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(-) Description

Title :  CHITINASE B FROM SERRATIA MARCESCENS IN COMPLEX WITH INHIBITOR PSAMMAPLIN
 
Authors :  D. Komander, D. M. Van Aalten
Date :  03 Nov 01  (Deposition) - 31 Oct 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Hydrolase, Chitin Degradation, Inhibitor Psammaplin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. N. Tabudravu, V. G. Eijsink, G. W. Gooday, M. Jaspars, D. Komander, M. Legg, B. Synstad, D. M. Van Aalten
Psammaplin A, A Chitinase Inhibitor Isolated From The Fijian Marine Sponge Aplysinella Rhax
Bioorg. Med. Chem. V. 10 1123 2002
PubMed-ID: 11836123  |  Reference-DOI: 10.1016/S0968-0896(01)00372-8

(-) 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

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:420 , HOH A:2326 , HOH A:2327 , HOH A:2328 , LYS B:386 , HOH B:2239BINDING SITE FOR RESIDUE SO4 A1499
2AC2SOFTWAREGLU A:383 , LYS A:386 , ARG B:420 , HOH B:2285BINDING SITE FOR RESIDUE SO4 B1500
3AC3SOFTWAREPRO B:281 , SER B:282 , HOH B:2196 , HOH B:2286BINDING SITE FOR RESIDUE SO4 B1501

(-) 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 1GPF)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1GPF)

(-) 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 d1gpfa2 A:3-291,A:380-446 Chitinase B, catalytic domain                                                                                                                                                                                                                                          d1gpfa3 A:292-379 Chitinase B                                                           d1gpfa2 A:3-291,A:380-446 Chitinase B, catalytic domain            d1gpfa1 A:447-499 Chitinase B, C-terminal domain      SCOP domains
               CATH domains 1gpfA01 A:3-290,A:381-448 Glycosidases                                                                                                                                                                                                                                                          1gpfA02 A:291-380  [code=3.10.50.10, no name defined]                                     1gpfA01 A:3-290,A:381-448 Glycosidases                              1gpfA03 A:449-499                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.hhhhhhh...........hhhhhhhhhhhhh.eeeeeeeee............hhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhh....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.hhhhhhhhhhhhhhhhh...eeeee............................hhhhhh....hhhhhhhhh......hhhhhhhhhhh....hhh.eeeeee.eeeee...............................hhhhhhh....eeehhhhhhhhhh...eeeeee....eeeeee....eeee..hhhhhhhhhhhhhhh...eeeeehhhhh...hhhhhhhhhhhhh...................hhhhh..................eeee..eeeee..............eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gpf 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 d1gpfb2 B:3-291,B:380-446 Chitinase B, catalytic domain                                                                                                                                                                                                                                          d1gpfb3 B:292-379 Chitinase B                                                           d1gpfb2 B:3-291,B:380-446 Chitinase B, catalytic domain            d1gpfb1 B:447-499 Chitinase B, C-terminal domain      SCOP domains
               CATH domains 1gpfB01 B:3-290,B:381-448 Glycosidases                                                                                                                                                                                                                                                          1gpfB02 B:291-380  [code=3.10.50.10, no name defined]                                     1gpfB01 B:3-290,B:381-448 Glycosidases                              1gpfB03 B:449-499                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.hhhhhhh...........hhhhhhhhhhhhh.eeeeeeeee............hhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhh....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.hhhhhhhhhhhhhhhhh...eeeee............................hhhhhh....hhhhhhhhh......hhhhhhhhhhh....hhh.eeeeee.eeeeee..............................hhhhhhhh...eeehhhhhhhhhh....eeeee....eeeeee....eeee..hhhhhhhhhhhhhhh...eeeeehhhhh...hhhhhhhhhhhhh..........................................eeee..eeeee..............eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gpf 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)
    → 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  (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  (0, 0)

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

(-) 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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  1gpf
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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 1ur8 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