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(-) Description

Title :  AUTOPHAGIN2
 
Authors :  N. Vidya, R. Mahmood, D. Sivakumar, S. Alex
Date :  28 Jan 06  (Deposition) - 14 Feb 06  (Release) - 14 Feb 06  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Apg4A (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  N. Vidya, R. Mahomood, D. Sivakumar, S. Alex
Atg4A
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYSTEINE PROTEASE ATG4A
    ChainsA
    EC Number3.4.22.-
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    SynonymAUTOPHAGY-RELATED PROTEIN 4 HOMOLOG A, HAPG4A, AUTOPHAGIN-2, AUTOPHAGY-RELATED CYSTEINE ENDOPEPTIDASE 2, AUT-LIKE 2 CYSTEINE ENDOPEPTIDASE

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2FUY)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (13, 13)

Theoretical Model (13, 13)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003722321aENSE00001837761X:107334898-107335066169ATG4A_HUMAN1-441A:1-44
1.2ENST000003722322ENSE00001642643X:107369307-107369417111ATG4A_HUMAN4-41381A:4-4138
1.4ENST000003722324ENSE00001713101X:107372011-10737208272ATG4A_HUMAN41-65251A:41-6525
1.5ENST000003722325ENSE00001652224X:107374490-10737458899ATG4A_HUMAN65-98341A:65-9834
1.6ENST000003722326ENSE00001771808X:107377287-107377388102ATG4A_HUMAN98-132351A:98-13235
1.7ENST000003722327ENSE00001796296X:107377569-10737764173ATG4A_HUMAN132-156251A:132-15625
1.8ENST000003722328ENSE00001651608X:107380321-10738040080ATG4A_HUMAN156-183281A:156-18328
1.9bENST000003722329bENSE00001779238X:107381034-107381221188ATG4A_HUMAN183-245631A:183-24563
1.10ENST0000037223210ENSE00001644003X:107381343-10738142179ATG4A_HUMAN246-272271A:246-27227
1.11dENST0000037223211dENSE00001776484X:107393382-107393527146ATG4A_HUMAN272-320491A:272-32049
1.12aENST0000037223212aENSE00002155558X:107395032-10739508857ATG4A_HUMAN321-339191A:321-33919
1.13bENST0000037223213bENSE00001690116X:107396209-107396317109ATG4A_HUMAN340-376371A:340-37637
1.14cENST0000037223214cENSE00001891122X:107396872-1073979011030ATG4A_HUMAN376-398231A:376-39823

(-) Sequences/Alignments

Theoretical Model
   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:398
 aligned with ATG4A_HUMAN | Q8WYN0 from UniProtKB/Swiss-Prot  Length:398

    Alignment length:398
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390        
          ATG4A_HUMAN     1 MESVLSKYEDQITIFTDYLEEYPDTDELVWILGKQHLLKTEKSKLLSDISARLWFTYRRKFSPIGGTGPSSDAGWGCMLRCGQMMLAQALICRHLGRDWSWEKQKEQPKEYQRILQCFLDRKDCCYSIHQMAQMGVGEGKSIGEWFGPNTVAQVLKKLALFDEWNSLAVYVSMDNTVVIEDIKKMCRVLPLSADTAGDRPPDSLTASNQSKGTSAYCSAWKPLLLIVPLRLGINQINPVYVDAFKECFKMPQSLGALGGKPNNAYYFIGFLGDELIFLDPHTTQTFVDTEENGTVNDQTFHCLQSPQRMNILNLDPSVALGFFCKEEKDFDNWCSLVQKEILKENLRMFELVQKHPSHWPPFVPPAKPEVTTTGAEFIDSTEQLEEFDLEEDFEILSV 398
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh...........eee..eeehhhhhhhhhhhhhhhh....eee................hhhhhhhhhhhhhhhhhhhh............hhhhhhhhhh.........hhhhhhhhhhhh........hhhhhhhhhhhhhh.......eeee....eeehhhhhhhhh...................................eeeeeeee......hhhhhhhhhhhhh...eeeeeeee..eeeeeeeee..eeeee....eee...........hhhhh.....eeee.hhh..eeeeeeee.hhhhhhhhhhhhhhhh........eee............hhhhhhh........................... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1a------------------------------------Exon 1.4  PDB: A:41-65   --------------------------------Exon 1.6  PDB: A:98-132            -----------------------Exon 1.8  PDB: A:156-183    --------------------------------------------------------------Exon 1.10  PDB: A:246-272  ------------------------------------------------Exon 1.12a         Exon 1.13b  PDB: A:340-376           ---------------------- Transcript 1 (1)
           Transcript 1 (2) ---Exon 1.2  PDB: A:4-41 UniProt: 4-41   -----------------------Exon 1.5  PDB: A:65-98            ---------------------------------Exon 1.7  PDB: A:132-156 --------------------------Exon 1.9b  PDB: A:183-245 UniProt: 183-245                     --------------------------Exon 1.11d  PDB: A:272-320 UniProt: 272-320      -------------------------------------------------------Exon 1.14c              Transcript 1 (2)
                 2fuy A   1 MESVLSKYEDQITIFTDYLEEYPDTDELVWILGKQHLLKTEKSKLLSDISARLWFTYRRKFSPIGGTGPSSDAGWGCMLRCGQMMLAQALICRHLGRDWSWEKQKEQPKEYQRILQCFLDRKDCCYSIHQMAQMGVGEGKSIGEWFGPNTVAQVLKKLALFDEWNSLAVYVSMDNTVVIEDIKKMCRVLPLSADTAGDRPPDSLTASNQSKGTSAYCSAWKPLLLIVPLRLGINQINPVYVDAFKECFKMPQSLGALGGKPNNAYYFIGFLGDELIFLDPHTTQTFVDTEENGTVNDQTFHCLQSPQRMNILNLDPSVALGFFCKEEKDFDNWCSLVQKEILKENLRMFELVQKHPSHWPPFVPPAKPEVTTTGAEFIDSTEQLEEFDLEEDFEILSV 398
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390        

   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 2FUY)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Theoretical Model(hide GO term definitions)
Chain A   (ATG4A_HUMAN | Q8WYN0)
molecular function
    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: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).
biological process
    GO:0006501    C-terminal protein lipidation    The covalent attachment of a lipid group to the carboxy terminus of a protein.
    GO:0000045    autophagosome assembly    The formation of a double membrane-bounded structure, the autophagosome, that occurs when a specialized membrane sac, called the isolation membrane, starts to enclose a portion of the cytoplasm.
    GO:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    GO:0000422    autophagy of mitochondrion    The autophagic process in which mitochondria are delivered to the vacuole and degraded in response to changing cellular conditions.
    GO:0044804    autophagy of nucleus    A selective form of autophagy, by which damaged or non-essential parts of the nucleus, or even an entire nucleus is degraded.
    GO:0051697    protein delipidation    The breakage of covalent bonds to detach lipid groups from a protein.
    GO:0016485    protein processing    Any protein maturation process achieved by the cleavage of a peptide bond or bonds within a protein. Protein maturation is the process leading to the attainment of the full functional capacity of a protein.
    GO:0006612    protein targeting to membrane    The process of directing proteins towards a membrane, usually using signals contained within the protein.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
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.

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        ATG4A_HUMAN | Q8WYN02p82

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