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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ARGINASE-1 COMPLEXED WITH INHIBITOR 14
 
Authors :  A. Cousido-Siah, A. Mitschler, F. X. Ruiz, D. L. Whitehouse, A. Golebio M. Ji, M. Zhang, P. Beckett, R. Sheeler, M. Andreoli, B. Conway, K. Mahb H. Schroeter, M. C. Van Zandt, A. Podjarny
Date :  12 Nov 12  (Deposition) - 20 Mar 13  (Release) - 10 Apr 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (3x)
Biol. Unit 2:  B  (3x)
Keywords :  Metalloenzyme, Alpha/Beta Fold, Hydrolase, Arginine Metabolism, Manganese, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Van Zandt, D. L. Whitehouse, A. Golebiowski, M. K. Ji, M. Zhang, R. P. Beckett, G. E. Jagdmann, T. R. Ryder, R. Sheeler, M. Andreoli, B. Conway, K. Mahboubi, G. D'Angelo, A. Mitschler, A. Cousido-Siah, F. X. Ruiz, E. I. Howard, A. D. Podjarny, H. Schroeter
Discovery Of (R)-2-Amino-6-Borono-2-(2-(Piperidin-1-Yl)Ethyl)Hexanoic Acid And Congeners As Highly Potent Inhibitors Of Human Arginases I And Ii For Treatment Of Myocardial Reperfusion Injury.
J. Med. Chem. V. 56 2568 2013
PubMed-ID: 23472952  |  Reference-DOI: 10.1021/JM400014C

(-) Compounds

Molecule 1 - ARGINASE-1
    Chains: A, B
    EC Number: 3.5.3.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    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
1MN4Ligand/IonMANGANESE (II) ION
2X8A2Ligand/Ion[(5R)-5-CARBOXY-5-(METHYLAMINO)-7-(PIPERIDIN-1-YL)HEPTYL](TRIHYDROXY)BORATE(1-)
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2X8A3Ligand/Ion[(5R)-5-CARBOXY-5-(METHYLAMINO)-7-(PIPERIDIN-1-YL)HEPTYL](TRIHYDROXY)BORATE(1-)
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1MN-1Ligand/IonMANGANESE (II) ION
2X8A3Ligand/Ion[(5R)-5-CARBOXY-5-(METHYLAMINO)-7-(PIPERIDIN-1-YL)HEPTYL](TRIHYDROXY)BORATE(1-)

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:101 , ASP A:124 , HIS A:126 , ASP A:128 , ASN A:130 , SER A:137 , HIS A:141 , ASP A:181 , ASP A:183 , ASP A:232 , ASP A:234 , THR A:246 , GLU A:277 , MN A:902 , MN A:903 , HOH A:1002 , HOH A:1023 , HOH A:1057 , HOH A:1230BINDING SITE FOR RESIDUE X8A A 901
2AC2SOFTWAREASP A:124 , HIS A:126 , ASP A:232 , ASP A:234 , X8A A:901 , MN A:903BINDING SITE FOR RESIDUE MN A 902
3AC3SOFTWAREHIS A:101 , ASP A:124 , ASP A:128 , ASP A:232 , X8A A:901 , MN A:902BINDING SITE FOR RESIDUE MN A 903
4AC4SOFTWAREHIS B:101 , ASP B:124 , HIS B:126 , ASP B:128 , ASN B:130 , SER B:137 , HIS B:141 , ASP B:181 , ASP B:183 , ASP B:232 , ASP B:234 , THR B:246 , GLU B:277 , MN B:402 , MN B:403 , HOH B:502 , HOH B:546 , HOH B:562BINDING SITE FOR RESIDUE X8A B 401
5AC5SOFTWAREASP B:124 , HIS B:126 , ASP B:232 , ASP B:234 , X8A B:401 , MN B:403BINDING SITE FOR RESIDUE MN B 402
6AC6SOFTWAREHIS B:101 , ASP B:124 , ASP B:128 , ASP B:232 , X8A B:401 , MN B:402BINDING SITE FOR RESIDUE MN B 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:98 -Gly A:99
2Gly B:98 -Gly B:99

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HXQ)

(-) 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 d4hxqa_ A: Arginase                                                                                                                                                                                                                                                                                                        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.hhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hxq A   5 SRTIGIIGAPFSKGQPRGGVEEGPTVLRKAGLLEKLKEQECDVKDYGDLPFADIPNDSPFQIVKNPRSVGKASEQLAGKVAEVKKNGRISLVLGGDHSLAIGSISGHARVHPDLGVIWVDAHTDINTPLTTTSGNLHGQPVSFLLKELKGKIPDVPGFSWVTPCISAKDIVYIGLRDVDPGEHYILKTLGIKYFSMTEVDRLGIGKVMEETLSYLLGRKKRPIHLSFDVDGLDPSFTPATGTPVVGGLTYREGLYITEEIYKTGLLSGLDIMEVNPSLGKTPEEVTRTVNTAVAITLACFGLAREGNHKPIDYL 318
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314    


Chain B from PDB  Type:PROTEIN  Length:314
                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains d4hxqb_ B: Arginase                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee........hhhhhhhhhhhhhhhhhhhhhhh..eeeeeee................hhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh...eeeee...............hhhhhhhhhhhhhhh................hhh.eeeeee...hhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhh................hhhhhhhhhhhhhhh..eeeeeee..hhhhh.hhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hxq B   5 SRTIGIIGAPFSKGQPRGGVEEGPTVLRKAGLLEKLKEQECDVKDYGDLPFADIPNDSPFQIVKNPRSVGKASEQLAGKVAEVKKNGRISLVLGGDHSLAIGSISGHARVHPDLGVIWVDAHTDINTPLTTTSGNLHGQPVSFLLKELKGKIPDVPGFSWVTPCISAKDIVYIGLRDVDPGEHYILKTLGIKYFSMTEVDRLGIGKVMEETLSYLLGRKKRPIHLSFDVDGLDPSFTPATGTPVVGGLTYREGLYITEEIYKTGLLSGLDIMEVNPSLGKTPEEVTRTVNTAVAITLACFGLAREGNHKPIDYL 318
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314
   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 Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (49, 49)

Asymmetric Unit(hide GO term definitions)

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  4hxq
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  ARGI1_HUMAN | P05089
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  3.5.3.1
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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 4fck 4gsm 4gsv 4gsz 4gwc 4gwd 4hww 4ie1

(-) Related Entries Specified in the PDB File

1d3v 2aeb 4hww 4hze