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(-) Description

Title :  CHITINASE A FROM SERRATIA MARCESCENS ATCC990 IN COMPLEX WITH CHITOBIO-THIAZOLINE THIOAMIDE.
 
Authors :  E. J. Taylor, R. J. Dennis, J. M. Macdonald, C. A. Tarling, S. Knapp, S. G. Withers, G. J. Davies
Date :  29 Jun 09  (Deposition) - 16 Mar 10  (Release) - 12 Oct 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Chitin Hydrolysis, Chitin Degradation, Polysaccharide Degradation, Carbohydrate Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. M. Macdonald, C. A. Tarling, E. J. Taylor, R. J. Dennis, D. S. Myers, S. Knapp, G. J. Davies, S. G. Withers
Chitinase Inhibition By Chitobiose And Chitotriose Thiazolines.
Angew. Chem. Int. Ed. Engl. V. 49 2599 2010
PubMed-ID: 20209544  |  Reference-DOI: 10.1002/ANIE.200906644

(-) Compounds

Molecule 1 - CHITINASE A
    Atcc990
    ChainsA
    EC Number3.2.1.14
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B (NOVAGEN)
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentRESIDUES 2-520
    Organism ScientificSERRATIA MARCESCENS
    Organism Taxid615
    SynonymSMCHI18A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1DIO1Ligand/Ion1,4-DIETHYLENE DIOXIDE
2NAG4Ligand/IonN-ACETYL-D-GLUCOSAMINE
3NGT1Ligand/Ion3AR,5R,6S,7R,7AR-5-HYDROXYMETHYL-2-METHYL-5,6,7,7A-TETRAHYDRO-3AH-PYRANO[3,2-D]THIAZOLE-6,7-DIOL
4PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:167 , ILE A:207 , THR A:276 , GLU A:473 , NAG A:1563 , HOH A:2553 , HOH A:2554 , HOH A:2555 , HOH A:2556BINDING SITE FOR RESIDUE NAG A1562
2AC2SOFTWAREPHE A:191 , TRP A:275 , THR A:276 , GLU A:473 , ILE A:476 , TRP A:539 , GLU A:540 , NAG A:1562 , NGT A:1564 , HOH A:2494 , HOH A:2557 , HOH A:2558 , HOH A:2559BINDING SITE FOR RESIDUE NAG A1563
3AC3SOFTWARETYR A:163 , PHE A:191 , TRP A:275 , ASP A:313 , GLU A:315 , TYR A:390 , ASP A:391 , ARG A:446 , TRP A:539 , NAG A:1563 , NAG A:1567BINDING SITE FOR RESIDUE NGT A1564
4AC4SOFTWAREVAL A:54 , ARG A:221 , GLU A:299 , HOH A:2043 , HOH A:2050BINDING SITE FOR RESIDUE DIO A1565
5AC5SOFTWAREILE A:31 , ALA A:32 , GLY A:34 , THR A:126 , HOH A:2015 , HOH A:2561 , HOH A:2562 , HOH A:2564BINDING SITE FOR RESIDUE PEG A1566
6AC6SOFTWARETRP A:275 , GLU A:315 , PHE A:316 , ASP A:391 , ARG A:446 , NGT A:1564 , NAG A:1568 , HOH A:2444 , HOH A:2566BINDING SITE FOR RESIDUE NAG A1567
7AC7SOFTWARELYS A:369 , ASP A:391 , PHE A:396 , TYR A:418 , NAG A:1567 , HOH A:2423 , HOH A:2567 , HOH A:2568 , HOH A:2569BINDING SITE FOR RESIDUE NAG A1568

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:115 -A:120
2A:195 -A:218

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Gly A:190 -Phe A:191
2Glu A:315 -Phe A:316
3Trp A:539 -Glu A:540

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2WM0)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CHITINASE_18PS01095 Chitinases family 18 active site.CHIA_SERMA307-315  1A:307-315

(-) Exons   (0, 0)

(no "Exon" information available for 2WM0)

(-) 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:538
 aligned with A6XFF7_SERMA | A6XFF7 from UniProtKB/TrEMBL  Length:521

    Alignment length:538
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 521                  
                                    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       501       511       521         -        
         A6XFF7_SERMA     2 AAPGKPTIAWGNTKFAIVEVDQAATAYNNLVKVKNAADVSVSWNLWNGDTGTTAKILLNGKEAWSGPSTGSSGTANFKVNKGGRYQMQVALCNADGCTASDATEIVVADTDGSHLAPLKEPLLEKNKPYKQNSGKVVGSYFVEWGVYGRNFTVDKIPAQNLTHLLYGFIPICGGNGINDSLKEIEGSFQALQRSCQGREDFKVSIHDPFAALQKAQKGVTAWDDPYKGNFGQLMALKQAHPDLKILPSIGGWTLSDPFFFMGDKVKRDRFVGSVKEFLQTWKFFDGVDIDWEFPGGKGANPNLGSPQDGETYVLLMKELRAMLDQLSAETGRKYELTSAISAGKDKIDKVAYNVAQNSMDHIFLMSYDFYGAFDLKNLGHQTALNAPAWKPDTAYTTVNGVNALLTQGVKPGKIVVGTAMYGRGWTGVNGYQNNIPFTGTATGPVKGTWENGIVDYRQIASQFMSGEWQYTYDATAEAPYVFKPSTGDLITFDDARSVQAKGKYVLDKQLGGLFSWEIDQ------------------   -
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2wm0A01 A:24-130 Immunoglobulins                                                                           2wm0A02 A:131-442,A:519-561 Glycosidases                                                                                                                                                                                                                                                                                2wm0A03 A:443-518  [code=3.10.50.10, no name defined]                       2wm0A02 A:131-442,A:519-561 Glycosidases    CATH domains
               Pfam domains ChitinaseA_N-2wm0A01 A:24-156                                                                                                        -Glyco_hydro_18-2wm0A02 A:158-544                                                                                                                                                                                                                                                                                                                                                                   ----------------- Pfam domains
         Sec.struct. author ......ee.....eee.eee.....hhhhheee...eeeeeeee........eeeeee..eeeeeee....eeeeeeee...eeeeeeeeeee..eeee...eeeeee...........................eeeeeee.hhhh....hhhhhhhhhh.eeeeeee........hhhhhhh.hhhhhhhhhh...........hhhhhhh.............hhhhhhhhhhhhhh...eeeeeee....hhhhhhh.hhhhhhhhhhhhhhhhhhh....eeeee................hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhh..hhhhhhhhh.eeeee..............................hhhhhhhhhhhhh.hhh.eeeeee.eeeeee........hhhhh...ee........eeehhhhhhhh.....eeeee....eeeeee....eeee..hhhhhhhhhhhhhhhh..eeeeehhhhh.hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wm0 A  24 AAPGKPTIAWGNTKFAIVEVDQAATAYNNLVKVKNAADVSVSWNLWNGDTGTTAKILLNGKEAWSGPSTGSSGTANFKVNKGGRYQMQVALCNADGCTASDATEIVVADTDGSHLAPLKEPLLEKNKPYKQNSGKVVGSYFVEWGVYGRNFTVDKIPAQNLTHLLYGFIPICGGNGINDSLKEIEGSFQALQRSCQGREDFKVSIHDPFAALQKAQKGVTAWDDPYKGNFGQLMALKQAHPDLKILPSIGGWTLSDPFFFMGDKVKRDRFVGSVKEFLQTWKFFDGVDIDWEFPGGKGANPNLGSPQDGETYVLLMKELRAMLDQLSAETGRKYELTSAISAGKDKIDKVAYNVAQNSMDHIFLMSYDFYGAFDLKNLGHQTALNAPAWKPDTAYTTVNGVNALLTQGVKPGKIVVGTAMYGRGWTGVNGYQNNIPFTGTATGPVKGTWENGIVDYRQIASQFMSGEWQYTYDATAEAPYVFKPSTGDLITFDDARSVQAKGKYVLDKQLGGLFSWEIDADNGDILNSMNASLGNSAG 561
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553        

Chain A from PDB  Type:PROTEIN  Length:538
 aligned with CHIA_SERMA | P07254 from UniProtKB/Swiss-Prot  Length:563

    Alignment length:538
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553        
           CHIA_SERMA    24 AAPGKPTIAWGNTKFAIVEVDQAATAYNNLVKVKNAADVSVSWNLWNGDAGTTAKILLNGKEAWSGPSTGSSGTANFKVNKGGRYQMQVALCNADGCTASDATEIVVADTDGSHLAPLKEPLLEKNKPYKQNSGKVVGSYFVEWGVYGRNFTVDKIPAQNLTHLLYGFIPICGGNGINDSLKEIEGSFQALQRSCQGREDFKVSIHDPFAALQKAQKGVTAWDDPYKGNFGQLMALKQAHPDLKILPSIGGWTLSDPFFFMGDKVKRDRFVGSVKEFLQTWKFFDGVDIDWEFPGGKGANPNLGSPQDGETYVLLMKELRAMLDQLSAETGRKYELTSAISAGKDKIDKVAYNVAQNSMDHIFLMSYDFYGPFDLKNLGHQTALNAPAWKPDTAYTTVNGVNALLAQGVKPGKVVVGTAMYGRGWTGVNGYQNNIPFTGTATGPVKGTWKNGIVDYRQIAGQFMSGEWQYTYDATAEAPYVFKPSTGDLITFDDARSVQAKGKYVLDKQLGGLFSWEIDADNGDILNSMNASLGNSAG 561
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2wm0A01 A:24-130 Immunoglobulins                                                                           2wm0A02 A:131-442,A:519-561 Glycosidases                                                                                                                                                                                                                                                                                2wm0A03 A:443-518  [code=3.10.50.10, no name defined]                       2wm0A02 A:131-442,A:519-561 Glycosidases    CATH domains
               Pfam domains ChitinaseA_N-2wm0A01 A:24-156                                                                                                        -Glyco_hydro_18-2wm0A02 A:158-544                                                                                                                                                                                                                                                                                                                                                                   ----------------- Pfam domains
         Sec.struct. author ......ee.....eee.eee.....hhhhheee...eeeeeeee........eeeeee..eeeeeee....eeeeeeee...eeeeeeeeeee..eeee...eeeeee...........................eeeeeee.hhhh....hhhhhhhhhh.eeeeeee........hhhhhhh.hhhhhhhhhh...........hhhhhhh.............hhhhhhhhhhhhhh...eeeeeee....hhhhhhh.hhhhhhhhhhhhhhhhhhh....eeeee................hhhhhhhhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhh..hhhhhhhhh.eeeee..............................hhhhhhhhhhhhh.hhh.eeeeee.eeeeee........hhhhh...ee........eeehhhhhhhh.....eeeee....eeeeee....eeee..hhhhhhhhhhhhhhhh..eeeeehhhhh.hhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CHITINASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wm0 A  24 AAPGKPTIAWGNTKFAIVEVDQAATAYNNLVKVKNAADVSVSWNLWNGDTGTTAKILLNGKEAWSGPSTGSSGTANFKVNKGGRYQMQVALCNADGCTASDATEIVVADTDGSHLAPLKEPLLEKNKPYKQNSGKVVGSYFVEWGVYGRNFTVDKIPAQNLTHLLYGFIPICGGNGINDSLKEIEGSFQALQRSCQGREDFKVSIHDPFAALQKAQKGVTAWDDPYKGNFGQLMALKQAHPDLKILPSIGGWTLSDPFFFMGDKVKRDRFVGSVKEFLQTWKFFDGVDIDWEFPGGKGANPNLGSPQDGETYVLLMKELRAMLDQLSAETGRKYELTSAISAGKDKIDKVAYNVAQNSMDHIFLMSYDFYGAFDLKNLGHQTALNAPAWKPDTAYTTVNGVNALLTQGVKPGKIVVGTAMYGRGWTGVNGYQNNIPFTGTATGPVKGTWENGIVDYRQIASQFMSGEWQYTYDATAEAPYVFKPSTGDLITFDDARSVQAKGKYVLDKQLGGLFSWEIDADNGDILNSMNASLGNSAG 561
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553        

   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 2WM0)

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: E-set (290)

(-) Gene Ontology  (8, 15)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (A6XFF7_SERMA | A6XFF7)
molecular function
    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.

Chain A   (CHIA_SERMA | P07254)
molecular function
    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.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        A6XFF7_SERMA | A6XFF72wk2 2wly 2wlz
        CHIA_SERMA | P072541ctn 1ehn 1eib 1ffq 1ffr 1k9t 1nh6 1rd6 1x6l 1x6n 2wk2 2wly 2wlz

(-) Related Entries Specified in the PDB File

1ctn CHITINASE A (PH 5.5, 4 DEGREES C)
1ehn CRYSTAL STRUCTURE OF CHITINASE A MUTANT E315Q COMPLEXED WITH OCTA-N- ACETYLCHITOOCTAOSE (NAG)8.
1eib CRYSTAL STRUCTURE OF CHITINASE A MUTANT D313A COMPLEXED WITH OCTA-N- ACETYLCHITOOCTAOSE (NAG)8.
1ffq CRYSTAL STRUCTURE OF CHITINASE A COMPLEXED WITH ALLOSAMIDIN
1ffr CRYSTAL STRUCTURE OF CHITINASE A MUTANT Y390F COMPLEXEDWITH HEXA-N-ACETYLCHITOHEXAOSE (NAG)6
1k9t CHITINASE A COMPLEXED WITH TETRA-N- ACETYLCHITOTRIOSE
1nh6 STRUCTURE OF S. MARCESCENS CHITINASE A, E315L, COMPLEX WITHHEXASACCHARIDE
1rd6 CRYSTAL STRUCTURE OF S. MARCESCENS CHITINASE A MUTANT W167A
1x6l CRYSTAL STRUCTURE OF S. MARCESCENS CHITINASE A MUTANT W167A
1x6n CRYSTAL STRUCTURE OF S. MARCESCENS CHITINASE A MUTANT W167AIN COMPLEX WITH ALLOSAMIDIN
2wk2 CHITINASE A FROM SERRATIA MARCESCENS ATCC990 IN COMPLEX WITH CHITOTRIO-THIAZOLINE DITHIOAMIDE.
2wly CHITINASE A FROM SERRATIA MARCESCENS ATCC990 IN COMPLEX WITH CHITOTRIO-THIAZOLINE.
2wlz CHITINASE A FROM SERRATIA MARCESCENS ATCC990 IN COMPLEX WITH CHITOBIO-THIAZOLINE.