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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CO2+2-HUMAN ARGINASE I-AGPA COMPLEX
 
Authors :  E. L. D'Antonio, D. W. Christianson
Date :  25 May 12  (Deposition) - 20 Jun 12  (Release) - 23 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  B  (3x)
Keywords :  Arginase Fold, Hydrolase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. L. D'Antonio, D. W. Christianson
Binding Of The Unreactive Substrate Analog L-2-Amino-3-Guanidinopropionic Acid (Dinor-L-Arginine) To Human Arginase I.
Acta Crystallogr. , Sect. F V. 68 889 2012
PubMed-ID: 22869115  |  Reference-DOI: 10.1107/S1744309112027820

(-) Compounds

Molecule 1 - ARGINASE-1
    Chains: A, B
    EC Number: 3.5.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBS(KS)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: HUMAN ARGINASE I
    Gene: ARG1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LIVER-TYPE ARGINASE, TYPE I ARGINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): A 
Biological Unit 2 (3x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1CO4Ligand/IonCOBALT (II) ION
2GPA2Ligand/Ion2-AMINO-3-GUANIDINO-PROPIONIC ACID
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2GPA3Ligand/Ion2-AMINO-3-GUANIDINO-PROPIONIC ACID
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1CO-1Ligand/IonCOBALT (II) ION
2GPA3Ligand/Ion2-AMINO-3-GUANIDINO-PROPIONIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:126 , ASP A:128 , ASN A:130 , SER A:137 , HIS A:141 , GLY A:142 , ASP A:183 , GLU A:186 , THR A:246 , HOH A:506 , HOH A:513 , HOH A:575 , HOH A:628 , HOH A:631BINDING SITE FOR RESIDUE GPA A 401
2AC2SOFTWAREHIS A:101 , ASP A:124 , ASP A:128 , ASP A:232 , CO A:403 , HOH A:628BINDING SITE FOR RESIDUE CO A 402
3AC3SOFTWAREASP A:124 , HIS A:126 , ASP A:232 , ASP A:234 , CO A:402BINDING SITE FOR RESIDUE CO A 403
4AC4SOFTWAREHIS B:126 , ASP B:128 , ASN B:130 , SER B:137 , HIS B:141 , GLY B:142 , ASP B:183 , GLU B:186 , THR B:246 , HOH B:503 , HOH B:504 , HOH B:532 , HOH B:539 , HOH B:560 , HOH B:566 , HOH B:602BINDING SITE FOR RESIDUE GPA B 401
5AC5SOFTWAREHIS B:101 , ASP B:124 , ASP B:128 , ASP B:232 , CO B:403 , HOH B:604BINDING SITE FOR RESIDUE CO B 402
6AC6SOFTWAREASP B:124 , HIS B:126 , ASP B:232 , ASP B:234 , CO B:402 , HOH B:604BINDING SITE FOR RESIDUE CO B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4FCK)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4FCK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4FCK)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4FCK)

(-) Exons   (0, 0)

(no "Exon" information available for 4FCK)

(-) Sequences/Alignments

Asymmetric 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 d4fcka_ A: automated matches                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee........hhhhhhhhhhhh.hhhhhhhh...eeeeeee................hhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh...eeeee...............hhhhhhhhhhhhhhh................hhh.eeeeee...hhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhh................hhhhhhhhhhhhhhh..eeeeeee..hhhhh.hhhhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fck A   6 RTIGIIGAPFSKGQPRGGVEEGPTVLRKAGLLEKLKEQECDVKDYGDLPFADIPNDSPFQIVKNPRSVGKASEQLAGKVAEVKKNGRISLVLGGDHSLAIGSISGHARVHPDLGVIWVDAHTDINTPLTTTSGNLHGQPVSFLLKELKGKIPDVPGFSWVTPCISAKDIVYIGLRDVDPGEHYILKTLGIKYFSMTEVDRLGIGKVMEETLSYLLGRKKRPIHLSFDVDGLDPSFTPATGTPVVGGLTYREGLYITEEIYKTGLLSGLDIMEVNPSLGKTPEEVTRTVNTAVAITLACFGLAREGNHKPIDYLN 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 d4fckb_ B: automated matches                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.......hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee................hhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh...eeeee...............hhhhhhhhhhhhhhh................hhh.eeeeee...hhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhh................hhhhhhhhhhhhhhh..eeeeeee..hhhhh.hhhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4fck B   6 RTIGIIGAPFSKGQPRGGVEEGPTVLRKAGLLEKLKEQECDVKDYGDLPFADIPNDSPFQIVKNPRSVGKASEQLAGKVAEVKKNGRISLVLGGDHSLAIGSISGHARVHPDLGVIWVDAHTDINTPLTTTSGNLHGQPVSFLLKELKGKIPDVPGFSWVTPCISAKDIVYIGLRDVDPGEHYILKTLGIKYFSMTEVDRLGIGKVMEETLSYLLGRKKRPIHLSFDVDGLDPSFTPATGTPVVGGLTYREGLYITEEIYKTGLLSGLDIMEVNPSLGKTPEEVTRTVNTAVAITLACFGLAREGNHKPIDYLN 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)
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    → 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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4FCK)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4FCK)

(-) Gene Ontology  (49, 49)

Asymmetric Unit(hide GO term definitions)

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  ARGI1_HUMAN | P05089
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 Related Entries

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

UniProtKB/Swiss-Prot
        ARGI1_HUMAN | P05089: 1wva 1wvb 2aeb 2pha 2pho 2pll 2zav 3dj8 3e6k 3e6v 3f80 3gmz 3gn0 3kv2 3lp4 3lp7 3mfv 3mfw 3mjl 3sjt 3skk 3tf3 3th7 3the 3thh 3thj 4fci 4gsm 4gsv 4gsz 4gwc 4gwd 4hww 4hxq 4ie1

(-) Related Entries Specified in the PDB File

2pha THE SAME PROTEIN EXCEPT THAT IT IS UNLIGANDED AND CONTAINS A MN2+2-CLUSTER AS OPPOSED TO A CO2+2-CLUSTER.
4fci THE SAME PROTEIN HAVING THE SAME WEAK INHIBITOR BOUND (AGPA); HOWEVER, THIS PROTEIN HAS A MN2+2-CLUSTER.