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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ASPARTYL AMINOPEPTIDASE (DNPEP) IN COMPLEX WITH ASPARTIC ACID HYDROXAMATE
 
Authors :  A. Chaikuad, E. Pilka, M. Vollmar, T. Krojer, J. R. C. Muniz, F. Von Delf C. H. Arrowsmith, A. M. Edwards, J. Weigelt, C. Bountra, K. L. Kavanagh U. Oppermann, Structural Genomics Consortium (Sgc)
Date :  29 Feb 12  (Deposition) - 14 Mar 12  (Release) - 18 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (12x)
Biol. Unit 2:  A  (2x)
Keywords :  Structural Genomics, Structural Genomics Consortium, Sgc, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Chaikuad, E. S. Pilka, A. D. Riso, F. V. Delft, K. L. Kavanagh, C. Venien-Bryan, U. Oppermann, W. W. Yue
Structure Of Human Aspartyl Aminopeptidase Complexed With Substrate Analogue: Insight Into Catalytic Mechanism, Substrate Specificity And M18 Peptidase Family.
Bmc Struct. Biol. V. 12 14 2012
PubMed-ID: 22720794  |  Reference-DOI: 10.1186/1472-6807-12-14

(-) Compounds

Molecule 1 - ASPARTYL AMINOPEPTIDASE
    Chains: A
    EC Number: 3.4.11.21
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC-CTHF
    Expression System Strain: BL21(DE3)-R3-PRARE2
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: SEE REMARK 999
    Gene: ASPEP, DAP, DNPEP
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DNPEP

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 10)

Asymmetric Unit (4, 10)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
2MG1Ligand/IonMAGNESIUM ION
3SD41Ligand/IonN-HYDROXY-L-ASPARAGINE
4ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 84)
No.NameCountTypeFull Name
1GOL72Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
3SD412Ligand/IonN-HYDROXY-L-ASPARAGINE
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 14)
No.NameCountTypeFull Name
1GOL12Ligand/IonGLYCEROL
2MG-1Ligand/IonMAGNESIUM ION
3SD42Ligand/IonN-HYDROXY-L-ASPARAGINE
4ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:264 , GLU A:302 , HIS A:440 , ZN A:502 , SD4 A:504BINDING SITE FOR RESIDUE ZN A 501
02AC2SOFTWAREHIS A:94 , ASP A:264 , GLU A:302 , ASP A:346 , ZN A:501 , SD4 A:504BINDING SITE FOR RESIDUE ZN A 502
03AC3SOFTWAREHOH A:896 , HOH A:897BINDING SITE FOR RESIDUE MG A 503
04AC4SOFTWAREHIS A:94 , HIS A:170 , ASP A:264 , GLU A:301 , GLU A:302 , ASP A:346 , MET A:347 , HIS A:349 , LYS A:374 , TYR A:381 , GLY A:414 , THR A:415 , HIS A:440 , ZN A:501 , ZN A:502 , HOH A:866 , HOH A:891BINDING SITE FOR RESIDUE SD4 A 504
05AC5SOFTWARETHR A:67 , ARG A:68 , ASN A:69 , SER A:70 , ARG A:428BINDING SITE FOR RESIDUE GOL A 505
06AC6SOFTWAREPRO A:353 , ASN A:354 , TYR A:355 , LEU A:356 , ASP A:357 , HOH A:652BINDING SITE FOR RESIDUE GOL A 506
07AC7SOFTWAREARG A:105 , ASN A:362 , ARG A:364 , GLN A:403 , ASP A:404 , HOH A:783BINDING SITE FOR RESIDUE GOL A 507
08AC8SOFTWAREILE A:169 , HIS A:170 , ARG A:173 , HIS A:440BINDING SITE FOR RESIDUE GOL A 508
09AC9SOFTWAREARG A:424 , HOH A:864BINDING SITE FOR RESIDUE GOL A 509
10BC1SOFTWAREASP A:357 , LYS A:358 , ARG A:408 , ASP A:410 , HOH A:869BINDING SITE FOR RESIDUE GOL A 510

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Asp A:264 -Asn A:265

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4DYO)

(-) 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:457
 aligned with DNPEP_HUMAN | Q9ULA0 from UniProtKB/Swiss-Prot  Length:475

    Alignment length:467
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       
          DNPEP_HUMAN     7 GKARKEAVQTAAKELLKFVNRSPSPFHAVAECRNRLLQAGFSELKETEKWNIKPESKYFMTRNSSTIIAFAVGGQYVPGNGFSLIGAHTDSPCLRVKRRSRRSQVGFQQVGVETYGGGIWSTWFDRDLTLAGRVIVKCPTSGRLEQQLVHVERPILRIPHLAIHLQRNINENFGPNTEMHLVPILATAIQEELEKGTPEPGPLNAVDERHHSVLMSLLCAHLGLSPKDIVEMELCLADTQPAVLGGAYDEFIFAPRLDNLHSCFCALQALIDSCAGPGSLATEPHVRMVTLYDNEEVGSESAQGAQSLLTELVLRRISASCQHPTAFEEAIPKSFMISADMAHAVHPNYLDKHEENHRPLFHKGPVIKVNSKQRYASNAVSEALIREVANKVKVPLQDLMVRNDTPCGTTIGPILASRLGLRVLDLGSPQLAMHSIREMACTTGVLQTLTLFKGFFELFPSLSHNLL 473
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh..ee.............eeeeee...eeeeeee.........eeeeeee....eeeeeeeeeeee..eeeeeeeee...hhhhhh...eeeeeeeeee......eeeeeee...........hhhhh.................eeeehhhhhhhh..----------...hhhhhhhhhhhhh.hhh.eeeeeeeeee....eee.....eeee.hhhhhhhhhhhhhhhhhhh...........eeeeeee.hhhhh.........hhhhhhhhhhhh.....hhhhhhh...eeeee..ee.....hhhhh............eee.........hhhhhhhhhhhhhhhh...eee..........hhhhhhhhhhh.eeeeee.eee......eeeehhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dyo A   7 GKARKEAVQTAAKELLKFVNRSPSPFHAVAECRNRLLQAGFSELKETEKWNIKPESKYFMTRNSSTIIAFAVGGQYVPGNGFSLIGAHTDSPCLRVKRRSRRSQVGFQQVGVETYGGGIWSTWFDRDLTLAGRVIVKCPTSGRLEQQLVHVERPILRIPHLAIHLQRNINENFGPNTEMHLVPILATAIQEELEKGT----------ERHHSVLMSLLCAHLGLSPKDIVEMELCLADTQPAVLGGAYDEFIFAPRLDNLHSCFCALQALIDSCAGPGSLATEPHVRMVTLYDNEEVGSESAQGAQSLLTELVLRRISASCQHPTAFEEAIPKSFMISADMAHAVHPNYLDKHEENHRPLFHKGPVIKVNSKQRYASNAVSEALIREVANKVKVPLQDLMVRNDTPCGTTIGPILASRLGLRVLDLGSPQLAMHSIREMACTTGVLQTLTLFKGFFELFPSLAENLY 473
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196      |  -       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       
                                                                                                                                                                                                                              203        214
   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 4DYO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A   (DNPEP_HUMAN | Q9ULA0)
molecular function
    GO:0004177    aminopeptidase activity    Catalysis of the hydrolysis of N-terminal amino acid residues from in a polypeptide chain.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0006518    peptide metabolic process    The chemical reactions and pathways involving peptides, compounds of two or more amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0072562    blood microparticle    A phospholipid microvesicle that is derived from any of several cell types, such as platelets, blood cells, endothelial cells, or others, and contains membrane receptors as well as other proteins characteristic of the parental cell. Microparticles are heterogeneous in size, and are characterized as microvesicles free of nucleic acids.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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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