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(-) Description

Title :  INTERACTIONS OF A FAMILY 18 CHITINASE WITH THE DESIGNED INHIBITOR HM508, AND ITS DEGRADATION PRODUCT, CHITOBIONO-DELTA-LACTONE
 
Authors :  G. Vaaje-Kolstad, A. Vasella, M. G. Peter, C. Netter, D. R. Houston, B. Westereng, B. Synstad, V. G. H. Eijsink, D. M. F. Van Aalten
Date :  27 Oct 03  (Deposition) - 27 Apr 04  (Release) - 15 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Chitinase, Inhibition, Lactone, Chitin Degradation, Glycosidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Vaaje-Kolstad, A. Vasella, M. G. Peter, C. Netter, D. R. Houston, B. Westereng, B. Synstad, V. G. H. Eijsink, D. M. F. Van Aalten
Interactions Of A Family 18 Chitinase With The Designed Inhibitor Hm508 And Its Degradation Product, Chitobiono- Delta-Lactone.
J. Biol. Chem. V. 279 3612 2004
PubMed-ID: 14597613  |  Reference-DOI: 10.1074/JBC.M310057200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHITINASE B
    Chains: A, B
    EC Number: 3.2.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: SERRATIA MARCESCENS
    Organism Taxid: 615
    Strain: BJL200

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 20)

Asymmetric/Biological Unit (4, 20)
No.NameCountTypeFull Name
1GDL2Ligand/Ion2-ACETAMIDO-2-DEOXY-D-GLUCONO-1,5-LACTONE
2GOL9Ligand/IonGLYCEROL
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
4SO47Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:420 , HOH A:2306 , HOH A:2343 , HOH A:2344 , HOH A:2345 , LYS B:386BINDING SITE FOR RESIDUE SO4 A1503
02AC2SOFTWAREPRO A:14 , ASN A:16 , GLN A:17 , VAL A:28 , ARG A:333BINDING SITE FOR RESIDUE SO4 A1504
03AC3SOFTWAREPRO A:281 , SER A:282 , HOH A:2347 , HOH A:2348BINDING SITE FOR RESIDUE SO4 A1505
04AC4SOFTWARELYS A:386 , ARG B:420 , HOH B:2394 , HOH B:2395 , HOH B:2396BINDING SITE FOR RESIDUE SO4 B1507
05AC5SOFTWAREPRO B:281 , SER B:282 , HOH B:2264 , HOH B:2397 , HOH B:2398BINDING SITE FOR RESIDUE SO4 B1508
06AC6SOFTWAREASN B:16 , GLN B:17 , VAL B:28 , ARG B:333 , HOH B:2035BINDING SITE FOR RESIDUE SO4 B1509
07AC7SOFTWAREARG B:294 , HOH B:2284 , HOH B:2400 , NAG B:2501 , GDL B:2502BINDING SITE FOR RESIDUE SO4 B1510
08AC8SOFTWAREPRO A:260 , PHE A:263 , SER A:264 , ARG A:439 , TYR A:440 , THR A:441 , HOH A:2210 , HOH A:2342BINDING SITE FOR RESIDUE GOL A1499
09AC9SOFTWAREASN A:55 , SER A:56 , PRO A:64 , ASN A:109 , THR A:436 , HOH A:2095 , HOH A:2099BINDING SITE FOR RESIDUE GOL A1500
10BC1SOFTWAREARG A:343 , GLN A:347 , ARG A:410BINDING SITE FOR RESIDUE GOL A1501
11BC2SOFTWAREPRO B:260 , PHE B:263 , SER B:264 , HOH B:2254 , HOH B:2386BINDING SITE FOR RESIDUE GOL B1500
12BC3SOFTWARETYR B:323 , LEU B:325 , VAL B:326 , GLY B:327 , GLU B:329 , VAL B:332BINDING SITE FOR RESIDUE GOL B1501
13BC4SOFTWAREPHE A:190 , SER A:193 , ARG A:194 , TRP B:479 , THR B:483 , SER B:484 , ASP B:489 , HOH B:2387BINDING SITE FOR RESIDUE GOL B1502
14BC5SOFTWAREARG B:162 , ALA B:204 , PRO B:205 , ASP B:207 , LYS B:284BINDING SITE FOR RESIDUE GOL B1503
15BC6SOFTWARETRP A:479 , GLY A:480 , TYR A:481 , ILE A:482 , PHE B:190 , PHE B:191 , ARG B:194 , HOH B:2388 , HOH B:2389BINDING SITE FOR RESIDUE GOL B1504
16BC7SOFTWAREPRO B:454 , ALA B:455 , HOH B:2390 , HOH B:2391 , HOH B:2392 , HOH B:2393BINDING SITE FOR RESIDUE GOL B1505
17BC8SOFTWARETYR A:10 , PHE A:51 , GLY A:96 , TRP A:97 , TYR A:98 , ASP A:142 , GLU A:144 , MET A:212 , TYR A:214 , ASP A:215 , TYR A:292 , ARG A:294 , TRP A:403 , GLN A:407 , HOH A:2084 , HOH A:2123 , HOH A:2177 , HOH A:2350BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG A2501 THROUGH GDL A2502
18BC9SOFTWARETYR B:10 , PHE B:51 , TRP B:97 , TYR B:98 , ASP B:142 , GLU B:144 , MET B:212 , TYR B:214 , ASP B:215 , TYR B:292 , ARG B:294 , TRP B:403 , GLN B:407 , SO4 B:1510 , HOH B:2404 , HOH B:2406BINDING SITE FOR POLY-SACCHARIDE RESIDUES NAG B2501 THROUGH GDL B2502

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:328 -A:331
2B:328 -B:331

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Ser A:50 -Phe A:51
2Glu A:144 -Tyr A:145
3Ser A:261 -Pro A:262
4Asp A:316 -Pro A:317
5Trp A:403 -His A:404
6Ser B:50 -Phe B:51
7Glu B:144 -Tyr B:145
8Ser B:261 -Pro B:262
9Asp B:316 -Pro B:317
10Trp B:403 -His B:404

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1UR8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1UR8)

(-) Exons   (0, 0)

(no "Exon" information available for 1UR8)

(-) 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:497
 aligned with Q54276_SERMA | Q54276 from UniProtKB/TrEMBL  Length:499

    Alignment length:497
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       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       
         Q54276_SERMA     3 TRKAVIGYYFIPTNQINNYTETDTSVVPFPVSNITPAKAKQLTHINFSFLDINSNLECAWDPATNDAKARDVVNRLTALKAHNPSLRIMFSIGGWYYSNDLGVSHANYVNAVKTPASRAKFAQSCVRIMKDYGFDGVDIDWEYPQAAEVDGFIAALQEIRTLLNQQTITDGRQALPYQLTIAGAGGAFFLSRYYSKLAQIVAPLDYINLMTYDLAGPWEKVTNHQAALFGDAAGPTFYNALREANLGWSWEELTRAFPSPFSLTVDAAVQQHLMMEGVPSAKIVMGVPFYGRAFKGVSGGNGGQYSSHSTPGEDPYPSTDYWLVGCEECVRDKDPRIASYRQLEQMLQGNYGYQRLWNDKTKTPYLYHAQNGLFVTYDDAESFKYKAKYIKQQQLGGVMFWHLGQDNRNGDLLAALDRYFNAADYDDSQLDMGTGLRYTGVGPGNLPIMTAPAYVPGTTYAQGALVSYQGYVWQTKWGYITSAPGSDSAWLKVGRVA 499
               SCOP domains d1ur8a2 A:3-291,A:380-446 Chitinase B, catalytic domain                                                                                                                                                                                                                                          d1ur8a3 A:292-379 Chitinase B                                                           d1ur8a2 A:3-291,A:380-446 Chitinase B, catalytic domain            d1ur8a1 A:447-499 Chitinase B, C-terminal domain      SCOP domains
               CATH domains 1ur8A01 A:3-290,A:381-448 Glycosidases                                                                                                                                                                                                                                                          1ur8A02 A:291-380  [code=3.10.50.10, no name defined]                                     1ur8A01 A:3-290,A:381-448 Glycosidases                              1ur8A03 A:449-499                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.hhhhhhh...........hhhhhhhhhhhhh.eeeeeeeee............hhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhh....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.hhhhhhhhhhhhhhhhh...eeeee............................hhhhhh....hhhhhhhhh......hhhhhhhhhhh....hhh.eeeeee.eeeeee..............................hhhhhhh....eeehhhhhhhhhh....eeeee....eeeeee....eeee....hhhhhhhhhhhhh...eeeeehhhhh...hhhhhhhhhhhhh..........................................eeee..eeeee..............eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ur8 A   3 TRKAVIGYYFIPTNQINNYTETDTSVVPFPVSNITPAKAKQLTHINFSFLDINSNLECAWDPATNDAKARDVVNRLTALKAHNPSLRIMFSIGGWYYSNDLGVSHANYVNAVKTPASRAKFAQSCVRIMKDYGFDGVDIDWEYPQAAEVDGFIAALQEIRTLLNQQTITDGRQALPYQLTIAGAGGAFFLSRYYSKLAQIVAPLDYINLMTYDLAGPWEKVTNHQAALFGDAAGPTFYNALREANLGWSWEELTRAFPSPFSLTVDAAVQQHLMMEGVPSAKIVMGVPFYGRAFKGVSGGNGGQYSSHSTPGEDPYPSTDYWLVGCEECVRDKDPRIASYRQLEQMLQGNYGYQRLWNDKTKTPYLYHAQNGLFVTYDDAESFKYKAKYIKQQQLGGVMFWHLGQDNRNGDLLAALDRYFNAADYDDSQLDMGTGLRYTGVGPGNLPIMTAPAYVPGTTYAQGALVSYQGYVWQTKWGYITSAPGSDSAWLKVGRVA 499
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       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       


Chain B from PDB  Type:PROTEIN  Length:497
 aligned with Q54276_SERMA | Q54276 from UniProtKB/TrEMBL  Length:499

    Alignment length:497
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       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       
         Q54276_SERMA     3 TRKAVIGYYFIPTNQINNYTETDTSVVPFPVSNITPAKAKQLTHINFSFLDINSNLECAWDPATNDAKARDVVNRLTALKAHNPSLRIMFSIGGWYYSNDLGVSHANYVNAVKTPASRAKFAQSCVRIMKDYGFDGVDIDWEYPQAAEVDGFIAALQEIRTLLNQQTITDGRQALPYQLTIAGAGGAFFLSRYYSKLAQIVAPLDYINLMTYDLAGPWEKVTNHQAALFGDAAGPTFYNALREANLGWSWEELTRAFPSPFSLTVDAAVQQHLMMEGVPSAKIVMGVPFYGRAFKGVSGGNGGQYSSHSTPGEDPYPSTDYWLVGCEECVRDKDPRIASYRQLEQMLQGNYGYQRLWNDKTKTPYLYHAQNGLFVTYDDAESFKYKAKYIKQQQLGGVMFWHLGQDNRNGDLLAALDRYFNAADYDDSQLDMGTGLRYTGVGPGNLPIMTAPAYVPGTTYAQGALVSYQGYVWQTKWGYITSAPGSDSAWLKVGRVA 499
               SCOP domains d1ur8b2 B:3-291,B:380-446 Chitinase B, catalytic domain                                                                                                                                                                                                                                          d1ur8b3 B:292-379 Chitinase B                                                           d1ur8b2 B:3-291,B:380-446 Chitinase B, catalytic domain            d1ur8b1 B:447-499 Chitinase B, C-terminal domain      SCOP domains
               CATH domains 1ur8B01 B:3-290,B:381-448 Glycosidases                                                                                                                                                                                                                                                          1ur8B02 B:291-380  [code=3.10.50.10, no name defined]                                     1ur8B01 B:3-290,B:381-448 Glycosidases                              1ur8B03 B:449-499                                   CATH domains
           Pfam domains (1) --Glyco_hydro_18-1ur8B01 B:5-408                                                                                                                                                                                                                                                                                                                                                                                      --------------------------------------------CBM_5_12-1ur8B03 B:453-492              ------- Pfam domains (1)
           Pfam domains (2) --Glyco_hydro_18-1ur8B02 B:5-408                                                                                                                                                                                                                                                                                                                                                                                      --------------------------------------------CBM_5_12-1ur8B04 B:453-492              ------- Pfam domains (2)
         Sec.struct. author ...eeeeeee.hhhhhhh...........hhhhhhhhhhh...eeeeeeeee............hhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhh....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeeeee.hhhhhhhhhhhhhhhhh...eeeee............................hhhhhh....hhhhhhhhh......hhhhhhhhhhhh...hhh.eeeeee.eeeeee..............................hhhhhhh....eeehhhhhhhhhh....eeeee....eeeeee....eeee..hhhhhhhhhhhhhhh...eeeeehhhhh...hhhhhhhhhhhhh..........................................eeee..eeeee..............eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ur8 B   3 TRKAVIGYYFIPTNQINNYTETDTSVVPFPVSNITPAKAKQLTHINFSFLDINSNLECAWDPATNDAKARDVVNRLTALKAHNPSLRIMFSIGGWYYSNDLGVSHANYVNAVKTPASRAKFAQSCVRIMKDYGFDGVDIDWEYPQAAEVDGFIAALQEIRTLLNQQTITDGRQALPYQLTIAGAGGAFFLSRYYSKLAQIVAPLDYINLMTYDLAGPWEKVTNHQAALFGDAAGPTFYNALREANLGWSWEELTRAFPSPFSLTVDAAVQQHLMMEGVPSAKIVMGVPFYGRAFKGVSGGNGGQYSSHSTPGEDPYPSTDYWLVGCEECVRDKDPRIASYRQLEQMLQGNYGYQRLWNDKTKTPYLYHAQNGLFVTYDDAESFKYKAKYIKQQQLGGVMFWHLGQDNRNGDLLAALDRYFNAADYDDSQLDMGTGLRYTGVGPGNLPIMTAPAYVPGTTYAQGALVSYQGYVWQTKWGYITSAPGSDSAWLKVGRVA 499
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (3, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (3, 6)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Glyco_hydro_tim (488)
(-)
Clan: no clan defined [family: CBM_5_12] (10)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q54276_SERMA | Q54276)
molecular function
    GO:0030246    carbohydrate binding    Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.
    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: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: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.
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.

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  1ur8
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  Q54276_SERMA | Q54276
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  3.2.1.14
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 Related Entries

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

UniProtKB/Swiss-Prot
        Q54276_SERMA | Q54276: 1e6n 1goi 1ogb
UniProtKB/TrEMBL
        Q54276_SERMA | Q54276: 1e15 1e6p 1e6r 1e6z 1gpf 1ur9 1w1p 1w1t 1w1v 1w1y

(-) Related Entries Specified in the PDB File

1e15 CHITINASE B FROM SERRATIA MARCESCENS
1e6n CHITINASE B FROM SERRATIA MARCESCENS INACTIVE MUTANT E144Q IN COMPLEX WITH N- ACETYLGLUCOSAMINE-PENTAMER
1e6p CHITINASE B FROM SERRATIA MARCESCENS INACTIVE MUTANT E144Q
1e6r CHITINASE B FROM SERRATIA MARCESCENS WILDTYPE IN COMPLEX WITH INHIBITOR ALLOSAMIDIN
1e6z CHITINASE B FROM SERRATIA MARCESCENS WILDTYPE IN COMPLEX WITH CATALYTIC INTERMEDIATE
1goi CRYSTAL STRUCTURE OF THE D140N MUTANT OF CHITINASE B FROM SERRATIA MARCESCENS AT 1. 45 A RESOLUTION
1gpf CHITINASE B FROM SERRATIA MARCESCENS IN COMPLEX WITH INHIBITOR PSAMMAPLIN
1ogb STRUCTURE OF THE D142N MUTANT OF THE FAMILY 18 CHITINASE CHIB FROM SERRATIA MARCESCENS AND ITS COMPLEX WITH ALLOSAMIDIN