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Theoretical Model  (Jmol Viewer)

(-) Description

Title :  HEXOSAMINIDASE BETA CHAIN, GLYCOSYL HYDROLASE FAMILY 20, THEORETICAL MODEL
 
Authors :  I. Tews, A. Perrakis, A. Oppenheim, Z. Dauter, K. S. Wilson, C. E. Vorgias
Date :  07 Jun 96  (Deposition) - 11 Jan 97  (Release) - 11 Jan 97  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Glycosyl Hydrolase, Hexosaminidase, Sandhoff Disease, Ba8- Barrel (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  I. Tews, A. Perrakis, A. Oppenheim, Z. Dauter, K. S. Wilson, C. E. Vorgias
Bacterial Chitobiase Structure Provides Insight Into Catalytic Mechanism And The Basis Of Tay-Sachs Disease.
Nat. Struct. Biol. V. 3 638 1996
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HEXOSAMINIDASE
    ChainsA
    EC Number3.2.1.30
    FragmentBETA CHAIN
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS

 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 1QBD)

(-) Sites  (0, 0)

(no "Site" information available for 1QBD)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1QBD)

(-) Cis Peptide Bonds  (7, 7)

Theoretical Model
No.Residues
1Ser A:261 -Leu A:262
2Thr A:291 -Pro A:292
3Phe A:344 -Pro A:345
4Gly A:401 -Ser A:402
5Ala A:416 -Pro A:417
6Gly A:490 -Glu A:491
7Trp A:503 -Pro A:504

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (7, 7)

Theoretical Model (7, 7)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_003249I207VHEXB_HUMANPolymorphism10805890AI207V
2UniProtVAR_011704S255RHEXB_HUMANDisease (GM2G2)  ---AS255R
3UniProtVAR_003250C309YHEXB_HUMANDisease (GM2G2)  ---AC309Y
4UniProtVAR_003251P417LHEXB_HUMANDisease (GM2G2)28942073AP417L
5UniProtVAR_003252Y456SHEXB_HUMANDisease (GM2G2)  ---AY456S
6UniProtVAR_011705P504SHEXB_HUMANDisease (GM2G2)  ---AP504S
7UniProtVAR_003253R505QHEXB_HUMANDisease (GM2G2)  ---AR505Q

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1QBD)

(-) Exons   (9, 9)

Theoretical Model (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2aENST000002614162aENSE00001083771chr5:73980969-73981384416HEXB_HUMAN1-1001000--
1.3aENST000002614163aENSE00000753141chr5:73985153-73985298146HEXB_HUMAN100-149500--
1.4bENST000002614164bENSE00000753143chr5:73989464-7398952966HEXB_HUMAN149-171230--
1.5ENST000002614165ENSE00000459979chr5:73992518-7399256447HEXB_HUMAN171-186160--
1.6ENST000002614166ENSE00000753190chr5:73992821-73992931111HEXB_HUMAN187-223371A:193-22331
1.7bENST000002614167bENSE00001031132chr5:74001044-74001145102HEXB_HUMAN224-257341A:224-25734
1.8aENST000002614168aENSE00001031135chr5:74009331-74009460130HEXB_HUMAN258-301441A:258-30144
1.9aENST000002614169aENSE00001031133chr5:74011335-74011515181HEXB_HUMAN301-361611A:301-36161
1.10aENST0000026141610aENSE00001083763chr5:74012412-7401249887HEXB_HUMAN361-390301A:361-390 (gaps)30
1.11ENST0000026141611ENSE00001083768chr5:74014116-7401418873HEXB_HUMAN390-414251A:390-41425
1.12aENST0000026141612aENSE00001083759chr5:74014622-74014796175HEXB_HUMAN415-473591A:415-47359
1.13bENST0000026141613bENSE00001263703chr5:74016253-7401634391HEXB_HUMAN473-503311A:473-50331
1.14aENST0000026141614aENSE00001083760chr5:74016468-74016572105HEXB_HUMAN503-538361A:503-51614
1.15cENST0000026141615cENSE00001171600chr5:74016943-74017113171HEXB_HUMAN538-556190--

(-) 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:323
 aligned with HEXB_HUMAN | P07686 from UniProtKB/Swiss-Prot  Length:556

    Alignment length:324
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512    
           HEXB_HUMAN   193 TIIDSPRFSHRGILIDTSRHYLPVKIILKTLDAMAFNKFNVLHWHIVDDQSFPYQSITFPELSNKGSYSLSHVYTPNDVRMVIEYARLRGIRVLPEFDTPGHTLSWGKGQKDLLTPCYSRQNKLDSFGPINPTLNTTYSFLTTFFKEISEVFPDQFIHLGGDEVEFKCWESNPKIQDFMRQKGFGTDFKKLESFYIQKVLDIIATINKGSIVWQEVFDDKAKLAPGTIVEVWKDSAYPEELSRVTASGFPVILSAPWYLDLISYGQDWRKYYKVEPLDFGGTQKQKQLFIGGEACLWGEYVDATNLTPRLWPRASAVGERLWSS 516
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..........eeeeee.......hhhhhhhhhhhhh....eeeee..............hhhhh............hhhhhhhhhhhhh..eeeee.......hhhh...........................hhhhhhhhhhhhhhhhh......eee............hhhhhhhh...-.....hhhhhhhhhhhhhhhhh...eeeehhhhh.........eeee.......hhhhhhhhh..eeee..............hhhhhh.................eeeeee......hhhhhhhh..hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------V-----------------------------------------------R-----------------------------------------------------Y-----------------------------------------------------------------------------------------------------------L--------------------------------------S-----------------------------------------------SQ----------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.6  PDB: A:193-223       Exon 1.7b  PDB: A:224-257         Exon 1.8a  PDB: A:258-301 UniProt: 258-301  -----------------------------------------------------------Exon 1.10a UniProt: 361-390   ------------------------Exon 1.12a  PDB: A:415-473 UniProt: 415-473                -----------------------------Exon 1.14a     Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------------------------------------------Exon 1.9a  PDB: A:301-361 UniProt: 301-361                   ----------------------------Exon 1.11  PDB: A:390-414----------------------------------------------------------Exon 1.13b  PDB: A:473-503     ------------- Transcript 1 (2)
                 1qbd A 193 TIIDSPRFSHRGILIDTSRHYLPVKIILKTLDAMAFNKFNVLHWHIVDDQSFPYQSITFPELSNKGSYSLSHVYTPNDVRMVIEYARLRGIRVLPEFDTPGHTLSWGKGQKDLLTPCYSRQNKLDSFGPINPTLNTTYSFLTTFFKEISEVFPDQFIHLGGDEVEFKCWESNPKIQDFMRQKG-GTDFKKLESFYIQKVLDIIATINKGSIVWQEVFDDKAKLAPGTIVEVWKDSAYPEELSRVTASGFPVILSAPWYLDLISYGQDWRKYYKVEPLDFGGTQKQKQLFIGGEACLWGEYVDATNLTPRLWPRASAVGERLWSS 516
                                   202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372  | |  382       392       402       412       422       432       442       452       462       472       482       492       502       512    
                                                                                                                                                                                                                375 |                                                                                                                                           
                                                                                                                                                                                                                  377                                                                                                                                           

   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 1QBD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1QBD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1QBD)

(-) Gene Ontology  (42, 42)

Theoretical Model(hide GO term definitions)
Chain A   (HEXB_HUMAN | P07686)
molecular function
    GO:0008375    acetylglucosaminyltransferase activity    Catalysis of the transfer of an N-acetylglucosaminyl residue from UDP-N-acetyl-glucosamine to a sugar.
    GO:0004563    beta-N-acetylhexosaminidase activity    Catalysis of the hydrolysis of terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides.
    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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0004553    hydrolase activity, hydrolyzing O-glycosyl compounds    Catalysis of the hydrolysis of any O-glycosyl bond.
    GO:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
biological process
    GO:0043615    astrocyte cell migration    The orderly movement of an astrocyte, a class of large neuroglial (macroglial) cells in the central nervous system, the largest and most numerous neuroglial cells in the brain and spinal cord.
    GO:0005975    carbohydrate metabolic process    The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
    GO:0006874    cellular calcium ion homeostasis    Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell.
    GO:0044267    cellular protein metabolic process    The chemical reactions and pathways involving a specific protein, rather than of proteins in general, occurring at the level of an individual cell. Includes cellular protein modification.
    GO:0030207    chondroitin sulfate catabolic process    The chemical reactions and pathways resulting in the breakdown of chondroitin sulfate, any member of a group of 10-60 kDa glycosaminoglycans, widely distributed in cartilage and other mammalian connective tissues, the repeat units of which consist of beta-(1,4)-linked D-glucuronyl beta-(1,3)-N-acetyl-D-galactosamine sulfate.
    GO:0006689    ganglioside catabolic process    The chemical reactions and pathways resulting in the breakdown of ganglioside, a ceramide oligosaccharide carrying, in addition to other sugar residues, one or more sialic residues.
    GO:0030203    glycosaminoglycan metabolic process    The chemical reactions and pathways involving glycosaminoglycans, any one of a group of polysaccharides that contain amino sugars. Formerly known as mucopolysaccharides, they include hyaluronic acid and chondroitin, which provide lubrication in joints and form part of the matrix of cartilage. The three-dimensional structure of these molecules enables them to trap water, which forms a gel and gives glycosaminoglycans their elastic properties.
    GO:0006687    glycosphingolipid metabolic process    The chemical reactions and pathways involving glycosphingolipids, any compound with residues of sphingoid and at least one monosaccharide.
    GO:0030214    hyaluronan catabolic process    The chemical reactions and pathways resulting in the breakdown of hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine.
    GO:0042340    keratan sulfate catabolic process    The chemical reactions and pathways resulting in the breakdown of keratan sulfate, a glycosaminoglycan with repeat units consisting of beta-1,4-linked D-galactopyranosyl-beta-(1,4)-N-acetyl-D-glucosamine 6-sulfate and with variable amounts of fucose, sialic acid and mannose units; keratan sulfate chains are covalently linked by a glycosidic attachment through the trisaccharide galactosyl-galactosyl-xylose to peptidyl-threonine or serine residues.
    GO:0019915    lipid storage    The accumulation and maintenance in cells or tissues of lipids, compounds soluble in organic solvents but insoluble or sparingly soluble in aqueous solvents. Lipid reserves can be accumulated during early developmental stages for mobilization and utilization at later stages of development.
    GO:0007626    locomotory behavior    The specific movement from place to place of an organism in response to external or internal stimuli. Locomotion of a whole organism in a manner dependent upon some combination of that organism's internal state and external conditions.
    GO:0007040    lysosome organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of a lysosome. A lysosome is a cytoplasmic, membrane-bounded organelle that is found in most animal cells and that contains a variety of hydrolases.
    GO:0008049    male courtship behavior    The behavior of a male, for the purpose of attracting a sexual partner. An example of this process is found in Drosophila melanogaster.
    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:0042552    myelination    The process in which myelin sheaths are formed and maintained around neurons. Oligodendrocytes in the brain and spinal cord and Schwann cells in the peripheral nervous system wrap axons with compact layers of their plasma membrane. Adjacent myelin segments are separated by a non-myelinated stretch of axon called a node of Ranvier.
    GO:0050905    neuromuscular process    Any process pertaining to the functions of the nervous and muscular systems of an organism.
    GO:0050885    neuromuscular process controlling balance    Any process that an organism uses to control its balance, the orientation of the organism (or the head of the organism) in relation to the source of gravity. In humans and animals, balance is perceived through visual cues, the labyrinth system of the inner ears and information from skin pressure receptors and muscle and joint receptors.
    GO:0009313    oligosaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of oligosaccharides, molecules with between two and (about) 20 monosaccharide residues connected by glycosidic linkages.
    GO:0048477    oogenesis    The complete process of formation and maturation of an ovum or female gamete from a primordial female germ cell. Examples of this process are found in Mus musculus and Drosophila melanogaster.
    GO:0007341    penetration of zona pellucida    The infiltration by sperm of the zona pellucida to reach the oocyte. The process involves digestive enzymes from a modified lysosome called the acrosome, situated at the head of the sperm.
    GO:0008654    phospholipid biosynthetic process    The chemical reactions and pathways resulting in the formation of phospholipids, any lipid containing phosphoric acid as a mono- or diester.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0008360    regulation of cell shape    Any process that modulates the surface configuration of a cell.
    GO:0031323    regulation of cellular metabolic process    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways by which individual cells transform chemical substances.
    GO:0007605    sensory perception of sound    The series of events required for an organism to receive an auditory stimulus, convert it to a molecular signal, and recognize and characterize the signal. Sonic stimuli are detected in the form of vibrations and are processed to form a sound.
    GO:0019953    sexual reproduction    A reproduction process that creates a new organism by combining the genetic material of two organisms. It occurs both in eukaryotes and prokaryotes: in multicellular eukaryotic organisms, an individual is created anew; in prokaryotes, the initial cell has additional or transformed genetic material. In a process called genetic recombination, genetic material (DNA) originating from two different individuals (parents) join up so that homologous sequences are aligned with each other, and this is followed by exchange of genetic information. After the new recombinant chromosome is formed, it is passed on to progeny.
    GO:0007338    single fertilization    The union of male and female gametes to form a zygote.
    GO:0001501    skeletal system development    The process whose specific outcome is the progression of the skeleton over time, from its formation to the mature structure. The skeleton is the bony framework of the body in vertebrates (endoskeleton) or the hard outer envelope of insects (exoskeleton or dermoskeleton).
cellular component
    GO:0001669    acrosomal vesicle    A structure in the head of a spermatozoon that contains acid hydrolases, and is concerned with the breakdown of the outer membrane of the ovum during fertilization. It lies just beneath the plasma membrane and is derived from the lysosome.
    GO:0042582    azurophil granule    Primary lysosomal granule found in neutrophil granulocytes. Contains a wide range of hydrolytic enzymes and is released into the extracellular fluid.
    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:0043202    lysosomal lumen    The volume enclosed within the lysosomal membrane.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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    Ala A:416 - Pro A:417   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        HEXB_HUMAN | P076861nou 1now 1np0 1o7a 2gjx 2gk1 3lmy 5bro

(-) Related Entries Specified in the PDB File

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