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(-) Description

Title :  CRYSTAL STRUCTURE OF ENGINEERED NEUROLYSIN WITH THIMET OLIGOPEPTIDASE SPECIFICITY FOR NEUROTENSIN CLEAVAGE SITE.
 
Authors :  D. W. Rodgers, E. J. Lim
Date :  01 Dec 06  (Deposition) - 23 Jan 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Thermolysin-Like Domain, Substrate-Binding Channel, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. J. Lim, S. Sampath, J. Coll-Rodriguez, J. Schmidt, K. Ray, D. W. Rodgers
Swapping The Substrate Specificities Of The Neuropeptidases Neurolysin And Thimet Oligopeptidase.
J. Biol. Chem. V. 282 9722 2007
PubMed-ID: 17251185  |  Reference-DOI: 10.1074/JBC.M609897200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - NEUROLYSIN
    Chains: A
    EC Number: 3.4.24.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD
    Expression System Strain: TOP10
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: NLN
    Mutation: YES
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: NEUROTENSIN ENDOPEPTIDASE, MITOCHONDRIAL OLIGOPEPTIDASE M, MICROSOMAL ENDOPEPTIDASE, MEP

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1ZN1Ligand/IonZINC ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:474 , HIS A:478 , GLU A:503 , HOH A:888BINDING SITE FOR RESIDUE ZN A 679

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O3E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2O3E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O3E)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.NEUL_RAT494-503  1A:471-480

(-) Exons   (0, 0)

(no "Exon" information available for 2O3E)

(-) 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:665
 aligned with NEUL_RAT | P42676 from UniProtKB/Swiss-Prot  Length:704

    Alignment length:665
                                    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       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616       626       636       646       656       666       676       686       696     
             NEUL_RAT    37 MSSYTAAGRNVLRWDLSPEQIKTRTEQLIAQTKQVYDTVGTIALKEVTYENCLQVLADIEVTYIVERTMLDFPQHVSSDREVRAASTEADKKLSRFDIEMSMREDVFQRIVHLQETCDLEKIKPEARRYLEKSIKMGKRNGLHLSEHIRNEIKSMKKRMSELCIDFNKNLNEDDTSLVFSKAELGALPDDFIDSLEKTDEDKYKVTLKYPHYFPVMKKCCVPETRRKMEMAFHTRCKQENTAILQQLLPLRAQVAKLLGYNTHADFVLELNTAKSTSRVAAFLDDLSQKLKPLGEAEREFILSLKKKECEERGFEYDGKINAWDLHYYMTQTEELKYSVDQESLKEYFPIEVVTEGLLSIYQELLGLSFEQVPDAHVWNKSVSLYTVKDKATGEVLGQFYLDLYPREGKYNHAACFGLQPGCLLPDGSRMMSVAALVVNFSQPVAGRPSLLRHDEVRTYFHEFGHVMHQICAQTDFARFSGTNVETDFVEVPSQMLENWVWDVDSLRKLSKHYKDGHPITDELLEKLVASRLVNTGLLTLRQIVLSKVDQSLHTNATLDAASEYAKYCTEILGVAATPGTNMPATFGHLAGGYDGQYYGYLWSEVFSMDMFHSCFKKEGIMNPEVGMKYRNLILKPGGSLDGMDMLQNFLQREPNQKAFLMSRGL 701
               SCOP domains d2o3ea_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2o3eA01 A:14-152 Endopeptidase. Chain P; domain 1                                                                                          2o3eA02 A:153-361,A:513-678 Neurolysin, domain 3                                                                                                                                                                 2o3eA03 A:362-512 Collagenase (Catalytic Domain)                                                                                                       2o3eA02 A:153-361,A:513-678 Neurolysin, domain 3                                                                                                                       CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhh.......eeeee.hhhhhhhhhhhh.hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhheeeee...........eeeeeee.....eeeeeeee...........eeeeee............eeeeee..............hhhhhhhhhhhhhhhhhhhhh...hhhhh.........hhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhh.........hhhhhh...........hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh.hhhhhhhhhhhhhhhh....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2o3e A  14 MSSYTAAGRNVLRWDLSPEQIKTRTEQLIAQTKQVYDTVGTIALKEVTYENCLQVLADIEVTYIVERTMLDFPQHVSSDREVRAASTEADKKLSRFDIEMSMREDVFQRIVHLQETCDLEKIKPEARRYLEKSIKMGKRNGLHLSEHIRNEIKSMKKRMSELCIDFNKNLNEDDTSLVFSKAELGALPDDFIDSLEKTDEDKYKVTLKYPHYFPVMKKCCVPETRRKMEMAFHTRCKQENTAILQQLLPLRAQVAKLLGYNTHADFVLELNTAKSTSRVAAFLDDLSQKLKPLGEAEREFILSLKKKECEERGFEYDGKINAWDLHYYMTQTEELKYSVDQESLKEYFPIEVVTEGLLSIYQELLGLSFEQVPDAHVWNKSVSLYTVKDKATGEVLGQFYLDLYPREGKYNHAACFGLQPGCLLPDGSRMMSVAALVVNFSQPVAGRPSLLRHDEVETYFHEFGHVMHQICAQTDFARFSGTNVERDFVEVPSQMLENWVWDVDSLRKLSKHYKDGHPITDELLEKLVASRLVNTGLLTLRQIVLSKVDQSLHTNATLDAASEYAKYCTEILGVAATPGTNMPATFGHLAGGYDGQYYGYLWSEVFSMDMFHSCFKKEGIMNPEVGMKYRNLILKPGGSLDGMDMLQNFLQREPNQKAFLMSRGL 678
                                    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       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673
   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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2O3E)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NEUL_RAT | P42676)
molecular function
    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:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain 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: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:0070012    oligopeptidase activity    Catalysis of the hydrolysis of a peptide bond in an oligopeptide, i.e. a molecule containing a small number (2 to 20) of amino acid residues connected by peptide bonds.
    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.
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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0005758    mitochondrial intermembrane space    The region between the inner and outer lipid bilayers of the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NEUL_RAT | P42676: 1i1i 4fxy

(-) Related Entries Specified in the PDB File

1i1i NEUROLYSIN (ENDOPEPTIDASE 24.16) CRYSTAL STRUCTURE