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(-) Description

Title :  CRYSTAL STRUCTURE OF APO-MANNANASE 26A FROM PSUDOMONAS CELLULOSA
 
Authors :  A. J. Oakley, M. C. J. Wilce
Date :  22 Oct 03  (Deposition) - 11 Nov 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Endo Beta1-4 Mannanase, Mannanase 26A, Mannan Degrading Enzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. J. Oakley, M. C. J. Wilce
Structural Investigation Of Mannanase 26A From Pseudomonas Cellulosa Reveals An Induced Fit Mechanism And A Non-Substrate Ligand Binding Site
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - MANNANASE A
    Chains: A
    EC Number: 3.2.1.78
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PDB1
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: MAN26A
    Organism Scientific: CELLVIBRIO JAPONICUS
    Organism Taxid: 155077
    Synonym: MANNANASE 26A

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1MES1Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
2SO41Ligand/IonSULFATE ION
3ZN4Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:67 , HIS A:71 , GLU A:239 , HOH A:2108 , HOH A:2270 , HOH A:2387BINDING SITE FOR RESIDUE ZN A 1001
2AC2SOFTWAREASP A:222 , HOH A:2121 , HOH A:2192 , HOH A:2196 , HOH A:2218 , HOH A:2329BINDING SITE FOR RESIDUE ZN A 1002
3AC3SOFTWAREHIS A:79 , ASP A:111 , GLU A:121 , HOH A:2501BINDING SITE FOR RESIDUE ZN A 1003
4AC4SOFTWAREARG A:208 , HIS A:211 , GLU A:212 , ASP A:283 , GLU A:320BINDING SITE FOR RESIDUE ZN A 1004
5AC5SOFTWAREPHE A:259 , TRP A:260 , ASP A:261 , HOH A:2341 , HOH A:2377 , HOH A:2494BINDING SITE FOR RESIDUE SO4 A 2001
6AC6SOFTWARETYR A:132 , ALA A:133 , GLU A:198 , GLN A:199 , TYR A:415 , GLN A:416 , HOH A:2055 , HOH A:2379BINDING SITE FOR RESIDUE MES A 2002

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R7O)

(-) 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 1R7O)

(-) 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 1R7O)

(-) 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:353
 aligned with MANA_CELJU | P49424 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:379
                                    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         
           MANA_CELJU    42 VKPVTVKLVDSQATMETRSLFAFMQEQRRHSIMFGHQHETTQGLTITRTDGTQSDTFNAVGDFAAVYGWDTLSIVAPKAEGDIVAQVKKAYARGGIITVSSHFDNPKTDTQKGVWPVGTSWDQTPAVVDSLPGGAYNPVLNGYLDQVAEWANNLKDEQGRLIPVIFRLYHENTGSWFWWGDKQSTPEQYKQLFRYSVEYLRDVKGVRNFLYAYSPNNFWDVTEANYLERYPGDEWVDVLGFDTYGPVADNADWFRNVVANAALVARMAEARGKIPVISEIGIRAPDIEAGLYDNQWYRKLISGLKADPDAREIAFLLVWRNAPQGVPGPNGTQVPHYWVPANRPENINNGTLEDFQAFYADEFTAFNRDIEQVYQRPTL 420
               SCOP domains d1r7oa_ A: Mannanase A, ManA                                                                                                                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1r7oA00 A:42-420 Glycosidases                                                                                                                                                                                                                                                                                                                                                               CATH domains
               Pfam domains --------Glyco_hydro_26-1r7oA01 A:50-350                                                                                                                                                                                                                                                                              ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee........hhhhhhhhhhhhhhh...eeeeee................hhhhhhhh....eeeee.hhh........hhhhhhhhhhh..eeeee.......hhhhh..............hhhhh....hhhhhhhhhhhhhhhhhh..........eeee.................hhhhhhhhhhhhhhhhhhh.....eeeee........hhhhhhh.........ee..eeee....hhhhhhhhhhhhhhhhhhhhhhh.ee.eeeeeehhhhhhh.....hhhhhhhhhhhhh.hhhhh.eeee..--------------------------...hhhhhhhhhhhh..eehhhhh.......ee Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------GH26  PDB: A:56-409 UniProt: 56-409                                                                                                                                                                                                                                                                                                                               ----------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r7o A  42 VKPVTVKLVDSQATMETRSLFAFMQEQRRHSIMFGHQHETTQGLTITRTDGTQSDTFNAVGDFAAVYGWDTLSIVAPKAEGDIVAQVKKAYARGGIITVSSHFDNPKTDTQKGVWPVGTSWDQTPAVVDSLPGGAYNPVLNGYLDQVAEWANNLKDEQGRLIPVIFRLYHENTGSWFWWGDKQSTPEQYKQLFRYSVEYLRDVKGVRNFLYAYSPNNFWDVTEANYLERYPGDEWVDVLGFDTYGPVADNADWFRNVVANAALVARMAEARGKIPVISEIGIRAPDIEAGLYDNQWYRKLISGLKADPDAREIAFLLVWR--------------------------INNGTLEDFQAFYADEFTAFNRDIEQVYQRPTL 420
                                    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         -         -      |391       401       411         
                                                                                                                                                                                                                                                                                                                                                         361                        388
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: Glyco_hydro_tim (488)

(-) 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 1gw1 1j9y 1odz 2whm

(-) Related Entries Specified in the PDB File

1j9y THIS ENTRY IS A REASESSMENT OF STRUCTURE 1J9Y