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(-) Description

Title :  THE CRYSTAL STRUCTURE OF CHRYSONILIA SITOPHILA ENDO-BETA-D-1,4-MANNANASE
 
Authors :  A. M. D. Goncalves, C. S. Silva, D. De Sanctis, I. Bento
Date :  01 Jun 12  (Deposition) - 31 Oct 12  (Release) - 07 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Endo-Mannanase, Glycosyl Hydrolase, Gh5 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. M. D. Goncalves, C. S. Silva, T. I. Madeira, R. Coelho, D. De Sanctis M. V. San Romao, I. Bento
Endo-Beta-D-1, 4-Mannanase From Chrysonilia Sitophila Displays A Novel Loop Arrangement For Substrate Selectivity
Acta Crystallogr. , Sect. D V. 68 1468 2012
PubMed-ID: 23090396  |  Reference-DOI: 10.1107/S0907444912034646

(-) Compounds

Molecule 1 - ENDO-BETA-D-1,4-MANNANASE
    Chains: A
    EC Number: 3.2.1.78
    Organism Scientific: NEUROSPORA SITOPHILA
    Organism Taxid: 40126
    Other Details: NAG LINKED TO N63, NAG LINKED TO N319
    Other Details - Source: COMMON NAME RED BREAD-MOULD, PORTUGUESE COLLECTION OF FUNGUS (IBET), DEPOSITED AT THE DEUTSCHE SAMMLUNG VON MIKROORGANISMEN UND ZELLKULTUREN GMBH, GERMANY, UNDER THE CODE DSM 16514

 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
1ACT2Ligand/IonACETATE ION
2CL1Ligand/IonCHLORIDE ION
3NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
4TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:319 , GLU A:324 , SER A:352 , TYR A:353 , HOH A:2449BINDING SITE FOR RESIDUE NAG A1390
2AC2SOFTWAREASN A:180 , GLU A:181 , TYR A:268 , TRP A:271 , GLU A:301 , TRP A:344 , ACT A:1393 , HOH A:2223 , HOH A:2387 , HOH A:2524BINDING SITE FOR RESIDUE TRS A1391
3AC3SOFTWAREPHE A:23 , ALA A:333 , ILE A:334 , LEU A:338 , GLY A:340 , ASP A:341 , HIS A:377 , VAL A:381BINDING SITE FOR RESIDUE ACT A1392
4AC4SOFTWAREGLU A:181 , ARG A:183 , TRP A:271 , TRP A:272 , TRS A:1391 , HOH A:2280 , HOH A:2286 , HOH A:2387BINDING SITE FOR RESIDUE ACT A1393
5AC5SOFTWARETYR A:29 , GLN A:345 , HIS A:357BINDING SITE FOR RESIDUE CL A1394
6AC6SOFTWAREASN A:63 , ILE A:67 , GLY A:70 , LEU A:71 , PRO A:72 , TYR A:74 , VAL A:136 , HOH A:2142 , HOH A:2238 , HOH A:2520 , HOH A:2521 , HOH A:2522BINDING SITE FOR CHAIN A OF SUGAR BOUND TO ASN A 63 RESIDUES 1388 TO 1389

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:184 -A:199

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:71 -Pro A:72
2Trp A:344 -Gln A:345

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4AWE)

(-) 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:381
 aligned with I4IY26_NEUSI | I4IY26 from UniProtKB/TrEMBL  Length:385

    Alignment length:383
                                                                                                                                                                                                                                                                                                                                                                                                                      385  
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384|  
         I4IY26_NEUSI     5 GFVTTEGDHFKLDGKDFYFAGSNAYYFPFNDQPDIEKGMTAARAAGLTVFRTWGFNDKNRTYIPTGLPQYGNEGAGDPTNTVFQWFEADGTQTIDVSPFDKVVDSATKTGIKLIVALTNNWADYGGMDVYTVNLGGKYHDDFYTVPKIKEAFKRYVKAMVTRYRDSEAILAWELANEARCGADGTRNLPRSEKGCTTETVTGWIEEMSAYVKSLDGNHLVTWGGEGGFNRGEDEEDGFYNGADGGDFDRELGLRNVDFGTMHLYPDWWSKSIEWSNQWIHDHAASGRAANKPVVLEEYGWMTDKGRLDQLGQVKNETRLEVVGGWQKIAIQEKLAGDMYWQFGYGGYSYGRNHDDSFTIYLEDDEAKELVYKHAKKVQKLN--   -
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee..eeee..ee..eeeee..hhhhhhhhhhhhhhhhhhhh...eeeee...eee........................eee.....eee.hhhhhhhhhhhhhhh.eeeee.........hhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh....eeeee......................hhhhhhhhhhhhhhhhhhhh...eee..........--............hhhhhhh......eeeeehhhhhh.hhhhhhhhhhhhhhhhhhhh..eeeeee...hhhhhhhhhh.....hhhhhhhhhhhhhhhhh..eeee..ee...............ee....hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4awe A   5 GFVTTEGDHFKLDGKDFYFAGSNAYYFPFNDQPDIEKGMTAARAAGLTVFRTWGFNDKNRTYIPTGLPQYGNEGAGDPTNTVFQWFEADGTQTIDVSPFDKVVDSATKTGIKLIVALTNNWADYGGMDVYTVNLGGKYHDDFYTVPKIKEAFKRYVKAMVTRYRDSEAILAWELANEARCGADGTRNLPRSEKGCTTETVTGWIEEMSAYVKSLDGNHLVTWGGEGGFNRG--EEDGFYNGADGGDFDRELGLRNVDFGTMHLYPDWWSKSIEWSNQWIHDHAASGRAANKPVVLEEYGWMTDKGRLDQLGQVKNETRLEVVGGWQKIAIQEKLAGDMYWQFGYGGYSYGRNHDDSFTIYLEDDEAKELVYKHAKKVQKLNER 387
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234|  |   244       254       264       274       284       294       304       314       324       334       344       354       364       374       384   
                                                                                                                                                                                                                                                                235  |                                                                                                                                                     
                                                                                                                                                                                                                                                                   238
   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 4AWE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (I4IY26_NEUSI | I4IY26)
molecular function
    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:0016985    mannan endo-1,4-beta-mannosidase activity    Catalysis of the random hydrolysis of (1->4)-beta-D-mannosidic linkages in mannans, galactomannans, glucomannans, and galactoglucomannans.
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.

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