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(-) Description

Title :  SUBSTRATE DISTORTION BY BETA-MANNANASE FROM PSEUDOMONAS CELLULOSA
 
Authors :  V. Ducros, D. L. Zechel, H. J. Gilbert, L. Szabo, S. G. Withers, G. J. Davi
Date :  01 Mar 02  (Deposition) - 05 Sep 02  (Release) - 28 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Glycoside Hydrolase, Glycosidase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Ducros, D. L. Zechel, G. Murshudov, H. J. Gilbert, L. Szabo, D. Stoll S. G. Withers, G. J. Davies
Substrate Distortion By A Beta-Mannanase: Snapshots Of The Michaelis And Covalent-Intermediate Complexes Suggest A B2, 5 Conformation For The Transition State
Angew. Chem. Int. Ed. Engl. V. 41 2824 2002 (for further references see the PDB file header)

(-) Compounds

Molecule 1 - MANNAN ENDO-1,4-BETA-MANNOSIDASE
    Chains: A
    EC Number: 3.2.1.78
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector: PET21A
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: PSEUDOMONAS CELLULOSA
    Organism Taxid: 155077
    Other Details: COMPLEX WITH 2,4-DINITROPHENYL 2-DEOXY-2-FLUORO-BETA-MANNOTRIOSIDE
    Synonym: BETA-MANNANASE, MANNANASE A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 10)

Asymmetric/Biological Unit (7, 10)
No.NameCountTypeFull Name
1BMA2Ligand/IonBETA-D-MANNOSE
2MAF1Ligand/Ion2-DEOXY-2-FLUORO-ALPHA-D-MANNOSE
3MBF1Ligand/Ion2-DEOXY-2-FLUORO-BETA-D-MANNOSE
4NA1Ligand/IonSODIUM ION
5NIN1Ligand/IonDINITROPHENYLENE
6TRS2Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
7ZN2Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:67 , HIS A:71 , GLU A:239 , TRS A:1430BINDING SITE FOR RESIDUE ZN A1422
2AC2SOFTWAREARG A:69 , SER A:72 , ILE A:73 , ARG A:352 , GLU A:353 , ILE A:354BINDING SITE FOR RESIDUE NA A1423
3AC3SOFTWAREARG A:208 , HIS A:211 , ASP A:283 , GLU A:320BINDING SITE FOR RESIDUE ZN A1424
4AC4SOFTWAREHIS A:143 , TRP A:162 , HIS A:211 , TYR A:285 , GLU A:320 , ALA A:325 , TRP A:360 , TRP A:379 , BMA A:1426 , NIN A:1429 , HOH A:2372 , HOH A:2373 , HOH A:2374 , HOH A:2376BINDING SITE FOR RESIDUE MBF A1428
5AC5SOFTWARETRP A:162 , TRP A:217 , MAF A:1427 , MBF A:1428 , HOH A:2373 , HOH A:2376BINDING SITE FOR RESIDUE NIN A1429
6AC6SOFTWAREGLU A:67 , HIS A:71 , GLN A:232 , ARG A:235 , GLU A:239 , TRP A:276 , ZN A:1422 , HOH A:2377 , HOH A:2378 , HOH A:2379BINDING SITE FOR RESIDUE TRS A1430
7AC7SOFTWARETYR A:400 , ALA A:401 , ASP A:402 , GLU A:403 , THR A:405 , PHE A:407 , ASP A:410BINDING SITE FOR RESIDUE TRS A1431
8AC8SOFTWARELEU A:113 , ALA A:120 , GLU A:121 , HIS A:143 , HIS A:211 , TYR A:285 , GLU A:320 , TRP A:360 , ARG A:361 , HIS A:377 , MBF A:1428 , NIN A:1429 , HOH A:2097 , HOH A:2100 , HOH A:2157 , HOH A:2370 , HOH A:2371 , HOH A:2372BINDING SITE FOR CHAIN A OF POLYSACCHARIDE RESIDUES 1425 TO 1427

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1GW1)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ala A:117 -Pro A:118
2Trp A:156 -Pro A:157

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1GW1)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1GH26PS51764 Glycosyl hydrolases family 26 (GH26) domain profile.MANA_CELJU56-409  1A:56-409

(-) Exons   (0, 0)

(no "Exon" information available for 1GW1)

(-) 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:375
 aligned with MANA_CELJU | P49424 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:379
                                    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         
           MANA_CELJU    43 KPVTVKLVDSQATMETRSLFAFMQEQRRHSIMFGHQHETTQGLTITRTDGTQSDTFNAVGDFAAVYGWDTLSIVAPKAEGDIVAQVKKAYARGGIITVSSHFDNPKTDTQKGVWPVGTSWDQTPAVVDSLPGGAYNPVLNGYLDQVAEWANNLKDEQGRLIPVIFRLYHENTGSWFWWGDKQSTPEQYKQLFRYSVEYLRDVKGVRNFLYAYSPNNFWDVTEANYLERYPGDEWVDVLGFDTYGPVADNADWFRNVVANAALVARMAEARGKIPVISEIGIRAPDIEAGLYDNQWYRKLISGLKADPDAREIAFLLVWRNAPQGVPGPNGTQVPHYWVPANRPENINNGTLEDFQAFYADEFTAFNRDIEQVYQRPTLI 421
               SCOP domains d1gw1a_ A: Mannanase A, ManA                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1gw1A00 A:43-421 Glycosidases                                                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..ee........hhhhhhhhhhhhhhh...eeeeee................hhhhhhhh....eeeee.hhh........hhhhhhhhhhh..eeeee.......hhhhh.......................hhhhhhhhhhhhhhhhhh..........eeee.................hhhhhhhhhhhhhhhhhhh.....eeeee........hhhhhhh.........ee..eeee....hhhhhhhhhhhhhhhhhhhhhhh.ee...eeeehhhhhhh.....hhhhhhhhhhhhh.hhhhh.eeee..........----..........hhhhhhhhhhhhhhhhhhh..eehhhhh.......ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------GH26  PDB: A:56-409 UniProt: 56-409                                                                                                                                                                                                                                                                                                                               ------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1gw1 A  43 KPVTVKLVDSQATMETRSLFAFMQEQRRHSIMFGHQHETTQGLTITRTDGTQSDTFNAVGDFAAVYGWDTLSIVAPKAEGDIVAQVKKAYARGGIITVSSHFDNPKTDTQKGVWPVGTSWDQTPAVVDSLPGGAYNPVLNGYLDQVAEWANNLKDEQGRLIPVIFRLYHANTGSWFWWGDKQSTPEQYKQLFRYSVEYLRDVKGVRNFLYAYSPNNFWDVTEANYLERYPGDEWVDVLGFDTYGPVADNADWFRNVVANAALVARMAEARGKIPVISEIGIRAPDIEAGLYDNQWYRKLISGLKADPDAREIAFLLVWRNAPQGVPG----QVPHYWVPANRPENINNGTLEDFQAFYADEFTAFNRDIEQVYQRPTLI 421
                                    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      |  - |     382       392       402       412         
                                                                                                                                                                                                                                                                                                                                                                369  374
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1GW1)

(-) Gene Ontology  (10, 10)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (MANA_CELJU | P49424)
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:0051069    galactomannan metabolic process    The chemical reactions and pathways involving galactomannan, a polysaccharide composed of D-galactose and D-mannose. The mannose units form the backbone structure (a linear main chain) with the D-galactose as single side units.
    GO:0010391    glucomannan metabolic process    The chemical reactions and pathways involving glucomannan, a polysaccharide composed of D-glucose and D-mannose. The mannose units form the backbone structure (a linear main chain) with the D-glucose as single side-units.
    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.
    GO:0006080    substituted mannan metabolic process    The chemical reactions and pathways involving a mannan backbone composed of D-mannose unites, substituted with D-glucose and/or D-galactose units.

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 Related Entries

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

UniProtKB/Swiss-Prot
        MANA_CELJU | P49424: 1gvy 1j9y 1odz 1r7o 2whm

(-) Related Entries Specified in the PDB File

1gvy SUBSTRATE DISTORSION BY BETA-MANNANASE FROM PSEUDOMONAS CELLULOSA