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(-) Description

Title :  A20 OTU DOMAIN IN REVERSIBLY OXIDISED (SOH) STATE
 
Authors :  Y. Kulathu, F. J. Garcia, T. E. T. Mevissen, M. Busch, N. Arnaudo, K. S. Ca D. Barford, D. Komander
Date :  17 Jan 13  (Deposition) - 06 Mar 13  (Release) - 20 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.84
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Ubiquitin, Deubiquitinating Enzyme, Reversible Oxidation, Sulphenic Acid, Cys Protease (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Kulathu, F. J. Garcia, T. E. T. Mevissen, M. Busch, N. Arnaudo, K. S. Carroll, D. Barford, D. Komander
Regulation Of A20 And Other Otu Deubiquitinases By Reversible Oxidation
Nat. Commun. V. 4 1569 2013
PubMed-ID: 23463012  |  Reference-DOI: 10.1038/NCOMMS2567

(-) Compounds

Molecule 1 - A20P50
    ChainsA, B
    EC Number3.4.19.12, 6.3.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System VectorPGEX6P1
    Expression System Vector TypePLASMID
    FragmentOTU DOMAIN, RESIDUES 1-366
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCATALYTIC CYS103 IS REVERSIBLY OXIDISED FORMING A CYS SULPHENIC ACID (SOH).
    SynonymTUMOR NECROSIS FACTOR ALPHA-INDUCED PROTEIN 3, TNF ALPHA-INDUCED PROTEIN 3, A20, OTU DOMAIN-CONTAINING PROTEIN 7C, PUTATIVE DNA-BINDING PROTEIN A20, ZINC FINGER PROTEIN A20

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1CL6Ligand/IonCHLORIDE ION
2CSO2Mod. Amino AcidS-HYDROXYCYSTEINE
3EDO2Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:22 , THR A:25 , ASP A:117 , THR A:118 , ASP A:119 , LEU A:120 , VAL A:121 , HOH A:2068BINDING SITE FOR RESIDUE EDO A1357
2AC2SOFTWAREHIS A:44 , ARG A:45 , ARG A:204 , GLU A:242 , CYS A:243 , TYR A:244BINDING SITE FOR RESIDUE EDO A1358
3AC3SOFTWAREGLU A:311 , GLY B:281 , TRP B:317BINDING SITE FOR RESIDUE CL B1358
4AC4SOFTWARECYS B:86 , ARG B:87 , ARG B:278 , HOH B:2057BINDING SITE FOR RESIDUE CL B1359
5AC5SOFTWARETRP B:317 , ASP B:318 , HIS B:323BINDING SITE FOR RESIDUE CL B1360
6AC6SOFTWAREGLY A:230 , GLY A:231 , LYS A:287 , HOH A:2104 , HOH A:2108BINDING SITE FOR RESIDUE CL A1359
7AC7SOFTWARELYS B:287 , HOH B:2128BINDING SITE FOR RESIDUE CL B1361
8AC8SOFTWARELYS A:213 , MET A:214 , LEU A:227BINDING SITE FOR RESIDUE CL A1360

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3ZJE)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:267 -Pro A:268

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric/Biological Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020447A125VTNAP3_HUMANPolymorphism5029941A/BA125V
2UniProtVAR_022143F127CTNAP3_HUMANPolymorphism2230926A/BF127C
3UniProtVAR_076302C243YTNAP3_HUMANDisease (AISBL)  ---A/BC243Y

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1OTUPS50802 OTU domain profile.TNAP3_HUMAN92-263
 
  2A:92-263
B:92-263

(-) Exons   (6, 12)

Asymmetric/Biological Unit (6, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1cENST000002372891cENSE00001013057chr6:138188581-13818863151TNAP3_HUMAN-00--
1.3bENST000002372893bENSE00002202018chr6:138192350-138192659310TNAP3_HUMAN1-99992A:5-99
B:5-99
95
95
1.4ENST000002372894ENSE00002197706chr6:138195982-138196172191TNAP3_HUMAN99-162642A:99-162 (gaps)
B:99-153
64
55
1.5ENST000002372895ENSE00000764532chr6:138196825-138196972148TNAP3_HUMAN163-212502A:163-212 (gaps)
B:164-212 (gaps)
50
49
1.6bENST000002372896bENSE00000764533chr6:138197133-138197303171TNAP3_HUMAN212-269582A:212-269 (gaps)
B:212-269 (gaps)
58
58
1.7ENST000002372897ENSE00002165528chr6:138198213-138198393181TNAP3_HUMAN269-329612A:269-329
B:269-329
61
61
1.8bENST000002372898bENSE00000764536chr6:138199569-138200488920TNAP3_HUMAN329-6363082A:329-356
B:329-357
28
29
1.9ENST000002372899ENSE00000764537chr6:138201208-138201389182TNAP3_HUMAN636-696610--
1.10ENST0000023728910ENSE00000798910chr6:138202172-1382044492278TNAP3_HUMAN697-790940--

(-) 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:329
 aligned with TNAP3_HUMAN | P21580 from UniProtKB/Swiss-Prot  Length:790

    Alignment length:352
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354  
          TNAP3_HUMAN     5 VLPQALYLSNMRKAVKIRERTPEDIFKPTNGIIHHFKTMHRYTLEMFRTCQFCPQFREIIHKALIDRNIQATLESQKKLNWCREVRKLVALKTNGDGNCLMHATSQYMWGVQDTDLVLRKALFSTLKETDTRNFKFRWQLESLKSQEFVETGLCYDTRNWNDEWDNLIKMASTDTPMARSGLQYNSLEEIHIFVLCNILRRPIIVISDKMLRSLESGSNFAPLKVGGIYLPLHWPAQECYRYPIVLGYDSHHFVPLVTLKDSGPEIRAVPLVNRDRGRFEDLKVHFLTDPENEMKEKLLKEYLMVIEIPVQGWDHGTTHLINAAKLDEANLPKEINLVDDYFELVQHEYKKW 356
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhee........ee.hhhhh..ee......hhhhhhhhhhhhhhhhhhhhhhhh...........eee.......hhhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhh.----------...hhhhhhhhhhhhh.....----.......hhhhhhhhhhhhh..eeeee.......--------....eee.....hhhhh....eeeeee..eeeeeeee..-.....eee.eeee..eeee......hhhhhhhhhhhhhhhh.eeeeeee......eeeeeeee......hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------V-C-------------------------------------------------------------------------------------------------------------------Y----------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------OTU  PDB: A:92-263 UniProt: 92-263                                                                                                                                          --------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: A:5-99 UniProt: 1-99 [INCOMPLETE]                                              ---------------------------------------------------------------Exon 1.5  PDB: A:163-212 (gaps) UniProt: 163-212  --------------------------------------------------------Exon 1.7  PDB: A:269-329 UniProt: 269-329                    --------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------Exon 1.4  PDB: A:99-162 (gaps) UniProt: 99-162                  -------------------------------------------------Exon 1.6b  PDB: A:212-269 (gaps) UniProt: 212-269         -----------------------------------------------------------Exon 1.8b  PDB: A:329-356    Transcript 1 (2)
                 3zje A   5 VLPQALYLSNMRKAVKIRERTPEDIFKPTNGIIHHFKTMHRYTLEMFRTCQFCPQFREIIHKALIDRNIQATLESQKKLNWCREVRKLVALKTNGDGNcLMHATSQYMWSVQDTDLVLRKALFSTLKETDTRNFKFRWQLESLKS----------DTRNWNDEWDNLIKMASTDTP----GLQYNSLEEIHIFVLCNILRRPIIVISDKMLRSL--------LKVGGIYLPLHWPAQECYRYPIVLGYDSHHFVPLVTLKD-GPEIRAVPLVNRDRGRFEDLKVHFLTDPENEMKEKLLKEYLMVIEIPVQGWDHGTTHLINAAKLDEANLPKEINLVDDYFELVQHEYKKW 356
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144    |    -     | 164       174     |   -|      194       204       214   |     -  |    234       244       254       264| |    274       284       294       304       314       324       334       344       354  
                                                                                                                            103-CSO                                       149        160                 180  185                              218      227                                   265 |                                                                                         
                                                                                                                                                                                                                                                                                                267                                                                                         

Chain B from PDB  Type:PROTEIN  Length:324
 aligned with TNAP3_HUMAN | P21580 from UniProtKB/Swiss-Prot  Length:790

    Alignment length:353
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354   
          TNAP3_HUMAN     5 VLPQALYLSNMRKAVKIRERTPEDIFKPTNGIIHHFKTMHRYTLEMFRTCQFCPQFREIIHKALIDRNIQATLESQKKLNWCREVRKLVALKTNGDGNCLMHATSQYMWGVQDTDLVLRKALFSTLKETDTRNFKFRWQLESLKSQEFVETGLCYDTRNWNDEWDNLIKMASTDTPMARSGLQYNSLEEIHIFVLCNILRRPIIVISDKMLRSLESGSNFAPLKVGGIYLPLHWPAQECYRYPIVLGYDSHHFVPLVTLKDSGPEIRAVPLVNRDRGRFEDLKVHFLTDPENEMKEKLLKEYLMVIEIPVQGWDHGTTHLINAAKLDEANLPKEINLVDDYFELVQHEYKKWQ 357
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhee........ee.hhhhh..........hhhhhhhhhhhhhhhhhhhhhhhh...........eee.......hhhhhhhhhhhhh.....hhhhhhhhhhhhh..hhhhhhhhhhhhh......----------..hhhhhhhhhh.....----.......hhhhhhhhhhhhh..eeeee.--------------....eee.....hhhhh....eeeeee..eeeeeee...-.....eee.eeee..eeee......hhhhhhhhhhhhhhhh.eeeeeee......eeeeeeee...........hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------V-C-------------------------------------------------------------------------------------------------------------------Y------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------OTU  PDB: B:92-263 UniProt: 92-263                                                                                                                                          ---------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.3b  PDB: B:5-99 UniProt: 1-99 [INCOMPLETE]                                              ---------------------------------------------------------------Exon 1.5  PDB: B:164-212 (gaps) UniProt: 163-212  --------------------------------------------------------Exon 1.7  PDB: B:269-329 UniProt: 269-329                    ---------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------------------Exon 1.4  PDB: B:99-153 UniProt: 99-162 [INCOMPLETE]            -------------------------------------------------Exon 1.6b  PDB: B:212-269 (gaps) UniProt: 212-269         -----------------------------------------------------------Exon 1.8b  PDB: B:329-357     Transcript 1 (2)
                 3zje B   5 VLPQALYLSNMRKAVKIRERTPEDIFKPTNGIIHHFKTMHRYTLEMFRTCQFCPQFREIIHKALIDRNIQATLESQKKLNWCREVRKLVALKTNGDGNcLMHATSQYMWSVQDTDLVLRKALFSTLKETDTRNFKFRWQLESLKSQEFV----------WNDEWDNLIKMASTDTP----GLQYNSLEEIHIFVLCNILRRPIIVISD--------------LKVGGIYLPLHWPAQECYRYPIVLGYDSHHFVPLVTLKD-GPEIRAVPLVNRDRGRFEDLKVHFLTDPENEMKEKLLKEYLMVIEIPVQGWDHGTTHLINAAKLDEANLPKEINLVDDYFELVQHEYKKWQ 357
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144        |-       164       174     |   -|      194       204       | -         -  |    234       244       254       264| |    274       284       294       304       314       324       334       344       354   
                                                                                                                            103-CSO                                           153        164             180  185                        212            227                                   265 |                                                                                          
                                                                                                                                                                                                                                                                                                267                                                                                          

   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 3ZJE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3ZJE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3ZJE)

(-) Gene Ontology  (76, 76)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (TNAP3_HUMAN | P21580)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0070530    K63-linked polyubiquitin modification-dependent protein binding    Interacting selectively and non-covalently with a protein upon poly-ubiquitination formed by linkages between lysine residues at position 63 in the target protein.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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:0019900    kinase binding    Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
    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:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0002020    protease binding    Interacting selectively and non-covalently with any protease or peptidase.
    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:0043621    protein self-association    Interacting selectively and non-covalently with a domain within the same polypeptide.
    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:0004842    ubiquitin-protein transferase activity    Catalysis of the transfer of ubiquitin from one protein to another via the reaction X-Ub + Y --> Y-Ub + X, where both X-Ub and Y-Ub are covalent linkages.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0001922    B-1 B cell homeostasis    The process of regulating the proliferation and elimination of B cells of the B-1 subset such that the total number of B-1 B cells within a whole or part of an organism is stable over time in the absence of an outside stimulus. B-1 B cells are a distinct subset of B cells characterized as being CD5 positive, found predominantly in the peritoneum, pleural cavities, and spleen, and enriched for self-reactivity.
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0070301    cellular response to hydrogen peroxide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydrogen peroxide (H2O2) stimulus.
    GO:0071222    cellular response to lipopolysaccharide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0072666    establishment of protein localization to vacuole    The directed movement of a protein to a specific location in a vacuole.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    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:0050869    negative regulation of B cell activation    Any process that stops, prevents, or reduces the frequency, rate or extent of B cell activation.
    GO:2000349    negative regulation of CD40 signaling pathway    Any process that stops, prevents or reduces the frequency, rate or extent of signaling via the CD40 signaling pathway.
    GO:0043124    negative regulation of I-kappaB kinase/NF-kappaB signaling    Any process that stops, prevents, or reduces the frequency, rate or extent of -kappaB kinase/NF-kappaB signaling.
    GO:0032088    negative regulation of NF-kappaB transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of the transcription factor NF-kappaB.
    GO:0045779    negative regulation of bone resorption    Any process that stops, prevents, or reduces the frequency, rate or extent of bone resorption.
    GO:0060548    negative regulation of cell death    Any process that decreases the rate or frequency of cell death. Cell death is the specific activation or halting of processes within a cell so that its vital functions markedly cease, rather than simply deteriorating gradually over time, which culminates in cell death.
    GO:0002677    negative regulation of chronic inflammatory response    Any process that stops, prevents, or reduces the frequency, rate, or extent of a chronic inflammatory response.
    GO:0045736    negative regulation of cyclin-dependent protein serine/threonine kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity.
    GO:2000352    negative regulation of endothelial cell apoptotic process    Any process that stops, prevents or reduces the frequency, rate or extent of endothelial cell apoptotic process.
    GO:1902042    negative regulation of extrinsic apoptotic signaling pathway via death domain receptors    Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors.
    GO:0050728    negative regulation of inflammatory response    Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
    GO:0045824    negative regulation of innate immune response    Any process that stops, prevents, or reduces the frequency, rate or extent of the innate immune response.
    GO:0032691    negative regulation of interleukin-1 beta production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-1 beta production.
    GO:0032703    negative regulation of interleukin-2 production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-2 production.
    GO:0032715    negative regulation of interleukin-6 production    Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-6 production.
    GO:0070429    negative regulation of nucleotide-binding oligomerization domain containing 1 signaling pathway    Any process that stops, prevents, or reduces the frequency, rate, or extent of the nucleotide-binding oligomerization domain containing 1 (NOD1) pathway.
    GO:0070433    negative regulation of nucleotide-binding oligomerization domain containing 2 signaling pathway    Any process that stops, prevents, or reduces the frequency, rate, or extent of the nucleotide-binding oligomerization domain containing 2 (NOD2) pathway.
    GO:0090291    negative regulation of osteoclast proliferation    Any process that decreases the rate, frequency, or extent of the multiplication or reproduction of osteoclasts, resulting in the expansion of an osteoclast cell population.
    GO:0031397    negative regulation of protein ubiquitination    Any process that stops, prevents, or reduces the frequency, rate or extent of the addition of ubiquitin groups to a protein.
    GO:0048662    negative regulation of smooth muscle cell proliferation    Any process that stops, prevents or reduces the rate or extent of smooth muscle cell proliferation.
    GO:0034136    negative regulation of toll-like receptor 2 signaling pathway    Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor 2 signaling pathway.
    GO:0034140    negative regulation of toll-like receptor 3 signaling pathway    Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor 3 signaling pathway.
    GO:0034144    negative regulation of toll-like receptor 4 signaling pathway    Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor 4 signaling pathway.
    GO:0034148    negative regulation of toll-like receptor 5 signaling pathway    Any process that stops, prevents, or reduces the frequency, rate, or extent of toll-like receptor 5 signaling pathway.
    GO:0032720    negative regulation of tumor necrosis factor production    Any process that stops, prevents, or reduces the frequency, rate, or extent of tumor necrosis factor production.
    GO:0032480    negative regulation of type I interferon production    Any process that stops, prevents, or reduces the frequency, rate, or extent of type I interferon production. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
    GO:0070423    nucleotide-binding oligomerization domain containing signaling pathway    Any series of molecular signals generated as a consequence of binding to a nucleotide-binding oligomerization domain containing (NOD) protein.
    GO:1903364    positive regulation of cellular protein catabolic process    Any process that activates or increases the frequency, rate or extent of cellular protein catabolic process.
    GO:2000347    positive regulation of hepatocyte proliferation    Any process that activates or increases the frequency, rate or extent of hepatocyte proliferation.
    GO:0045732    positive regulation of protein catabolic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0035871    protein K11-linked deubiquitination    A protein deubiquitination process in which a K11-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 11 of the ubiquitin monomers, is removed from a protein.
    GO:0071108    protein K48-linked deubiquitination    A protein deubiquitination process in which a K48-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 48 of the ubiquitin monomers, is removed from a protein.
    GO:0070936    protein K48-linked ubiquitination    A protein ubiquitination process in which a polymer of ubiquitin, formed by linkages between lysine residues at position 48 of the ubiquitin monomers, is added to a protein. K48-linked ubiquitination targets the substrate protein for degradation.
    GO:0070536    protein K63-linked deubiquitination    A protein deubiquitination process in which a K63-linked ubiquitin chain, i.e. a polymer of ubiquitin formed by linkages between lysine residues at position 63 of the ubiquitin monomers, is removed from a protein.
    GO:0016579    protein deubiquitination    The removal of one or more ubiquitin groups from a protein.
    GO:0071947    protein deubiquitination involved in ubiquitin-dependent protein catabolic process    The removal of one or more ubiquitin groups from a protein as part of a process of ubiquitin-dependent protein catabolism.
    GO:0051259    protein oligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of component monomers; protein oligomers may be composed of different or identical monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0016567    protein ubiquitination    The process in which one or more ubiquitin groups are added to a protein.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0050691    regulation of defense response to virus by host    Any host process that modulates the frequency, rate, or extent of the antiviral response of a host cell or organism.
    GO:0002634    regulation of germinal center formation    Any process that modulates the frequency, rate, or extent of germinal center formation.
    GO:0050727    regulation of inflammatory response    Any process that modulates the frequency, rate or extent of the inflammatory response, the immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents.
    GO:0010803    regulation of tumor necrosis factor-mediated signaling pathway    Any process that modulates the rate or extent of the tumor necrosis factor-mediated signaling pathway. The tumor necrosis factor-mediated signaling pathway is the series of molecular signals generated as a consequence of tumor necrosis factor binding to a cell surface receptor.
    GO:0061043    regulation of vascular wound healing    Any process that modulates the rate, frequency, or extent of blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels and contribute to the series of events that restore integrity to damaged vasculature.
    GO:0002237    response to molecule of bacterial origin    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 stimulus by molecules of bacterial origin such as peptides derived from bacterial flagellin.
    GO:0032495    response to muramyl dipeptide    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 muramyl dipeptide stimulus. Muramyl dipeptide is derived from peptidoglycan.
    GO:0072573    tolerance induction to lipopolysaccharide    Tolerance induction directed at lipopolysaccharide antigens.
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: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:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    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)

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        TNAP3_HUMAN | P215802eqe 2eqf 2eqg 2vfj 3dkb 3oj3 3oj4 3vuw 3vux 3vuy 3zjd 3zjf 3zjg 4zrh 4zs5 5dod 5lrx

(-) Related Entries Specified in the PDB File

3zjd A20 OTU DOMAIN IN REDUCED, ACTIVE STATE AT 1.87 A RESOLUTION
3zjf A20 OTU DOMAIN WITH IRREVERSIBLY OXIDISED CYS103 FROM 270 MIN H2O2 SOAK.
3zjg A20 OTU DOMAIN WITH IRREVERSIBLY OXIDISED CYS103 FROM 60 MIN H2O2 SOAK.