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(-) Description

Title :  ALTERING THE BINUCLEAR MANGANESE CLUSTER OF ARGINASE DIMINISHES THERMOSTABILITY AND CATALYTIC FUNCTION
 
Authors :  L. R. Scolnick, Z. F. Kanyo, D. W. Christianson
Date :  07 May 97  (Deposition) - 13 May 98  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.74
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Hydrolase, Urea Cycle, Arginine Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. R. Scolnick, Z. F. Kanyo, R. C. Cavalli, D. E. Ash, D. W. Christianson
Altering The Binuclear Manganese Cluster Of Arginase Diminishes Thermostability And Catalytic Function.
Biochemistry V. 36 10558 1997
PubMed-ID: 9265637  |  Reference-DOI: 10.1021/BI970800V
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ARGINASE
    Cellular Location: CYTOPLASM
    Cell Line: BL21
    Chains: A, B, C
    EC Number: 3.5.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Gene: PARG-X
    Expression System Plasmid: PRSET C
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PARGR-2
    Mutation: YES
    Organ: LIVER
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1MN3Ligand/IonMANGANESE (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:124 , HIS A:126 , ASP A:232 , ASP A:234 , HOH A:543BINDING SITE FOR RESIDUE MN A 500
2AC2SOFTWAREASP B:124 , HIS B:126 , ASP B:232 , ASP B:234BINDING SITE FOR RESIDUE MN B 501
3AC3SOFTWAREASP C:124 , HIS C:126 , ASP C:232 , ASP C:234BINDING SITE FOR RESIDUE MN C 502
4MNAUNKNOWNASN A:101 , ASP A:124 , HIS A:126 , ASP A:128 , ASP A:232 , ASP A:234BI-MANGANESE NUCLEAR BINDING SITE.
5MNBUNKNOWNASN B:101 , ASP B:124 , HIS B:126 , ASP B:128 , ASP B:232 , ASP B:234BI-MANGANESE NUCLEAR BINDING SITE.
6MNCUNKNOWNASN C:101 , ASP C:124 , HIS C:126 , ASP C:128 , ASP C:232 , ASP C:234BI-MANGANESE NUCLEAR BINDING SITE.

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5RLA)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:98 -Gly A:99
2Gly B:98 -Gly B:99
3Gly C:98 -Gly C:99

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5RLA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5RLA)

(-) Exons   (0, 0)

(no "Exon" information available for 5RLA)

(-) 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:314
                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d5rlaa_ A: Arginase                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 5rlaA00 A:6-319  [code=3.40.800.10, no name defined]                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...........hhhhhhhhhh..hhhhhhh....eeeeee.................hhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhh....eeeee................hhh.hhhhh.hhh.....................eeeeee....hhhhhhhhh...eeeehhhhhhh.hhhhhhhhhhhhh......eeeeeehhh..................hhhhhhhhhhhhhh..eeeeeee...hhh...hhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5rla A   6 KPIEIIGAPFSKGQPRGGVEKGPAALRKAGLVEKLKETEYNVRDHGDLAFVDVPNDSPFQIVKNPRSVGKANEQLAAVVAETQKNGTISVVLGGDNSMAIGSISGHARVHPDLCVIWVDAHTDINTPLTTSSGNLHGQPVAFLLKELKGKFPDVPGFSWVTPCISAKDIVYIGLRDVDPGEHYIIKTLGIKYFSMTEVDKLGIGKVMEETFSYLLGRKKRPIHLSFDVDGLDPVFTPATGTPVVGGLSYREGLYITEEIYKTGLLSGLDIMEVNPTLGKTPEEVTRTVNTAVALTLSCFGTKREGNHKPETDYL 319
                                    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    


Chain B from PDB  Type:PROTEIN  Length:314
                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d5rlab_ B: Arginase                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 5rlaB00 B:6-319  [code=3.40.800.10, no name defined]                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...........hhhhhhhhhh..hhhhhhh....eeeeee.................hhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhh....eeeee................hhh.hhhhh.hhh.....................eeeeee....hhhhhhhhh...eeeehhhhhhh.hhhhhhhhhhhhh......eeeeeehhh..................hhhhhhhhhhhhhh..eeeeeee...hhh...hhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5rla B   6 KPIEIIGAPFSKGQPRGGVEKGPAALRKAGLVEKLKETEYNVRDHGDLAFVDVPNDSPFQIVKNPRSVGKANEQLAAVVAETQKNGTISVVLGGDNSMAIGSISGHARVHPDLCVIWVDAHTDINTPLTTSSGNLHGQPVAFLLKELKGKFPDVPGFSWVTPCISAKDIVYIGLRDVDPGEHYIIKTLGIKYFSMTEVDKLGIGKVMEETFSYLLGRKKRPIHLSFDVDGLDPVFTPATGTPVVGGLSYREGLYITEEIYKTGLLSGLDIMEVNPTLGKTPEEVTRTVNTAVALTLSCFGTKREGNHKPETDYL 319
                                    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    


Chain C from PDB  Type:PROTEIN  Length:314
                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d5rlac_ C: Arginase                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 5rlaC00 C:6-319  [code=3.40.800.10, no name defined]                                                                                                                                                                                                                                                                       CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee...........hhhhhhhhhh..hhhhhhh....eee....................hhhhhhhhhhhhhhhhhhhh...eeeee...hhhhhhhhhhhhhh....eeeee................hhh...hhh.hhh..................hhheeeeee....hhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhh......eeeeeehhh..................hhhhhhhhhhhhhh..eeeeeee...hhh...hhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5rla C   6 KPIEIIGAPFSKGQPRGGVEKGPAALRKAGLVEKLKETEYNVRDHGDLAFVDVPNDSPFQIVKNPRSVGKANEQLAAVVAETQKNGTISVVLGGDNSMAIGSISGHARVHPDLCVIWVDAHTDINTPLTTSSGNLHGQPVAFLLKELKGKFPDVPGFSWVTPCISAKDIVYIGLRDVDPGEHYIIKTLGIKYFSMTEVDKLGIGKVMEETFSYLLGRKKRPIHLSFDVDGLDPVFTPATGTPVVGGLSYREGLYITEEIYKTGLLSGLDIMEVNPTLGKTPEEVTRTVNTAVALTLSCFGTKREGNHKPETDYL 319
                                    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
   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, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5RLA)

(-) Gene Ontology  (47, 47)

Asymmetric/Biological Unit(hide GO term definitions)

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  ARGI1_RAT | P07824
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 Related Entries

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

UniProtKB/Swiss-Prot
        ARGI1_RAT | P07824: 1d3v 1hq5 1hqf 1hqg 1hqh 1hqx 1p8m 1p8n 1p8o 1p8p 1p8q 1p8r 1p8s 1r1o 1rla 1t4p 1t4r 1t4s 1t4t 1t5f 1t5g 1ta1 1tbh 1tbj 1tbl 1zpe 1zpg 2rla 3e8q 3e8z 3e9b 3rla 4rla

(-) Related Entries Specified in the PDB File

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