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(-) Description

Title :  CRYSTAL STRUCTURE OF AN ASPARTOACYLASE FROM RATTUS NORVEGICUS
 
Authors :  E. Bitto, G. E. Wesenberg, G. N. Phillips Jr. , C. A. Bingman, Center Fo Eukaryotic Structural Genomics (Cesg)
Date :  28 Apr 06  (Deposition) - 20 Jun 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A,B  (2x)
Keywords :  Aspartoacylase Family, Aminoacylase-2, Acy-2, Acy2_rat, Structural Genomics, Psi, Protein Structure Initiative, Center For Eukaryotic Structural Genomics, Cesg, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Bitto, C. A. Bingman, G. E. Wesenberg, J. G. Mccoy, G. N. Phillips
Structure Of Aspartoacylase, The Brain Enzyme Impaired In Canavan Disease.
Proc. Natl. Acad. Sci. Usa V. 104 456 2007
PubMed-ID: 17194761  |  Reference-DOI: 10.1073/PNAS.0607817104

(-) Compounds

Molecule 1 - ASPA PROTEIN
    Chains: A, B
    EC Number: 3.5.1.15
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PVP 16
    Expression System Strain: BL834 P(RARE2)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: BC078813, UNIPROT-Q9R1T5
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 21)

Asymmetric Unit (3, 21)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
2SO45Ligand/IonSULFATE ION
3ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 19)
No.NameCountTypeFull Name
1MSE14Mod. Amino AcidSELENOMETHIONINE
2SO45Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 38)
No.NameCountTypeFull Name
1MSE28Mod. Amino AcidSELENOMETHIONINE
2SO410Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:20 , GLU A:23 , HIS A:115 , HOH A:748BINDING SITE FOR RESIDUE ZN A 601
2AC2SOFTWAREHIS B:20 , GLU B:23 , HIS B:115 , HOH B:733BINDING SITE FOR RESIDUE ZN B 602
3AC3SOFTWAREASP A:73 , LEU A:74 , LYS A:102 , TYR A:163 , HOH A:836 , ARG B:308 , THR B:310BINDING SITE FOR RESIDUE SO4 A 701
4AC4SOFTWAREARG A:196 , LYS A:199 , HIS A:200BINDING SITE FOR RESIDUE SO4 A 702
5AC5SOFTWARECYS A:60 , THR A:61 , HOH A:772 , HOH A:779 , HOH A:796 , HOH A:970 , HOH A:989 , THR B:61 , HOH B:801BINDING SITE FOR RESIDUE SO4 A 703
6AC6SOFTWAREHIS B:20 , ARG B:62 , ASP B:67 , ASN B:69 , ARG B:70 , TYR B:287 , LYS B:290 , HOH B:733 , HOH B:926BINDING SITE FOR RESIDUE SO4 B 704
7AC7SOFTWAREARG B:196 , LYS B:199 , HIS B:200 , HOH B:920BINDING SITE FOR RESIDUE SO4 B 705

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2GU2)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Gly A:100 -Pro A:101
2Ala A:147 -Pro A:148
3Gly A:179 -Pro A:180
4Gly B:100 -Pro B:101
5Ala B:147 -Pro B:148
6Gly B:179 -Pro B:180

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2GU2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2GU2)

(-) Exons   (0, 0)

(no "Exon" information available for 2GU2)

(-) 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:307
 aligned with ACY2_RAT | Q9R1T5 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:307
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       
             ACY2_RAT     4 CVAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVHRAGLEVKPFITNPRAVEKCTRYIDCDLNRVFDLENLSKEMSEDLPYEVRRAQEINHLFGPKNSDDAYDVVFDLHNTTSNMGCTLILEDSRNDFLIQMFHYIKTCMAPLPCSVYLIEHPSLKYATTRSIAKYPVGIEVGPQPHGVLRADILDQMRRMLKHALDFIQRFNEGKEFPPCAIDVYKIMEKVDYPRNESGDVAAVIHPNLQDQDWKPLHPGDPVFVSLDGKVIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTKLTLNAKSIRST 310
               SCOP domains d2gu2a1 A:4-310 Aspartoacylase AspA                                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eeeeee.....hhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhh.......hhhhh.hhhhhh.......hhhhhhhhhhhhhhh.........eeeeeee.....eeeeee....hhhhhhhhhhhhhhhh...eeeee.........hhhhhh.eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeeeeeeee............ee................eeee.....eee.......eee...hhhhh.....eeeeeeeeeee..eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gu2 A   4 CVAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVHRAGLEVKPFITNPRAVEKCTRYIDCDLNRVFDLENLSKEmSEDLPYEVRRAQEINHLFGPKNSDDAYDVVFDLHNTTSNmGCTLILGDSGNDFLIQmFHYIKTCmAPLPCSVYLIEHPSLKYATTRSIAKYPVGIEVGPQPHGVLRADILDQmRRmLKHALDFIQRFNEGKEFPPCAIDVYKImEKVDYPRNESGDVAAVIHPNLQDQDWKPLHPGDPVFVSLDGKVIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTKLTLNAKSIRST 310
                                    13        23        33        43        53        63        73       |83        93       103       113       123       133    |  143  |    153       163       173       183       193|  |   203       213       223 |     233       243       253       263       273       283       293       303       
                                                                                                        81-MSE                                 121-MSE          138-MSE 146-MSE                                         194-MSE                        225-MSE                                                                                 
                                                                                                                                                                                                                           197-MSE                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:307
 aligned with ACY2_RAT | Q9R1T5 from UniProtKB/Swiss-Prot  Length:312

    Alignment length:307
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       
             ACY2_RAT     4 CVAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVHRAGLEVKPFITNPRAVEKCTRYIDCDLNRVFDLENLSKEMSEDLPYEVRRAQEINHLFGPKNSDDAYDVVFDLHNTTSNMGCTLILEDSRNDFLIQMFHYIKTCMAPLPCSVYLIEHPSLKYATTRSIAKYPVGIEVGPQPHGVLRADILDQMRRMLKHALDFIQRFNEGKEFPPCAIDVYKIMEKVDYPRNESGDVAAVIHPNLQDQDWKPLHPGDPVFVSLDGKVIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTKLTLNAKSIRST 310
               SCOP domains d2gu2b_ B: Aspartoacylase AspA                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee....eeeeee.....hhhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhh......hhhhh.hhhhhh.......hhhhhhhhhhhhhhh.........eeeeeee.....eeeeee....hhhhhhhhhhhhhhhh....eeee..hhhhhh.hhhhhh.eeeeeeee.......hhhhhhhhhhhhhhhhhhhhhhhh......eeeeeeeeeeee............ee................eeee.....eee.......eee...hhhhh.....eeeeeeeeeee..eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gu2 B   4 CVAEEPIKKIAIFGGTHGNELTGVFLVTHWLKNGAEVHRAGLEVKPFITNPRAVEKCTRYIDCDLNRVFDLENLSKEmSEDLPYEVRRAQEINHLFGPKNSDDAYDVVFDLHNTTSNmGCTLILGDSGNDFLIQmFHYIKTCmAPLPCSVYLIEHPSLKYATTRSIAKYPVGIEVGPQPHGVLRADILDQmRRmLKHALDFIQRFNEGKEFPPCAIDVYKImEKVDYPRNESGDVAAVIHPNLQDQDWKPLHPGDPVFVSLDGKVIPLGGDCTVYPVFVNEAAYYEKKEAFAKTTKLTLNAKSIRST 310
                                    13        23        33        43        53        63        73       |83        93       103       113       123       133    |  143  |    153       163       173       183       193|  |   203       213       223 |     233       243       253       263       273       283       293       303       
                                                                                                        81-MSE                                 121-MSE          138-MSE 146-MSE                                         194-MSE                        225-MSE                                                                                 
                                                                                                                                                                                                                           197-MSE
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2GU2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2GU2)

(-) Gene Ontology  (10, 10)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (ACY2_RAT | Q9R1T5)
molecular function
    GO:0019807    aspartoacylase activity    Catalysis of the reaction: N-acyl-L-aspartate + H2O = a fatty acid anion + L-aspartate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0016811    hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides    Catalysis of the hydrolysis of any non-peptide carbon-nitrogen bond in a linear amide.
    GO:0016788    hydrolase activity, acting on ester bonds    Catalysis of the hydrolysis of any ester bond.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0022010    central nervous system myelination    The process in which neuronal axons and dendrites become coated with a segmented lipid-rich sheath (myelin) to enable faster and more energetically efficient conduction of electrical impulses. The sheath is formed by the cell membranes of oligodendrocytes in the central nervous system. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0048714    positive regulation of oligodendrocyte differentiation    Any process that activates or increases the frequency, rate or extent of oligodendrocyte differentiation.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ACY2_RAT | Q9R1T5: 2q4z

(-) Related Entries Specified in the PDB File

2i3c ASPARTOACYLASE FROM HOMO SAPIENS