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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CHITINASE IN COMPLEX WITH GLUCOALLOSAMIDIN B
 
Authors :  F. V. Rao, D. R. Houston, R. G. Boot, J. M. F. G. Aerts, S. Sakuda, D. M. F. Van Aalten
Date :  10 Mar 03  (Deposition) - 11 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A
Keywords :  Human Chitinase, Hydrolase, Structure, Glucoallosamidin B, Allosamidin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  F. V. Rao, D. R. Houston, R. G. Boot, J. M. F. G. Aerts, S. Sakuda, D. M. F. Van Aalten
Crystal Structures Of Allosamidin Derivatives In Complex With Human Macrophage Chitinase
J. Biol. Chem. V. 278 20110 2003
PubMed-ID: 12639956  |  Reference-DOI: 10.1074/JBC.M300362200

(-) Compounds

Molecule 1 - CHITOTRIOSIDASE
    CellMACROPHAGE
    ChainsA
    EC Number3.2.1.14
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsGLUCOALLOSAMIDIN B
    SynonymENDOCHITINASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1ALI1Ligand/IonMETHYL N-ACETYL ALLOSAMINE
2NA11Ligand/IonMETHYL N-ACETYL ALLOSAMINE
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:31 , GLY A:98 , TRP A:99 , ASN A:100 , MET A:300 , TRP A:358 , NA1 A:1387 , ALI A:1389BINDING SITE FOR RESIDUE NAG A1388
2AC2SOFTWARETRP A:31 , ARG A:35 , ASN A:100 , GLU A:297 , ARG A:374 , NAG A:1388 , HOH A:2063BINDING SITE FOR RESIDUE NA1 A1387
3AC3SOFTWARETYR A:27 , TRP A:99 , ASP A:138 , GLU A:140 , ALA A:183 , MET A:210 , TYR A:212 , ASP A:213 , TYR A:267 , MET A:356 , TRP A:358 , NAG A:1388BINDING SITE FOR RESIDUE ALI A1389

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:26 -A:51
2A:307 -A:370

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Ala A:57 -Phe A:58
2Glu A:140 -Tyr A:141
3Trp A:358 -Ala A:359

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric/Biological Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_049190R40HCHIT1_HUMANPolymorphism35920428AR40H
2UniProtVAR_065914E74KCHIT1_HUMANPolymorphism137852607AE74K
3UniProtVAR_022138G102SCHIT1_HUMANPolymorphism2297950AG102S
4UniProtVAR_049191Q171HCHIT1_HUMANPolymorphism12562058AQ171H

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHITINASE_18PS01095 Chitinases family 18 active site.CHIT1_HUMAN132-140  1A:132-140

(-) Exons   (9, 9)

Asymmetric/Biological Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.8aENST000003672298aENSE00001443882chr1:203198799-20319874060CHIT1_HUMAN1-990--
1.9ENST000003672299ENSE00001608418chr1:203197690-20319766130CHIT1_HUMAN9-19110--
1.10ENST0000036722910ENSE00001767547chr1:203194998-203194797202CHIT1_HUMAN19-86681A:22-8665
1.11ENST0000036722911ENSE00001697138chr1:203194232-20319417657CHIT1_HUMAN86-105201A:86-10520
1.12bENST0000036722912bENSE00001666970chr1:203192788-203192623166CHIT1_HUMAN105-160561A:105-16056
1.13ENST0000036722913ENSE00000907172chr1:203192387-203192263125CHIT1_HUMAN161-202421A:161-20242
1.14aENST0000036722914aENSE00001687399chr1:203191453-203191330124CHIT1_HUMAN202-243421A:202-24342
1.15aENST0000036722915aENSE00000907170chr1:203188977-203188792186CHIT1_HUMAN244-305621A:244-30562
1.16ENST0000036722916ENSE00000907169chr1:203188457-203188344114CHIT1_HUMAN306-343381A:306-34338
1.17cENST0000036722917cENSE00001130578chr1:203186993-203186867127CHIT1_HUMAN344-386431A:344-38643
1.19cENST0000036722919cENSE00001443883chr1:203186261-2031852071055CHIT1_HUMAN386-466811A:386-3861

(-) 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:365
 aligned with CHIT1_HUMAN | Q13231 from UniProtKB/Swiss-Prot  Length:466

    Alignment length:365
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381     
          CHIT1_HUMAN    22 AKLVCYFTNWAQYRQGEARFLPKDLDPSLCTHLIYAFAGMTNHQLSTTEWNDETLYQEFNGLKKMNPKLKTLLAIGGWNFGTQKFTDMVATANNRQTFVNSAIRFLRKYSFDGLDLDWEYPGSQGSPAVDKERFTTLVQDLANAFQQEAQTSGKERLLLSAAVPAGQTYVDAGYEVDKIAQNLDFVNLMAYDFHGSWEKVTGHNSPLYKRQEESGAAASLNVDAAVQQWLQKGTPASKLILGMPTYGRSFTLASSSDTRVGAPATGSGTPGPFTKEGGMLAYYEVCSWKGATKQRIQDQKVPYIFRDNQWVGFDDVESFKTKVSYLKQKGLGGAMVWALDLDDFAGFSCNQGRYPLIQTLRQELS 386
               SCOP domains d1hkia1 A:22-266,A:335-386 Chitotriosidase                                                                                                                                                                                                           d1hkia2 A:267-334 Chitotriosidase                                   d1hkia1 A:22-266,A:335-386 Chitotriosidase           SCOP domains
               CATH domains 1hkiA01 A:22-266,A:335-386 Glycosidases                                                                                                                                                                                                              1hkiA02 A:267-334  [code=3.10.50.10, no name defined]               1hkiA01 A:22-266,A:335-386 Glycosidases              CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhh.hhhhh......eeeeeeeee..........hhhhhhhhhhhhhhhh...eeeeeee.hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..eeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeee..hhhhhhhhhhhhhhhhhh.eeee................................hhhhhhhhhhh.......eeeeee.eeeeeee...........eeee............eehhhhhhh...eeeee....eeeeee..eeee..hhhhhhhhhhhhhhh...eeeeehhhhh...........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------H---------------------------------K---------------------------S--------------------------------------------------------------------H----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------CHITINASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.10  PDB: A:22-86 UniProt: 19-86 [INCOMPLETE]              ------------------Exon 1.12b  PDB: A:105-160 UniProt: 105-160             Exon 1.13  PDB: A:161-202 UniProt: 161-202-----------------------------------------Exon 1.15a  PDB: A:244-305 UniProt: 244-305                   Exon 1.16  PDB: A:306-343             Exon 1.17c  PDB: A:344-386 UniProt: 344-386 Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------Exon 1.11           ------------------------------------------------------------------------------------------------Exon 1.14a  PDB: A:202-243                ----------------------------------------------------------------------------------------------------------------------------------------------1 Transcript 1 (2)
                 1hki A  22 AKLVCYFTNWAQYRQGEARFLPKDLDPSLCTHLIYAFAGMTNHQLSTTEWNDETLYQEFNGLKKMNPKLKTLLAIGGWNFGTQKFTDMVATANNRQTFVNSAIRFLRKYSFDGLDLDWEYPGSQGSPAVDKERFTTLVQDLANAFQQEAQTSGKERLLLSAAVPAGQTYVDAGYEVDKIAQNLDFVNLMAYDFHGSWEKVTGHNSPLYKRQEQSGAAASLNVDAAVQQWLQKGTPASKLILGMPTYGRSFTLASSSDTRVGAPATGSGTPGPFTKEGGMLAYYEVCSWKGATKQRIQDQKVPYIFRDNQWVGFDDVESFKTKVSYLKQKGLGGAMVWALDLDDFAGFSCNQGRYPLIQTLRQELS 386
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381     

   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  (2, 2)

Asymmetric/Biological Unit

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CHIT1_HUMAN | Q13231)
molecular function
    GO:0008061    chitin binding    Interacting selectively and non-covalently with chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
    GO:0004568    chitinase activity    Catalysis of the hydrolysis of (1->4)-beta linkages of N-acetyl-D-glucosamine (GlcNAc) polymers of chitin and chitodextrins.
    GO:0008843    endochitinase activity    Catalysis of the hydrolysis of nonterminal (1->4)-beta linkages of N-acetyl-D-glucosamine (GlcNAc) polymers of chitin and chitodextrins. Typically, endochitinases cleave randomly within the chitin chain.
    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.
biological process
    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:0006032    chitin catabolic process    The chemical reactions and pathways resulting in the breakdown of chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
    GO:0006030    chitin metabolic process    The chemical reactions and pathways involving chitin, a linear polysaccharide consisting of beta-(1->4)-linked N-acetyl-D-glucosamine residues.
    GO:0006955    immune response    Any immune system process that functions in the calibrated response of an organism to a potential internal or invasive threat.
    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:0000272    polysaccharide catabolic process    The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
    GO:0009617    response to bacterium    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus from a bacterium.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CHIT1_HUMAN | Q132311guv 1hkj 1hkk 1hkm 1lg1 1lg2 1lq0 1waw 1wb0 4wjx 4wk9 4wka 4wkf 4wkh 5hbf

(-) Related Entries Specified in the PDB File

1guv STRUCTURE OF HUMAN CHITOTRIOSIDASE
1hkj CRYSTAL STRUCTURE OF HUMAN CHITINASE IN COMPLEX WITH METHYLALLOSAMIDIN
1hkk HIGH RESOULTION CRYSTAL STRUCTURE OF HUMAN CHITINASE IN COMPLEX WITH ALLOSAMIDIN
1hkm HIGH RESOULTION CRYSTAL STRUCTURE OF HUMAN CHITINASE IN COMPLEX WITH DEMETHYLALLOSAMIDIN
1lg1 CRYSTAL STRUCTURE OF HUMAN CHITOTRIOSIDASE IN COMPLEX WITHCHITOBIOSE
1lg2 CRYSTAL STRUCTURE OF HUMAN CHITOTRIOSIDASE IN COMPLEX WITHETHYLENE GLYCOL