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(-) Description

Title :  CRYSTAL STRUCTURE OF SULFATE-BOUND HUMAN L-ASPARAGINASE PROTEIN
 
Authors :  J. Nomme, A. Lavie
Date :  18 Mar 14  (Deposition) - 26 Mar 14  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.13
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ntn Enzyme, Homodimer, Hydrolase, L-Asparagine (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Nomme, Y. Su, M. Konrad, A. Lavie
Structures Of Apo And Product-Bound Human L-Asparaginase: Insights Into The Mechanism Of Autoproteolysis And Substrat Hydrolysis.
Biochemistry V. 51 6816 2012
PubMed-ID: 22861376  |  Reference-DOI: 10.1021/BI300870G

(-) Compounds

Molecule 1 - ISOASPARTYL PEPTIDASE/L-ASPARAGINASE
    ChainsA, B
    EC Number3.4.19.5, 3.5.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET14B
    Expression System StrainBL21 (DE3) C41
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneALP, ASRGL1, CRASH
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymASPARAGINASE-LIKE PROTEIN 1, BETA-ASPARTYL-PEPTIDASE, ISOASPARTYL DIPEPTIDASE, L-ASPARAGINE AMIDOHYDROLASE, ISOASPARTYL PEPTIDASE/L-ASPARAGINASE ALPHA CHAIN, ISOASPARTYL PEPTIDASE/L- ASPARAGINASE BETA CHAIN

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 19)

Asymmetric/Biological Unit (3, 19)
No.NameCountTypeFull Name
1IOD4Ligand/IonIODIDE ION
2NA2Ligand/IonSODIUM ION
3SO413Ligand/IonSULFATE ION

(-) Sites  (19, 19)

Asymmetric Unit (19, 19)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA A:12 , GLY A:13 , LEU A:262 , SER A:280 , THR A:281 , HOH A:567 , LEU B:262BINDING SITE FOR RESIDUE SO4 A 401
02AC2SOFTWARETHR A:168 , GLY A:188 , ILE A:189 , ARG A:196 , GLY A:220 , HIS A:221 , GLY A:222 , HOH A:507BINDING SITE FOR RESIDUE SO4 A 402
03AC3SOFTWAREASP A:212 , ILE A:213 , ILE A:238 , GLU A:239 , LYS A:270BINDING SITE FOR RESIDUE SO4 A 403
04AC4SOFTWAREMET A:193 , ALA B:128BINDING SITE FOR RESIDUE SO4 A 404
05AC5SOFTWAREGLN A:124 , PHE A:125 , ALA A:128 , HOH A:555 , MET B:193BINDING SITE FOR RESIDUE SO4 A 405
06AC6SOFTWAREGLY A:73 , GLU A:74 , VAL A:75 , GLY A:136 , GLU A:137 , VAL A:140 , HOH A:533BINDING SITE FOR RESIDUE SO4 A 406
07AC7SOFTWARETHR A:32 , TYR A:35 , ARG A:39 , LEU A:307 , PRO A:308BINDING SITE FOR RESIDUE SO4 A 407
08AC8SOFTWAREGLY A:10 , LEU A:166 , PRO A:284 , IOD A:410BINDING SITE FOR RESIDUE IOD A 408
09AC9SOFTWARELYS A:227 , PRO B:113 , IOD B:407BINDING SITE FOR RESIDUE IOD A 409
10BC1SOFTWAREASN A:62 , LEU A:166 , GLY A:167 , IOD A:408BINDING SITE FOR RESIDUE IOD A 410
11BC2SOFTWARELEU A:55 , GLU A:56 , ASP A:58 , PHE A:61 , ALA A:63 , CYS A:65BINDING SITE FOR RESIDUE NA A 411
12BC3SOFTWARETHR B:168 , THR B:186 , GLY B:188 , ARG B:196 , ASP B:199 , GLY B:220 , GLY B:222BINDING SITE FOR RESIDUE SO4 B 401
13BC4SOFTWARETHR B:32 , TYR B:35 , GLY B:36 , ARG B:39 , LEU B:307BINDING SITE FOR RESIDUE SO4 B 402
14BC5SOFTWAREASP B:212 , ILE B:213 , GLU B:239 , LYS B:270 , HOH B:524BINDING SITE FOR RESIDUE SO4 B 403
15BC6SOFTWAREHIS B:0 , MET B:1 , CYS B:176 , LYS B:177 , GLY B:178 , HOH B:590BINDING SITE FOR RESIDUE SO4 B 404
16BC7SOFTWARELYS A:17 , TYR B:254 , SER B:257 , ARG B:258BINDING SITE FOR RESIDUE SO4 B 405
17BC8SOFTWAREGLU B:74 , VAL B:75 , GLY B:136 , LEU B:139BINDING SITE FOR RESIDUE SO4 B 406
18BC9SOFTWARELYS A:227 , IOD A:409 , SER B:88BINDING SITE FOR RESIDUE IOD B 407
19CC1SOFTWARELEU B:55 , GLU B:56 , ASP B:58 , PHE B:61 , ALA B:63 , CYS B:65BINDING SITE FOR RESIDUE NA B 408

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PVQ)

(-) 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:294
                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..................eeeeeee....eeeeeeee....hhhhhhhhhhhhh...eeehhhhhhhhhhh.....hhhhh.hhhhhhhhhh...eeeeee.....eeeeeee....................eeee...eeeeeeehhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeee....eeeee......eeeee..eeeee......eeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4pvq A   0 HMNPIVVVHGGGAGPISKDRKERVHQGMVRAATVGYGILREGGSAVDAVEGAVVALEDDPEFNAGCGSVLNTNGEVEMDASIMDGKDLSAGAVSAVQCIANPIKLARLVMEKTPHCFLTDQGAAQFAAAMGVPEIPGEKLVTERNKKRLEKLGTVGAVALDCKGNVAYATSTGGIVNKMVGRVGDSPCLGAGGYADNDIGAVSTTGHGESILKVNLARLTLFHIEQGKTVEEAADLSLGYMKSRVKGLGGLIVVSKTGDWVAKWTSTSMPWAAAKDGKLHFGIDPDDTTITDLP 308
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149||     174       184       194       204       214       224       234       244       254       264       274       284       294       304    
                                                                                                                                                                                150|                                                                                                                                              
                                                                                                                                                                                 166                                                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.........hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..................eeeeeee....eeeeeeee....hhhhhhhhhhhhh...eeehhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh...eeeeee.....eeeeeee....................eeee...eeeeeeehhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeee....eeeee......eeeee..eeeee......eeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pvq B   0 HMNPIVVVHGGGAGPISKDRKERVHQGMVRAATVGYGILREGGSAVDAVEGAVVALEDDPEFNAGCGSVLNTNGEVEMDASIMDGKDLSAGAVSAVQCIANPIKLARLVMEKTPHCFLTDQGAAQFAAAMGVPEIPGEKLVTERNKKRLEKEKLGTVGAVALDCKGNVAYATSTGGIVNKMVGRVGDSPCLGAGGYADNDIGAVSTTGHGESILKVNLARLTLFHIEQGKTVEEAADLSLGYMKSRVKGLGGLIVVSKTGDWVAKWTSTSMPWAAAKDGKLHFGIDPDDTTITDLP 308
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149  ||   172       182       192       202       212       222       232       242       252       262       272       282       292       302      
                                                                                                                                                                                  152|                                                                                                                                              
                                                                                                                                                                                   166                                                                                                                                              

   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  (0, 0)

(no "SCOP Domain" information available for 4PVQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        ASGL1_HUMAN | Q7L2663tkj 4et0 4o0c 4o0d 4o0e 4o0f 4o0g 4o0h 4osx 4osy 4pvp 4pvr 4pvs 4zm9

(-) Related Entries Specified in the PDB File

4pvp 4pvr 4pvs