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(-) Description

Title :  CRYSTAL STRUCTURE OF TRUNCATED PYROCOCCUS FURIOSUS L-ASPARAGINASE WITH PEPTIDE
 
Authors :  P. Sharma, R. Tomar, S. K. Nath, B. Kundu, Ashish
Date :  23 May 16  (Deposition) - 31 May 17  (Release) - 31 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.61
Chains :  Asym. Unit :  A,B,C,E
Biol. Unit 1:  A,B,C,E  (2x)
Keywords :  Truncated Pyrococcus Furiosus L-Asparaginase, Linkerless, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Sharma, R. Tomar, S. K. Nath, B. Kundu, Ashish
Crystal Structure Of Truncated Pyrococcus Furiosus L-Asparaginase With Peptide
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - L-ASPARAGINASE
    Chains: A
    EC Number: 3.5.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: N-TERMINAL DOMAIN UNP RESIDUES 1-178
    Gene: PF2047
    Organism Scientific: PYROCOCCUS FURIOSUS DSM 3638
    Organism Taxid: 186497
    Strain: DSM 3638
 
Molecule 2 - L-ASPARAGINASE
    Chains: B
    EC Number: 3.5.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-28A
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: C-TERMINAL DOMAIN UNP RESIDUES 202-326
    Gene: PF2047
    Organism Scientific: PYROCOCCUS FURIOSUS DSM 3638
    Organism Taxid: 186497
    Strain: DSM 3638
 
Molecule 3 - LEU-VAL-VAL-ASN
    Chains: C, E
    Engineered: YES
    Organism Scientific: PYROCOCCUS FURIOSUS
    Organism Taxid: 2261
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCE
Biological Unit 1 (2x): ABCE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1ASP1Mod. Amino AcidASPARTIC ACID
2CL2Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL
4IPA2Ligand/IonISOPROPYL ALCOHOL
Biological Unit 1 (3, 12)
No.NameCountTypeFull Name
1ASP2Mod. Amino AcidASPARTIC ACID
2CL-1Ligand/IonCHLORIDE ION
3GOL6Ligand/IonGLYCEROL
4IPA4Ligand/IonISOPROPYL ALCOHOL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:10 , THR A:11 , ASP A:51 , SER A:52 , GLY A:82 , THR A:83 , ASP A:84 , SER A:109 , MET A:110 , TYR B:273binding site for residue ASP A 201
2AC2SOFTWAREVAL A:71 , ASN A:99binding site for residue IPA A 203
3AC3SOFTWAREASP A:46 , LEU A:47 , ASN A:49binding site for residue IPA A 204
4AC4SOFTWAREGLY A:10 , THR A:11 , ALA A:13 , SER A:14 , SER A:24 , ASN A:49 , VAL A:50 , ASP A:51binding site for residue GOL A 205
5AC5SOFTWAREVAL A:71 , LYS A:72 , TYR A:74 , ASP A:75 , PRO A:101 , ILE A:102 , ASN B:319 , ARG B:325 , ASP B:326binding site for residue GOL A 206
6AC6SOFTWARESER A:165 , TYR A:168binding site for residue GOL A 207
7AC7SOFTWAREASP B:214binding site for residue CL B 401

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:39 -A:42

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5B5U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5B5U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5B5U)

(-) Exons   (0, 0)

(no "Exon" information available for 5B5U)

(-) 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:176
                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee.hhhh...........hhhhhhhhhh......eeeeeeeeehhhhhhhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhh.....eeeee...........hhhhhhhhhhhhhh....eeeeee..eeee...eee........eee......ee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b5u A   1 MKILLIGMGGTIASVKGENGYEASLSVKEVLDIAGIKDCEDCDFLDLKNVDSTLIQPEDWVDLAETLYKNVKKYDGIIVTHGTDTLAYTSSMISFMLRNPPIPIVFTGSMIPATEENSDAPLNLQTAIKFATSGIRGVYVAFNGKVMLGVRTSKVRTMSRDAFESINYPIIAELRD 201
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170    ||
                                                                                                                                                                                                        175|
                                                                                                                                                                                                         201


Chain B from PDB  Type:PROTEIN  Length:127
                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee......hhhhhhhhhhh..eeeeee...........hhhhhhhhhh....eeeee...........hhhhhhhhhh..ee....hhhhhhhhhhhhhh...hhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5b5u B 200 MAVLVIKLIPGLSGDIFRAAVELGYRGIVIEGYGAGGIPYRGSDLLQTIEELSKEIPIVMTTQAMYDGVDLTRYKVGRLALRAGVIPAGDMTKEATVTKLMWILGHTNNVEEIKVLMRKNLVGELRD 326
                                   209       219       229       239       249       259       269       279       289       299       309       319       


Chain C from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 5b5u C   1 LVVN   4


Chain E from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 5b5u E   1 LVVN   4
   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 5B5U)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5B5U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5B5U)

(-) Gene Ontology  (2, 2)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        Q8TZE8_PYRFU | Q8TZE8: 5b74
UniProtKB/TrEMBL
        Q8TZE8_PYRFU | Q8TZE8: 4nje 4q0m 4ra6 4ra9 5cbp

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