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(-) Description

Title :  HALLMARKS OF PROCESSIVE AND NON-PROCESSIVE GLYCOSIDE HYDROLASES REVEALED FROM COMPUTATIONAL AND CRYSTALLOGRAPHIC STUDIES OF THE SERRATIA MARCESCENS CHITINASES
 
Authors :  C. M. Payne, J. Baban, B. Synstad, P. H. Backe, A. S. Arvai, B. Dalhus, M. B V. G. H. Eijsink, M. Sorlie, G. T. Beckham, G. Vaaje-Kolstad
Date :  13 Jun 12  (Deposition) - 05 Sep 12  (Release) - 07 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.68
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. M. Payne, J. Baban, S. J. Horn, P. H. Backe, A. S. Arvai, B. Dalhus, M. Bjoras, V. G. H. Eijsink, M. Sorlie, G. T. Beckham, G. Vaaje-Kolstad
Hallmarks Of Processivity In Glycoside Hydrolases From Crystallographic And Computational Studies Of The Serratia Marcescens Chitinases.
J. Biol. Chem. V. 287 36322 2012
PubMed-ID: 22952223  |  Reference-DOI: 10.1074/JBC.M112.402149

(-) Compounds

Molecule 1 - CHITINASE C1
    Chains: A, B
    EC Number: 3.2.1.14
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES 1-328
    Organism Scientific: SERRATIA MARCESCENS
    Organism Taxid: 615

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2CA2Ligand/IonCALCIUM ION
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2CA-1Ligand/IonCALCIUM ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:15 , ILE A:17 , ASN A:93 , GLY A:132 , ASP A:134 , HOH A:2008BINDING SITE FOR RESIDUE CA A1329
2AC2SOFTWAREALA B:15 , ILE B:17 , ASN B:93 , GLY B:132 , ASP B:134 , HOH B:2006BINDING SITE FOR RESIDUE CA B1329
3AC3SOFTWAREASP A:40 , TYR A:42 , GLN A:44 , TRP A:300 , TRP A:304 , HOH A:2066 , HOH A:2067BINDING SITE FOR RESIDUE ACT A1330
4AC4SOFTWAREPHE A:30 , ASP A:139 , GLN A:206 , TYR A:208 , TRP A:300 , HOH A:2390 , HOH A:2391 , HOH A:2392BINDING SITE FOR RESIDUE ACT A1331
5AC5SOFTWAREPHE B:30 , ASP B:139 , GLN B:206 , TYR B:208 , TRP B:300 , HOH B:2240 , HOH B:2241BINDING SITE FOR RESIDUE ACT B1330
6AC6SOFTWARETYR A:237 , TYR A:238 , ARG A:286 , HOH A:2303 , HOH A:2341BINDING SITE FOR RESIDUE ACT A1332
7AC7SOFTWAREGLU B:318 , ARG B:322 , HOH B:2235BINDING SITE FOR RESIDUE ACT B1331

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4AXN)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:65 -Phe A:66
2Trp A:300 -Ser A:301
3Ala B:65 -Phe B:66
4Trp B:300 -Ser B:301

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4AXN)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4AXN)

(-) Exons   (0, 0)

(no "Exon" information available for 4AXN)

(-) 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:316
 aligned with Q700B8_SERMA | Q700B8 from UniProtKB/TrEMBL  Length:480

    Alignment length:316
                                    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      
         Q700B8_SERMA    13 DDAAIMPSIANKKILMGFWHNWAAGASDGYQQGQFANMNLTDIPTEYNVVAVAFMKGQGIPTFKPYNLSDTEFRRQVGVLNSQGRAVLISLGGADAHIELKTGDEDKLKDEIIRLVEVYGFDGLDIDLEQAAIGAANNKTVLPAALKKVKDHYAAQGKNFIISMAPEFPYLRTNGTYLDYINALEGYYDFIAPQYYNQGGDGIWVDELNAWITQNNDAMKEDFLYYLTESLVTGTRGYAKIPAAKFVIGLPSNNDAAATGYVVNKQAVYNAFSRLDAKNLSIKGLMTWSINWDNGKSKAGVAYNWEFKTRYAPLIQ 328
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh........eeeeeee..................hhhhh.....eeeeeee.............hhhhhhhhhhhhhhh..eeeeeeee..........hhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhhhhhhhh.....eeee...hhhh.....hhhhhhhh.....ee..........eeee....eeee.....hhhhhhhhhhhhhhhh.......hhhh.eeeee.............hhhhhhhhhhhhhh.....eeeeehhhhhh..........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4axn A  13 DDAAIMPSIANKKILMGFWHNWAAGASDGYQQGQFANMNLTDIPTEYNVVAVAFMKGQGIPTFKPYNLSDTEFRRQVGVLNSQGRAVLISLGGADAHIELKTGDEDKLKDEIIRLVEVYGFDGLDIDLEQAAIGAANNKTVLPAALKKVKDHYAAQGKNFIISMAPEFPYLRTNGTYLDYINALEGYYDFIAPQYYNQGGDGIWVDELNAWITQNNDAMKEDFLYYLTESLVTGTRGYAKIPAAKFVIGLPSNNDAAATGYVVNKQAVYNAFSRLDAKNLSIKGLMTWSINWDNGKSKAGVAYNWEFKTRYAPLIQ 328
                                    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      


Chain B from PDB  Type:PROTEIN  Length:316
 aligned with Q700B8_SERMA | Q700B8 from UniProtKB/TrEMBL  Length:480

    Alignment length:316
                                    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      
         Q700B8_SERMA    13 DDAAIMPSIANKKILMGFWHNWAAGASDGYQQGQFANMNLTDIPTEYNVVAVAFMKGQGIPTFKPYNLSDTEFRRQVGVLNSQGRAVLISLGGADAHIELKTGDEDKLKDEIIRLVEVYGFDGLDIDLEQAAIGAANNKTVLPAALKKVKDHYAAQGKNFIISMAPEFPYLRTNGTYLDYINALEGYYDFIAPQYYNQGGDGIWVDELNAWITQNNDAMKEDFLYYLTESLVTGTRGYAKIPAAKFVIGLPSNNDAAATGYVVNKQAVYNAFSRLDAKNLSIKGLMTWSINWDNGKSKAGVAYNWEFKTRYAPLIQ 328
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh........eeeeeee..................hhhhh.....eeeeeee.............hhhhhhhhhhhhhhh..eeeeeeee..........hhhhhhhhhhhhhhhhh..eeeeee.hhhh...hhhhhhhhhhhhhhhhhhh.....eeee...hhhh.....hhhhhhhh.....ee..........eeee....eeee.....hhhhhhhhhhhhhhhh.......hhhh.eeeee.............hhhhhhhhhhhhhh.....eeeeehhhhhh..........hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4axn B  13 DDAAIMPSIANKKILMGFWHNWAAGASDGYQQGQFANMNLTDIPTEYNVVAVAFMKGQGIPTFKPYNLSDTEFRRQVGVLNSQGRAVLISLGGADAHIELKTGDEDKLKDEIIRLVEVYGFDGLDIDLEQAAIGAANNKTVLPAALKKVKDHYAAQGKNFIISMAPEFPYLRTNGTYLDYINALEGYYDFIAPQYYNQGGDGIWVDELNAWITQNNDAMKEDFLYYLTESLVTGTRGYAKIPAAKFVIGLPSNNDAAATGYVVNKQAVYNAFSRLDAKNLSIKGLMTWSINWDNGKSKAGVAYNWEFKTRYAPLIQ 328
                                    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
   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 4AXN)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4AXN)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4AXN)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q700B8_SERMA | Q700B8)
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.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
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: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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