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(-) Description

Title :  SOLUTION STRUCTURE OF UCHL1 S18Y VARIANT
 
Authors :  H. Tse
Date :  19 Jun 11  (Deposition) - 20 Jun 12  (Release) - 20 Jun 12  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
NMR Structure *:  A  (1x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Tse, K. Sze, H. Hu
Backbone And Side-Chain (1)H, (15)N And (13)C Resonance Assignments Of S18Y Mutant Of Ubiquitin Carboxy-Terminal Hydrolase L1
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - UBIQUITIN CARBOXYL-TERMINAL HYDROLASE ISOZYME L1
    ChainsA
    EC Number3.4.19.12
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainROSETTA BL21
    Expression System Taxid562
    Expression System VectorPET22B
    Expression System Vector TypeVECTOR
    GeneUCHL1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymUCH-L1, NEURON CYTOPLASMIC PROTEIN 9.5, PGP 9.5, PGP9.5, UBIQUITIN THIOESTERASE L1

 Structural Features

(-) Chains, Units

  1
NMR Structure (20x)A
NMR Structure * (1x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2LEN)

(-) Sites  (0, 0)

(no "Site" information available for 2LEN)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (5, 5)

NMR Structure (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_070875E7AUCHL1_HUMANDisease (SPG79)397515634AE7A
2UniProtVAR_015677S18YUCHL1_HUMANPolymorphism5030732AY18Y
3UniProtVAR_015678I93MUCHL1_HUMANDisease (PARK5)121917767AI93M
4UniProtVAR_078119R178QUCHL1_HUMANDisease (SPG79)768996179AR178Q
5UniProtVAR_078120A216DUCHL1_HUMANDisease (SPG79)  ---AA216D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
NMR Structure * (5, 5)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_070875E7AUCHL1_HUMANDisease (SPG79)397515634AE7A
2UniProtVAR_015677S18YUCHL1_HUMANPolymorphism5030732AY18Y
3UniProtVAR_015678I93MUCHL1_HUMANDisease (PARK5)121917767AI93M
4UniProtVAR_078119R178QUCHL1_HUMANDisease (SPG79)768996179AR178Q
5UniProtVAR_078120A216DUCHL1_HUMANDisease (SPG79)  ---AA216D

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

NMR Structure (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UCH_1PS00140 Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site.UCHL1_HUMAN84-100  1A:84-100
NMR Structure * (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1UCH_1PS00140 Ubiquitin carboxyl-terminal hydrolase family 1 cysteine active-site.UCHL1_HUMAN84-100  1A:84-100

(-) Exons   (9, 9)

NMR Structure (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.4aENST000002844404aENSE00001014976chr4:41258850-41259026177UCHL1_HUMAN1-11111A:1-1111
1.5aENST000002844405aENSE00001700600chr4:41259132-4125914312UCHL1_HUMAN12-1541A:12-154
1.5dENST000002844405dENSE00002143077chr4:41259626-41259754129UCHL1_HUMAN16-58431A:16-5843
1.6bENST000002844406bENSE00001720890chr4:41262664-41262814151UCHL1_HUMAN59-109511A:59-10951
1.7aENST000002844407aENSE00001014975chr4:41263732-4126381786UCHL1_HUMAN109-137291A:109-13729
1.8ENST000002844408ENSE00001014973chr4:41263893-4126394048UCHL1_HUMAN138-153161A:138-15316
1.9aENST000002844409aENSE00001014969chr4:41265242-4126530867UCHL1_HUMAN154-176231A:154-17623
1.10aENST0000028444010aENSE00001014974chr4:41266120-4126617859UCHL1_HUMAN176-195201A:176-19520
1.11hENST0000028444011hENSE00001852993chr4:41270004-41270446443UCHL1_HUMAN196-223281A:196-22328

(-) Sequences/Alignments

NMR Structure
   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:231
 aligned with UCHL1_HUMAN | P09936 from UniProtKB/Swiss-Prot  Length:223

    Alignment length:231
                                                                                                                                                                                                                                                        223        
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220  |      - 
          UCHL1_HUMAN     1 MQLKPMEINPEMLNKVLSRLGVAGQWRFVDVLGLEEESLGSVPAPACALLLLFPLTAQHENFRKKQIEELKGQEVSPKVYFMKQTIGNSCGTIGLIHAVANNQDKLGFEDGSVLKQFLSETEKMSPEDRAKCFEKNEAIQAAHDAVAQEGQCRVDDKVNFHFILFNNVDGHLYELDGRMPFPVNHGASSEDTLLKDAAKVCREFTEREQGEVRFSAVALCKAA--------   -
               SCOP domains d2lena_ A: Ubiquitin carboxyl-terminal hydrolase isozyme l1                                                                                                                                                                             SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhh.....eeee.....hhhhhh......eeeeeee..hhhhhhhhhhhhhhh....................hhhhhhhhhhhh.........hhhhhhhhhhh..hhhhhhhhhh..hhhhhhhhhhhhhh..........eeeeeeee..eeeeee......ee....hhhhhhhhhhhhhhhhhhhh.hhhhheeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ------A----------Y--------------------------------------------------------------------------M------------------------------------------------------------------------------------Q-------------------------------------D--------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------UCH_1            ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4a  1.5aExon 1.5d  PDB: A:16-58 UniProt: 16-58     Exon 1.6b  PDB: A:59-109 UniProt: 59-109           ----------------------------Exon 1.8        ----------------------Exon 1.10a          Exon 1.11h  PDB: A:196-223  -------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------Exon 1.7a  PDB: A:109-137    ----------------Exon 1.9a              ------------------------------------------------------- Transcript 1 (2)
                 2len A   1 MQLKPMEINPEMLNKVLYRLGVAGQWRFVDVLGLEEESLGSVPAPACALLLLFPLTAQHENFRKKQIEELKGQEVSPKVYFMKQTIGNSCGTIGLIHAVANNQDKLGFEDGSVLKQFLSETEKMSPEDRAKCFEKNEAIQAAHDAVAQEGQCRVDDKVNFHFILFNNVDGHLYELDGRMPFPVNHGASSEDTLLKDAAKVCREFTEREQGEVRFSAVALCKAALEHHHHHH 231
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230 

   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)

NMR Structure

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (42, 42)

NMR Structure(hide GO term definitions)
Chain A   (UCHL1_HUMAN | P09936)
molecular function
    GO:0031694    alpha-2A adrenergic receptor binding    Interacting selectively and non-covalently with an alpha-2A adrenergic receptor.
    GO:0004197    cysteine-type endopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    GO:0008234    cysteine-type peptidase activity    Catalysis of the hydrolysis of peptide bonds in a polypeptide chain by a mechanism in which the sulfhydryl group of a cysteine residue at the active center acts as a nucleophile.
    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:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0008242    omega peptidase activity    Catalysis of the removal of terminal peptide residues that are substituted, cyclized or linked by isopeptide bonds (peptide linkages other than those of alpha-carboxyl to alpha-amino groups).
    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:0004843    thiol-dependent ubiquitin-specific protease activity    Catalysis of the thiol-dependent hydrolysis of a peptide bond formed by the C-terminal glycine of ubiquitin and another protein.
    GO:0036459    thiol-dependent ubiquitinyl hydrolase activity    Catalysis of the thiol-dependent hydrolysis of an ester, thioester, amide, peptide or isopeptide bond formed by the C-terminal glycine of ubiquitin.
    GO:0043130    ubiquitin binding    Interacting selectively and non-covalently with ubiquitin, a protein that when covalently bound to other cellular proteins marks them for proteolytic degradation.
    GO:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0007628    adult walking behavior    The behavior of an adult relating to the progression of that organism along the ground by the process of lifting and setting down each leg.
    GO:0007412    axon target recognition    The process in which an axon recognizes and binds to a set of cells with which it may form stable connections.
    GO:0019896    axonal transport of mitochondrion    The directed movement of mitochondria along microtubules in nerve cell axons.
    GO:0007409    axonogenesis    De novo generation of a long process of a neuron, that carries efferent (outgoing) action potentials from the cell body towards target cells. Refers to the morphogenesis or creation of shape or form of the developing axon.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0042755    eating behavior    The specific behavior of an organism relating to the intake of food, any substance (usually solid) that can be metabolized by an organism to give energy and build tissue.
    GO:0048747    muscle fiber development    The process whose specific outcome is the progression of the muscle fiber over time, from its formation to the mature structure. In skeletal muscle, fibers are formed by the maturation of myotubes. They can be classed as slow, intermediate/fast or fast.
    GO:0043407    negative regulation of MAP kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of MAP kinase activity.
    GO:0050905    neuromuscular process    Any process pertaining to the functions of the nervous and muscular systems of an organism.
    GO:0043161    proteasome-mediated ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of ubiquitin, and mediated by the proteasome.
    GO:0016579    protein deubiquitination    The removal of one or more ubiquitin groups from a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0016241    regulation of macroautophagy    Any process that modulates the frequency, rate or extent of macroautophagy.
    GO:0002931    response to ischemia    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a inadequate blood supply.
    GO:0019233    sensory perception of pain    The series of events required for an organism to receive a painful stimulus, convert it to a molecular signal, and recognize and characterize the signal. Pain is medically defined as the physical sensation of discomfort or distress caused by injury or illness, so can hence be described as a harmful stimulus which signals current (or impending) tissue damage. Pain may come from extremes of temperature, mechanical damage, electricity or from noxious chemical substances. This is a neurological process.
    GO:0006511    ubiquitin-dependent protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein or peptide by hydrolysis of its peptide bonds, initiated by the covalent attachment of a ubiquitin group, or multiple ubiquitin groups, to the protein.
cellular component
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:1904115    axon cytoplasm    Any cytoplasm that is part of a axon.
    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:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    GO:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0043209    myelin sheath    An electrically insulating fatty layer that surrounds the axons of many neurons. It is an outgrowth of glial cells: Schwann cells supply the myelin for peripheral neurons while oligodendrocytes supply it to those of the central nervous system.
    GO:0044306    neuron projection terminus    The specialized, terminal region of a neuron projection such as an axon or a dendrite.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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 Related Entries

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

UniProtKB/Swiss-Prot
        UCHL1_HUMAN | P099362etl 3ifw 3irt 3kvf 3kw5 4dm9 4jkj

(-) Related Entries Specified in the PDB File

2etl RELATED ID: 17260 RELATED DB: BMRB
3ifw
3irt
3kvf
3kw5