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(-) Description

Title :  CRYSTAL STRUCTURE OF CIRCULARLY PERMUTED HUMAN ASPARAGINASE-LIKE PROTEIN 1
 
Authors :  W. Z. Li, Y. Zhang
Date :  02 May 15  (Deposition) - 17 Feb 16  (Release) - 24 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.51
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Circularly Permutated, Human Asparaginase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  W. Li, S. Irani, A. Crutchfield, K. Hodge, W. Matthews, P. Patel, Y. J. Zhang, E. Stone
Intramolecular Cleavage Of The Hasrgl1 Homodimer Occurs In Two Stages.
Biochemistry V. 55 960 2016
PubMed-ID: 26780688  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B01157

(-) Compounds

Molecule 1 - ISOASPARTYL PEPTIDASE/L-ASPARAGINASE
    ChainsA, B, C, D
    EC Number3.4.19.5, 3.5.1.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET28A
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    GeneASRGL1, ALP, CRASH
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCIRCULAR PERMUTATION
    SynonymASPARAGINASE-LIKE PROTEIN 1,BETA-ASPARTYL-PEPTIDASE, ISOASPARTYL DIPEPTIDASE,L-ASPARAGINE AMIDOHYDROLASE

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)AB  
Biological Unit 2 (1x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 25)

Asymmetric Unit (5, 25)
No.NameCountTypeFull Name
1BME10Ligand/IonBETA-MERCAPTOETHANOL
2DTT2Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
3FLC2Ligand/IonCITRATE ANION
4GLY4Mod. Amino AcidGLYCINE
5NA7Ligand/IonSODIUM ION
Biological Unit 1 (4, 9)
No.NameCountTypeFull Name
1BME5Ligand/IonBETA-MERCAPTOETHANOL
2DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
3FLC1Ligand/IonCITRATE ANION
4GLY2Mod. Amino AcidGLYCINE
5NA-1Ligand/IonSODIUM ION
Biological Unit 2 (4, 9)
No.NameCountTypeFull Name
1BME5Ligand/IonBETA-MERCAPTOETHANOL
2DTT1Ligand/Ion2,3-DIHYDROXY-1,4-DITHIOBUTANE
3FLC1Ligand/IonCITRATE ANION
4GLY2Mod. Amino AcidGLYCINE
5NA-1Ligand/IonSODIUM ION

(-) Sites  (25, 25)

Asymmetric Unit (25, 25)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELEU A:55 , GLU A:56 , ASP A:58 , PHE A:61 , ALA A:63 , CYS A:65binding site for residue NA A 401
02AC2SOFTWARETHR A:168 , GLY A:188 , ILE A:189 , ARG A:196 , ASP A:199 , SER A:200 , GLY A:220 , GLY A:222 , DTT A:407 , NA A:408 , HOH A:510binding site for residue GLY A 402
03AC3SOFTWAREGLU A:239 , LEU B:233 , PHE B:236binding site for residue BME A 403
04AC4SOFTWARESER A:88 , ALA A:89 , VAL A:108 , MET A:109 , THR A:112 , HIS A:114 , CYS A:115 , LYS B:227binding site for residue BME A 404
05AC5SOFTWAREBME A:406 , HOH A:519 , GLY B:36 , ARG B:39 , PRO B:308binding site for residue BME A 405
06AC6SOFTWAREGLY A:26 , ARG A:29 , ALA A:54 , ASP A:58 , BME A:405 , PRO B:308binding site for residue BME A 406
07AC7SOFTWAREGLY A:11 , THR A:168 , VAL A:190 , THR A:219 , GLY A:220 , GLY A:402binding site for residue DTT A 407
08AC8SOFTWARETHR A:168 , ASP A:199 , SER A:200 , THR A:218 , GLY A:402binding site for residue NA A 408
09AC9SOFTWARELEU B:55 , GLU B:56 , ASP B:58 , PHE B:61 , ALA B:63 , CYS B:65binding site for residue NA B 401
10AD1SOFTWARETHR B:168 , GLY B:188 , ARG B:196 , ASP B:199 , SER B:200 , GLY B:220 , GLY B:222 , FLC B:403 , HOH B:505 , HOH B:507binding site for residue GLY B 402
11AD2SOFTWAREGLY B:11 , ASN B:62 , ARG B:147 , THR B:168 , ILE B:189 , THR B:219 , GLY B:220 , GLY B:402binding site for residue FLC B 403
12AD3SOFTWARELYS A:227 , SER B:88 , ALA B:89 , VAL B:108 , MET B:109 , THR B:112 , HIS B:114 , CYS B:115binding site for residue BME B 404
13AD4SOFTWARELEU C:55 , GLU C:56 , ASP C:58 , PHE C:61 , ALA C:63 , CYS C:65binding site for residue NA C 401
14AD5SOFTWARETHR C:168 , GLY C:188 , ARG C:196 , ASP C:199 , SER C:200 , GLY C:220 , GLY C:222 , ILE C:225 , NA C:409 , HOH C:506binding site for residue GLY C 402
15AD6SOFTWARESER C:88 , ALA C:89 , VAL C:108 , MET C:109 , THR C:112 , HIS C:114 , CYS C:115 , LYS D:227binding site for residue BME C 403
16AD7SOFTWAREGLY C:36 , HOH C:509 , ALA D:54 , ASP D:57binding site for residue BME C 404
17AD8SOFTWAREVAL C:33 , GLY C:50 , ALA C:54 , HOH C:513 , THR D:32 , GLY D:36 , BME D:404binding site for residue BME C 405
18AD9SOFTWAREGLY C:26 , ARG C:29 , ALA C:54 , LEU C:55 , ASP C:58 , PRO D:308 , BME D:404binding site for residue BME C 406
19AE1SOFTWAREGLY C:11 , ASN C:62 , THR C:168 , THR C:219 , GLY C:220binding site for residue DTT C 407
20AE2SOFTWAREASP C:78 , ALA C:94 , LYS C:192 , ARG C:196binding site for residue NA C 408
21AE3SOFTWARETHR C:168 , ASP C:199 , SER C:200 , THR C:218 , GLY C:402binding site for residue NA C 409
22AE4SOFTWARELEU D:55 , GLU D:56 , ASP D:58 , PHE D:61 , ALA D:63 , CYS D:65binding site for residue NA D 401
23AE5SOFTWARETHR D:168 , GLY D:188 , ILE D:189 , ARG D:196 , ASP D:199 , SER D:200 , GLY D:220 , GLY D:222 , FLC D:403 , HOH D:509 , HOH D:511binding site for residue GLY D 402
24AE6SOFTWAREGLY D:11 , ASN D:62 , THR D:168 , GLY D:188 , ILE D:189 , THR D:219 , GLY D:220 , GLY D:402binding site for residue FLC D 403
25AE7SOFTWAREVAL C:53 , ALA C:54 , ASP C:57 , BME C:405 , BME C:406 , PRO D:308binding site for residue BME D 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ZM9)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4ZM9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ZM9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZM9)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZM9)

(-) 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:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.........hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..................eeeeeee.....eeeeeee....hhhhhhhhhhhhh....eehhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhh..eeeeee.....eeeeeee....................eeee...eeeeeeehhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeee....eeeee......eeeee..eeeee.....eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zm9 A   1 GNPIVVVHGGGAGPISKDRKERVHQGMVRAATVGYGILREGGSAVDAVEGAVVALEDDPEFNAGCGSVLNTNGEVEMDASIMDGKDLSAGAVSAVQCIANPIKLARLVMEKTPHCFLTDQGAAQFAAAMGVPEIPGEKLVTERNKKRLEKEKHETVGAVALDCKGNVAYATSTGGIVNKMVGRVGDSPCLGAGGYADNDIGAVSTTGHGESILKVNLARLTLFHIEQGKTVEEAADLSLGYMKSRVKGLGGLIVVSKTGDWVAKWTSTSMPWAAAKDGKLHFGIDPDDTTITDLPG 309
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   ||  173       183       193       203       213       223       233       243       253       263       273       283       293       303      
                                                                                                                                                                                   154|                                                                                                                                             
                                                                                                                                                                                    168                                                                                                                                             

Chain B from PDB  Type:PROTEIN  Length:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..................eeeeeee.....eeeeeee....hhhhhhhhhhhhh....eehhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhh..eeeeee.....eeeeeee....................eeee...eeeeeeehhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeee....eeeee......eeeee..eeeee......eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zm9 B   1 GNPIVVVHGGGAGPISKDRKERVHQGMVRAATVGYGILREGGSAVDAVEGAVVALEDDPEFNAGCGSVLNTNGEVEMDASIMDGKDLSAGAVSAVQCIANPIKLARLVMEKTPHCFLTDQGAAQFAAAMGVPEIPGEKLVTERNKKRLEKEKHETVGAVALDCKGNVAYATSTGGIVNKMVGRVGDSPCLGAGGYADNDIGAVSTTGHGESILKVNLARLTLFHIEQGKTVEEAADLSLGYMKSRVKGLGGLIVVSKTGDWVAKWTSTSMPWAAAKDGKLHFGIDPDDTTITDLPG 309
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   ||  173       183       193       203       213       223       233       243       253       263       273       283       293       303      
                                                                                                                                                                                   154|                                                                                                                                             
                                                                                                                                                                                    168                                                                                                                                             

Chain C 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.....eeeeeee....hhhhhhhhhhhhh....eehhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhh..eeeeee.....eeeeeee....................eeee...eeeeeeehhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeee....eeeee......eeeee..eeeee.....eeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zm9 C   1 GNPIVVVHGGGAGPISKDRKERVHQGMVRAATVGYGILREGGSAVDAVEGAVVALEDDPEFNAGCGSVLNTNGEVEMDASIMDGKDLSAGAVSAVQCIANPIKLARLVMEKTPHCFLTDQGAAQFAAAMGVPEIPGEKLVTERNKKRLEKEKHETVGAVALDCKGNVAYATSTGGIVNKMVGRVGDSPCLGAGGYADNDIGAVSTTGHGESILKVNLARLTLFHIEQGKTVEEAADLSLGYMKSRVKGLGGLIVVSKTGDWVAKWTSTSMPWAAAKDGKLHFGIDPDDTTITDLPG 309
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   ||  173       183       193       203       213       223       233       243       253       263       273       283       293       303      
                                                                                                                                                                                   154|                                                                                                                                             
                                                                                                                                                                                    168                                                                                                                                             

Chain D from PDB  Type:PROTEIN  Length:296
                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..................eeeeeee.....eeeeeee....hhhhhhhhhhhhh....eehhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhh..eeeeee.....eeeeeee....................eeee...eeeeeeehhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh..eeeeeee....eeeee......eeeee..eeeee......eeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zm9 D   1 GNPIVVVHGGGAGPISKDRKERVHQGMVRAATVGYGILREGGSAVDAVEGAVVALEDDPEFNAGCGSVLNTNGEVEMDASIMDGKDLSAGAVSAVQCIANPIKLARLVMEKTPHCFLTDQGAAQFAAAMGVPEIPGEKLVTERNKKRLEKEKHETVGAVALDCKGNVAYATSTGGIVNKMVGRVGDSPCLGAGGYADNDIGAVSTTGHGESILKVNLARLTLFHIEQGKTVEEAADLSLGYMKSRVKGLGGLIVVSKTGDWVAKWTSTSMPWAAAKDGKLHFGIDPDDTTITDLPG 309
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150   ||  173       183       193       203       213       223       233       243       253       263       273       283       293       303      
                                                                                                                                                                                   154|                                                                                                                                             
                                                                                                                                                                                    168                                                                                                                                             

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  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 4ZM9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZM9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZM9)

(-) Gene Ontology  (11, 11)

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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 4pvq 4pvr 4pvs

(-) Related Entries Specified in the PDB File

4et0