries Specified in the PDB File

1lxy CRYSTAL STRUCTURE OF ARGININE DEIMINASE COVALENTLY LINKED WITH L-CITRULLINE