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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ZN2+5-HUMAN ARGINASE I-ABH COMPLEX
 
Authors :  E. L. D'Antonio, Y. Hai, D. W. Christianson
Date :  28 Aug 12  (Deposition) - 26 Sep 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
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, Y. Hai, D. W. Christianson
Structure And Function Of Non-Native Metal Clusters In Huma Arginase I.
Biochemistry V. 51 8399 2012
PubMed-ID: 23061982  |  Reference-DOI: 10.1021/BI301145N

(-) 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, 11)

Asymmetric Unit (2, 11)
No.NameCountTypeFull Name
1ABH2Ligand/Ion2(S)-AMINO-6-BORONOHEXANOIC ACID
2ZN9Ligand/IonZINC ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1ABH3Ligand/Ion2(S)-AMINO-6-BORONOHEXANOIC ACID
2ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1ABH3Ligand/Ion2(S)-AMINO-6-BORONOHEXANOIC ACID
2ZN-1Ligand/IonZINC ION

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:312BINDING SITE FOR RESIDUE ZN A 401
02AC2SOFTWAREHIS A:101 , ASP A:124 , ASP A:128 , ASP A:232 , ZN A:403 , ABH A:405BINDING SITE FOR RESIDUE ZN A 402
03AC3SOFTWAREASP A:124 , HIS A:126 , ASP A:232 , ASP A:234 , ZN A:402 , ABH A:405BINDING SITE FOR RESIDUE ZN A 403
04AC4SOFTWAREHIS A:141 , GLU A:277 , ABH A:405 , HOH A:559BINDING SITE FOR RESIDUE ZN A 404
05AC5SOFTWAREHIS A:101 , ASP A:124 , HIS A:126 , ASP A:128 , ASN A:130 , SER A:137 , HIS A:141 , GLY A:142 , ASP A:183 , GLU A:186 , ASP A:232 , ASP A:234 , THR A:246 , GLU A:277 , ZN A:402 , ZN A:403 , ZN A:404 , HOH A:506 , HOH A:558BINDING SITE FOR RESIDUE ABH A 405
06AC6SOFTWAREHIS A:115 , ASP A:117 , PRO A:226 , HOH A:560BINDING SITE FOR RESIDUE ZN A 406
07AC7SOFTWAREHIS B:101 , ASP B:124 , ASP B:128 , ASP B:232 , ZN B:402 , ABH B:403BINDING SITE FOR RESIDUE ZN B 401
08AC8SOFTWAREASP B:124 , HIS B:126 , ASP B:232 , ASP B:234 , ZN B:401 , ABH B:403BINDING SITE FOR RESIDUE ZN B 402
09AC9SOFTWAREHIS B:101 , ASP B:124 , HIS B:126 , ASP B:128 , ASN B:130 , SER B:137 , HIS B:141 , GLY B:142 , ASP B:183 , ASP B:232 , ASP B:234 , THR B:246 , GLU B:277 , ZN B:401 , ZN B:402 , ZN B:404 , HOH B:502 , HOH B:505 , HOH B:525 , HOH B:538 , HOH B:541BINDING SITE FOR RESIDUE ABH B 403
10BC1SOFTWAREHIS B:141 , GLU B:277 , ABH B:403 , HOH B:538BINDING SITE FOR RESIDUE ZN B 404
11BC2SOFTWAREHIS B:115 , ASP B:117 , HOH B:543BINDING SITE FOR RESIDUE ZN B 405

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GSZ)

(-) 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:313
                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4gsza_ A: automated matches                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee........hhhhhhhhhhhhh.hhhhhhhh..eeeeeeee................hhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh...eeeee...............hhhhhhhhhhh....................hhh.eeee.....hhhhhhhhhhh..eeehhhhhhhhhhhhhhhhhhhhhh......eeeeee.hhh................hhhhhhhhhhhhhhh..eeeeeee..hhhhh.hhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gsz A   5 SRTIGIIGAPFSKGQPRGGVEEGPTVLRKAGLLEKLKEQECDVKDYGDLPFADIPNDSPFQIVKNPRSVGKASEQLAGKVAEVKKNGRISLVLGGDHSLAIGSISGHARVHPDLGVIWVDAHTDINTPLTTTSGNLHGQPVSFLLKELKGKIPDVPGFSWVTPCISAKDIVYIGLRDVDPGEHYILKTLGIKYFSMTEVDRLGIGKVMEETLSYLLGRKKRPIHLSFDVDGLDPSFTPATGTPVVGGLTYREGLYITEEIYKTGLLSGLDIMEVNPSLGKTPEEVTRTVNTAVAITLACFGLAREGNHKPIDY 317
                                    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:313
                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4gszb_ B: automated matches                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.......hhhhhhhhhhhhhhhhhhhhhh....eeeeee................hhhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh...eeeee...............hhhhhhhhhhhhhhh................hhh.eeeeee...hhhhhhhhhhhh.eeeehhhhhhhhhhhhhhhhhhhhh......eeeeee.hhh................hhhhhhhhhhhhhh...eeeeeee..hhhhh.hhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gsz B   5 SRTIGIIGAPFSKGQPRGGVEEGPTVLRKAGLLEKLKEQECDVKDYGDLPFADIPNDSPFQIVKNPRSVGKASEQLAGKVAEVKKNGRISLVLGGDHSLAIGSISGHARVHPDLGVIWVDAHTDINTPLTTTSGNLHGQPVSFLLKELKGKIPDVPGFSWVTPCISAKDIVYIGLRDVDPGEHYILKTLGIKYFSMTEVDRLGIGKVMEETLSYLLGRKKRPIHLSFDVDGLDPSFTPATGTPVVGGLTYREGLYITEEIYKTGLLSGLDIMEVNPSLGKTPEEVTRTVNTAVAITLACFGLAREGNHKPIDY 317
                                    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)
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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 4GSZ)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (49, 49)

Asymmetric Unit(hide GO term definitions)

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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 4gwc 4gwd 4hww 4hxq 4ie1

(-) Related Entries Specified in the PDB File

2aeb THE SAME PROTEIN-INHIBITOR COMPLEX EXCEPT THAT THERE ARE ONLY TWO MN2+ IONS
3thh THE SAME PROTEIN-INHIBITOR COMPLEX EXCEPT THAT THERE ARE ONLY TWO CO2+ IONS
4gsk
4gsv THE SAME PROTEIN-INHIBITOR COMPLEX EXCEPT THAT THERE ARE ONLY TWO NI2+ IONS