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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MN2+2,ZN2+-HUMAN ARGINASE I-ABH COMPLEX
 
Authors :  E. L. D'Antonio, Y. Hai, D. W. Christianson
Date :  01 Sep 12  (Deposition) - 26 Sep 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.53
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: 469008
    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  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1ABH2Ligand/Ion2(S)-AMINO-6-BORONOHEXANOIC ACID
2MN4Ligand/IonMANGANESE (II) ION
3ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1ABH3Ligand/Ion2(S)-AMINO-6-BORONOHEXANOIC ACID
2MN-1Ligand/IonMANGANESE (II) ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1ABH3Ligand/Ion2(S)-AMINO-6-BORONOHEXANOIC ACID
2MN-1Ligand/IonMANGANESE (II) ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:124 , HIS A:126 , ASP A:232 , ASP A:234 , MN A:402 , ABH A:404BINDING SITE FOR RESIDUE MN A 401
2AC2SOFTWAREHIS A:101 , ASP A:124 , ASP A:128 , ASP A:232 , MN A:401 , ABH A:404BINDING SITE FOR RESIDUE MN A 402
3AC3SOFTWAREHIS A:141 , GLU A:277 , ABH A:404 , HOH A:501BINDING SITE FOR RESIDUE ZN A 403
4AC4SOFTWAREHIS 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 , MN A:401 , MN A:402 , ZN A:403 , HOH A:505 , HOH A:511 , HOH A:512 , HOH A:542 , HOH A:592BINDING SITE FOR RESIDUE ABH A 404
5AC5SOFTWAREASP B:124 , HIS B:126 , ASP B:232 , ASP B:234 , MN B:402 , ABH B:404BINDING SITE FOR RESIDUE MN B 401
6AC6SOFTWAREHIS B:101 , ASP B:124 , ASP B:128 , ASP B:232 , MN B:401 , ABH B:404BINDING SITE FOR RESIDUE MN B 402
7AC7SOFTWAREHIS B:141 , GLU B:277 , ABH B:404 , HOH B:501BINDING SITE FOR RESIDUE ZN B 403
8AC8SOFTWAREHIS 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 , MN B:401 , MN B:402 , ZN B:403 , HOH B:506 , HOH B:508 , HOH B:512BINDING SITE FOR RESIDUE ABH B 404

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4GWD)

(-) 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 d4gwda_ A: automated matches                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee........hhhhhhhhhhhhhhhhhhhhhh..eeeeeeee................hhhhhhhhhhhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhhhh...eeeee...............hhhhhhhhhhhhhhh................hhh.eeee.....hhhhhhhhhhhh.eeehhhhhhhhhhhhhhhhhhhhhh......eeeeee.hhh................hhhhhhhhhhhhhhhh.eeeeeee..hhhhh.hhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gwd 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 d4gwdb_ B: automated matches                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee........hhhhhhhhhhhhhhhhhhhhh...eeeeeee................hhhhhhhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhh...eeeee...............hhhhhhhhhhhhhhh................hhh.eeee.....hhhhhhhhhhhh.eeehhhhhhhhhhhhhhhhhhhhhhh.....eeeeee.hhh................hhhhhhhhhhhhhhh..eeeeeee..hhhhh.hhhhhhhhhhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4gwd 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 4GWD)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (49, 49)

Asymmetric Unit(hide GO term definitions)

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  4gwd
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Access by UniProt ID/Accession number
  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 4hww 4hxq 4ie1

(-) Related Entries Specified in the PDB File

2aeb THE SAME PROTEIN/INHIBITOR COMPLEX EXCEPT THAT IT LACKS THE ZN2+ ION
4gsz THE SAME PROTEIN/INHIBITOR COMPLEX (IN THE ACTIVE SITE) EXCEPT THAT MN2+A AND MN2+B ARE REPLACED BY ZN2+ IONS
4gwc