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(-) Description

Title :  CHITINASE B FROM SERRATIA MARCESCENS INACTIVE MUTANT E144Q
 
Authors :  D. Komander, B. Synstad, V. G. H. Eijsink, D. M. F. Van Aalten
Date :  22 Aug 00  (Deposition) - 22 Jun 01  (Release) - 24 Aug 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  A  (1x)
Biol. Unit 3:  B  (1x)
Keywords :  Chitin Degradation, Hydrolase, Glycosidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. M. F. Van Aalten, D. Komander, B. Synstad, S. Gseidnes, M. G. Peter, V. G. H. Eijsink
Structural Insights Into The Catalytic Mechanism Of A Family 18 Exo-Chitinase
Proc. Natl. Acad. Sci. Usa V. 98 8979 2001
PubMed-ID: 11481469  |  Reference-DOI: 10.1073/PNAS.151103798

(-) Compounds

Molecule 1 - CHITINASE B
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: SERRATIA MARCESCENS
    Organism Taxid: 615

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): AB
Biological Unit 2 (1x): A 
Biological Unit 3 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 21)

Asymmetric Unit (2, 21)
No.NameCountTypeFull Name
1GOL18Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION
Biological Unit 1 (2, 21)
No.NameCountTypeFull Name
1GOL18Ligand/IonGLYCEROL
2SO43Ligand/IonSULFATE ION
Biological Unit 2 (2, 12)
No.NameCountTypeFull Name
1GOL11Ligand/IonGLYCEROL
2SO41Ligand/IonSULFATE ION
Biological Unit 3 (2, 9)
No.NameCountTypeFull Name
1GOL7Ligand/IonGLYCEROL
2SO42Ligand/IonSULFATE ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:420 , HOH A:2419 , HOH A:2483 , HOH A:2485 , LYS B:386 , ARG B:420BINDING SITE FOR RESIDUE SO4 A1510
02AC2SOFTWAREGLU A:383 , LYS A:386 , ARG B:420 , ASP B:426 , HOH B:2620 , HOH B:2621 , HOH B:2622 , HOH B:2623BINDING SITE FOR RESIDUE SO4 B1507
03AC3SOFTWARETHR B:26 , ARG B:343 , ARG B:410 , HOH B:2502 , HOH B:2624 , HOH B:2625 , HOH B:2626 , HOH B:2627BINDING SITE FOR RESIDUE SO4 B1508
04AC4SOFTWAREPRO A:260 , PHE A:263 , SER A:264 , ARG A:439 , TYR A:440 , THR A:441 , HOH A:2275 , HOH A:2473BINDING SITE FOR RESIDUE GOL A1499
05AC5SOFTWAREPHE A:51 , ASP A:142 , GLN A:144 , MET A:212 , TYR A:214 , TRP A:403 , HOH A:2474BINDING SITE FOR RESIDUE GOL A1500
06AC6SOFTWAREGLU A:221 , PHE A:239 , GOL A:1502 , GOL A:1505 , HOH A:2475 , HOH A:2476 , GLY B:480BINDING SITE FOR RESIDUE GOL A1501
07AC7SOFTWAREASP A:215 , LEU A:216 , ALA A:217 , TRP A:220 , GLU A:221 , GOL A:1501 , GOL A:1508 , HOH A:2477BINDING SITE FOR RESIDUE GOL A1502
08AC8SOFTWAREARG A:244 , PHE A:259 , PRO A:260 , SER A:261BINDING SITE FOR RESIDUE GOL A1503
09AC9SOFTWARETHR A:3 , ARG A:4 , HIS A:46 , ARG A:89 , HOH A:2107 , HOH A:2231 , HOH A:2479BINDING SITE FOR RESIDUE GOL A1504
10BC1SOFTWAREPHE A:190 , ARG A:194 , GOL A:1501 , TRP B:479 , ILE B:482 , THR B:483 , SER B:484 , HOH B:2599BINDING SITE FOR RESIDUE GOL A1505
11BC2SOFTWARETYR A:323 , VAL A:326 , GLY A:327 , VAL A:332 , HOH A:2322 , HOH A:2324BINDING SITE FOR RESIDUE GOL A1506
12BC3SOFTWARETYR A:214 , ASP A:215 , TYR A:292 , ARG A:294 , ILE A:339 , GOL A:1509 , HOH A:2480 , HOH A:2481BINDING SITE FOR RESIDUE GOL A1507
13BC4SOFTWARETRP A:97 , TRP A:220 , GOL A:1502 , GOL A:1509 , HOH A:2482 , TYR B:481BINDING SITE FOR RESIDUE GOL A1508
14BC5SOFTWAREASP A:215 , ASP A:316 , GOL A:1507 , GOL A:1508 , HOH A:2169 , HOH A:2482BINDING SITE FOR RESIDUE GOL A1509
15BC6SOFTWAREGLY A:480 , TYR A:481 , GLU B:221 , PHE B:239 , GOL B:1501 , HOH B:2608 , HOH B:2609BINDING SITE FOR RESIDUE GOL B1500
16BC7SOFTWARETRP A:479 , TYR A:481 , ILE A:482 , THR A:483 , ASP A:489 , PHE B:190 , PHE B:191 , ARG B:194 , GOL B:1500BINDING SITE FOR RESIDUE GOL B1501
17BC8SOFTWARETHR B:3 , ARG B:4 , THR B:45 , HIS B:46 , ARG B:89 , HOH B:2170 , HOH B:2320 , HOH B:2611BINDING SITE FOR RESIDUE GOL B1502
18BC9SOFTWAREASP B:142 , GLN B:144 , MET B:212 , TYR B:214 , TRP B:403 , HOH B:2612 , HOH B:2613BINDING SITE FOR RESIDUE GOL B1503
19CC1SOFTWAREARG B:162 , ALA B:204 , ASP B:207 , LYS B:284 , HOH B:2475BINDING SITE FOR RESIDUE GOL B1504
20CC2SOFTWAREPRO B:260 , PHE B:263 , SER B:264 , ARG B:439 , TYR B:440 , THR B:441 , HOH B:2616 , HOH B:2617BINDING SITE FOR RESIDUE GOL B1505
21CC3SOFTWARETYR B:323 , VAL B:326 , GLY B:327 , CYS B:328 , GLU B:329 , VAL B:332 , HOH B:2424 , HOH B:2427 , HOH B:2618 , HOH B:2619BINDING SITE FOR RESIDUE GOL B1506

(-) SS Bonds  (2, 2)

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

(-) Cis Peptide Bonds  (10, 10)

Asymmetric Unit
No.Residues
1Ser A:50 -Phe A:51
2Gln 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
7Gln 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 1E6P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1E6P)

(-) Exons   (0, 0)

(no "Exon" information available for 1E6P)

(-) Sequences/Alignments

Asymmetric 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:498
 aligned with Q54276_SERMA | Q54276 from UniProtKB/TrEMBL  Length:499

    Alignment length:498
                                    11        21        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       391       401       411       421       431       441       451       461       471       481       491        
         Q54276_SERMA     2 STRKAVIGYYFIPTNQINNYTETDTSVVPFPVSNITPAKAKQLTHINFSFLDINSNLECAWDPATNDAKARDVVNRLTALKAHNPSLRIMFSIGGWYYSNDLGVSHANYVNAVKTPASRAKFAQSCVRIMKDYGFDGVDIDWEYPQAAEVDGFIAALQEIRTLLNQQTITDGRQALPYQLTIAGAGGAFFLSRYYSKLAQIVAPLDYINLMTYDLAGPWEKVTNHQAALFGDAAGPTFYNALREANLGWSWEELTRAFPSPFSLTVDAAVQQHLMMEGVPSAKIVMGVPFYGRAFKGVSGGNGGQYSSHSTPGEDPYPSTDYWLVGCEECVRDKDPRIASYRQLEQMLQGNYGYQRLWNDKTKTPYLYHAQNGLFVTYDDAESFKYKAKYIKQQQLGGVMFWHLGQDNRNGDLLAALDRYFNAADYDDSQLDMGTGLRYTGVGPGNLPIMTAPAYVPGTTYAQGALVSYQGYVWQTKWGYITSAPGSDSAWLKVGRVA 499
               SCOP domains d1e6pa2 A:2-291,A:380-446 Chitinase B, catalytic domain                                                                                                                                                                                                                                           d1e6pa3 A:292-379 Chitinase B                                                           d1e6pa2 A:2-291,A:380-446 Chitinase B, catalytic domain            d1e6pa1 A:447-498 Chitinase B, C-terminal domain    - SCOP domains
               CATH domains 1e6pA01 A:2-290,A:381-448 Glycosidases                                                                                                                                                                                                                                                           1e6pA02 A:291-380  [code=3.10.50.10, no name defined]                                     1e6pA01 A:2-290,A:381-448 Glycosidases                              1e6pA03 A:449-499                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeeeeee.hhhhhh............hhhhhhhhhhhhh.eeeee................hhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhh....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..eeeee.......hhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.hhhhhhhhhhhhhhhhh...eeeee............................hhhhhh....hhhhhhhhh......hhhhhhhhhhh....hhh.eeeeee.eeeeee..............................hhhhhhh....eeehhhhhhhhhh...eeeeee....eeeeee....eeee....hhhhhhhhhhhhh...eeeeehhhhh...hhhhhhhhhhhhh...................hhhhh..................eeee..eeeee..............eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1e6p A   2 STRKAVIGYYFIPTNQINNYTETDTSVVPFPVSNITPAKAKQLTHINFSFLDINSNLECAWDPATNDAKARDVVNRLTALKAHNPSLRIMFSIGGWYYSNDLGVSHANYVNAVKTPASRAKFAQSCVRIMKDYGFDGVDIDWQYPQAAEVDGFIAALQEIRTLLNQQTITDGRQALPYQLTIAGAGGAFFLSRYYSKLAQIVAPLDYINLMTYDLAGPWEKVTNHQAALFGDAAGPTFYNALREANLGWSWEELTRAFPSPFSLTVDAAVQQHLMMEGVPSAKIVMGVPFYGRAFKGVSGGNGGQYSSHSTPGEDPYPSTDYWLVGCEECVRDKDPRIASYRQLEQMLQGNYGYQRLWNDKTKTPYLYHAQNGLFVTYDDAESFKYKAKYIKQQQLGGVMFWHLGQDNRNGDLLAALDRYFNAADYDDSQLDMGTGLRYTGVGPGNLPIMTAPAYVPGTTYAQGALVSYQGYVWQTKWGYITSAPGSDSAWLKVGRVA 499
                                    11        21        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       391       401       411       421       431       441       451       461       471       481       491        


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 d1e6pb2 B:3-291,B:380-446 Chitinase B, catalytic domain                                                                                                                                                                                                                                          d1e6pb3 B:292-379 Chitinase B                                                           d1e6pb2 B:3-291,B:380-446 Chitinase B, catalytic domain            d1e6pb1 B:447-499 Chitinase B, C-terminal domain      SCOP domains
               CATH domains 1e6pB01 B:3-290,B:381-448 Glycosidases                                                                                                                                                                                                                                                          1e6pB02 B:291-380  [code=3.10.50.10, no name defined]                                     1e6pB01 B:3-290,B:381-448 Glycosidases                              1e6pB03 B:449-499                                   CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee.hhhhhhh...........hhhhhhhhhhhhh.eeeee................hhhhhhhhhhhhhhhhhhh...eeeeeeehhhhhh....hhhhhhhhh.hhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhhhhhhhhhhhhhhhhhhh.......eeeeeee.hhhhhhhhhhhhhhhhh...eeeee............................hhhhhh....hhhhhhhhh......hhhhhhhhhhh....hhh.eeeeee.eeeeee..............................hhhhhhh....eeehhhhhhhhhh...eeeeee....eeeeee....eeee....hhhhhhhhhhhhh...eeeeehhhhh...hhhhhhhhhhhhh..........................................eeee..eeeee..............eeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e6p B   3 TRKAVIGYYFIPTNQINNYTETDTSVVPFPVSNITPAKAKQLTHINFSFLDINSNLECAWDPATNDAKARDVVNRLTALKAHNPSLRIMFSIGGWYYSNDLGVSHANYVNAVKTPASRAKFAQSCVRIMKDYGFDGVDIDWQYPQAAEVDGFIAALQEIRTLLNQQTITDGRQALPYQLTIAGAGGAFFLSRYYSKLAQIVAPLDYINLMTYDLAGPWEKVTNHQAALFGDAAGPTFYNALREANLGWSWEELTRAFPSPFSLTVDAAVQQHLMMEGVPSAKIVMGVPFYGRAFKGVSGGNGGQYSSHSTPGEDPYPSTDYWLVGCEECVRDKDPRIASYRQLEQMLQGNYGYQRLWNDKTKTPYLYHAQNGLFVTYDDAESFKYKAKYIKQQQLGGVMFWHLGQDNRNGDLLAALDRYFNAADYDDSQLDMGTGLRYTGVGPGNLPIMTAPAYVPGTTYAQGALVSYQGYVWQTKWGYITSAPGSDSAWLKVGRVA 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 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 Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1E6P)

(-) Gene Ontology  (9, 9)

Asymmetric 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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  Q54276_SERMA | Q54276
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 1e6r 1e6z 1gpf 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
1e6r CHITINASE B FROM SERRATIA MARCESCENS WILDTYPE IN COMPLEX WITH INHIBITOR ALLOSAMIDIN