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(-) Description

Title :  CRYSTAL STRUCTURE OF XANTHAN LYASE IN COMPLEX WITH MANNOSE
 
Authors :  Y. Maruyama, B. Mikami, W. Hashimoto, K. Murata
Date :  07 Nov 06  (Deposition) - 30 Jan 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A
Keywords :  Xanthan, Mannose, Polysaccharide Lyase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Maruyama, B. Mikami, W. Hashimoto, K. Murata
A Structural Factor Responsible For Substrate Recognition B Bacillus Sp. Gl1 Xanthan Lyase That Acts Specifically On Pyruvated Side Chains Of Xanthan
Biochemistry V. 46 781 2007
PubMed-ID: 17223699  |  Reference-DOI: 10.1021/BI0619775

(-) Compounds

Molecule 1 - XANTHAN LYASE
    Chains: A
    EC Number: 4.2.2.12
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET17B
    Expression System Strain: BL21(DE3)PLYSS
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 26-777
    Organism Scientific: BACILLUS SP.
    Organism Taxid: 84635
    Strain: GL1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1MAN1Ligand/IonALPHA-D-MANNOSE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:148 , TYR A:255 , ARG A:309 , ARG A:313 , ARG A:612 , HOH A:1044 , HOH A:1113 , HOH A:1128 , HOH A:1231BINDING SITE FOR RESIDUE MAN A 1001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2E22)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Tyr A:145 -Asn A:146
2Ala A:338 -Pro A:339
3Ala A:753 -Pro A:754

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2E22)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2E22)

(-) Exons   (0, 0)

(no "Exon" information available for 2E22)

(-) 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:752
 aligned with XANLY_BACGL | Q9AQS0 from UniProtKB/Swiss-Prot  Length:930

    Alignment length:752
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775  
          XANLY_BACGL    26 SDEFDALRIKWATLLTGGPALDPADSDIAARTDKLAQDANDYWEDMDLSSSRTYIWYALRGNGTSDNVNAVYERLRTMALAATTVGSSLYGNADLKEDILDALDWLYVNSYNSTRSRSAYNWWHWQLGIPMSLNDIAVLLYDDISAARMATYMDTIDYFTPSIGLTGANRAWQAIVVGVRAVIVKDAVKLAAARNGLSGTGIFPYATGGDGFYADGSFVQHTTFAYTGGYGSSVLETTANLMYLLSGSTWSVSDPNQSNVWQWIYEAYRPLLYKGAMMDMVRGREISRSYAQDHAVGHGIVASIVRLAQFAPAPHAAAFKQIAKRVIQEDTFSSFYGDVSTDTIRLAKAIVDDPSIAPAAAPNLYKQYAAMDRAVLQRPGFALGLALYSTRISSYESINSENGRGWYTGAGATYLYNQDLAQYSEDYWPTVDAYRIPGTTVASGTPIASGTGTSSWTGGVSLAGQYGASGMDLSYGAYNLSARKSWFMFDDEIVALGSGISSTAGIPIETVVDNRKLNGAGDNAWTANGAALSTGLGVAQTLTGVNWVHLAGNTADGSDIGYYFPGGATLQTKREARTGTWKQINNRPATPSTAVTRNYETMWIDHGTNPSGASYGYVLLPNKTSAQVGAYAADPAIEIVVNTSGVQSVKEKTLGLVGANFWTDTTQTADLITSNKKASVMTREIADERLEASVSDPTQANNGTIAIELARSAEGYSADPGITVTQLAPTIKFTVNVNGAKGKSFHASFQLG 777
               SCOP domains d2e22a1 A:26-386 automated matches                                                                                                                                                                                                                                                                                                                                       d2e22a3 A:387-659 automated matches                                                                                                                                                                                                                                              d2e22a2 A:660-777 automated matches                                                                                    SCOP domains
               CATH domains 2e22A01 A:26-386  [code=1.50.10.100, no name defined]                                                                                                                                                                                                                                                                                                                    2e22A02 A:387-659  [code=2.70.98.10, no name defined]                                                                                                                                                                                                                            2e22A03 A:660-777 Chondroitinase Ac; Chain A, domain 3                                                                 CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh..........hhhhh...hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.............ee.....eee...ee...hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhh.ee..ee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...........eeeeehhh.eeeeee..eeeeee.........................eeeee.......................eee..............eeeeee...eeeeeeeee......eeeeeeee....eeeeeeeee.....eeeeeeeeee........eee..ee......eeeeeeeeeeeee.........eeeeeeeeeeeeeeeeeeeehhhhhh.........eeeeeeeeeeeeee....eeeeeeeee..hhhhhhhhhhh..eeeeee...eeeeee....eeeeee.....eee..eee...eeeeeeee...eeeeeee........eeeeee...eeeeee...eeeee....eeeeee........eeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2e22 A  26 SDEFDALRIKWATLLTGGPALDPADSDIAARTDKLAQDANDYWEDMDLSSSRTYIWYALRGNGTSDNVNAVYERLRTMALAATTVGSSLYGNADLKEDILDALDWLYVNSYNSTRSRSAYNWWHWQLGIPMSLNDIAVLLYDDISAARMATYMDTIDYFTPSIGLTGANRAWQAIVVGVRAVIVKDAVKLAAARNGLSGTGIFPYATGGDGFYADGSFVQHTTFAYTGGYGSSVLETTANLMYLLSGSTWSVSDPNQSNVWQWIYEAYRPLLYKGAMMDMVRGREISRSYAQDHAVGHGIVASIVRLAQFAPAPHAAAFKQIAKRVIQEDTFSSFYGDVSTDTIRLAKAIVDDPSIAPAAAPNLYKQYAAMDRAVLQRPGFALGLALYSTRISSYESINSENGRGWYTGAGATYLYNQDLAQYSEDYWPTVDAYRIPGTTVASGTPIASGTGTSSWTGGVSLAGQYGASGMDLSYGAYNLSARKSWFMFDDEIVALGSGISSTAGIPIETVVDNRKLNGAGDNAWTANGAALSTGLGVAQTLTGVNWVHLAGNTADGSDIGYYFPGGATLQTKREARTGTWKQINNRPATPSTAVTRNYETMWIDHGTNPSGASYGYVLLPNKTSAQVGAYAADPAIEIVVNTSGVQSVKEKTLGLVGANFWTDTTQTADLITSNKKASVMTREIADERLEASVSDPTQANNGTIAIELARSAEGYSADPGITVTQLAPTIKFTVNVNGAKGKSFHASFQLG 777
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775
   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  (3, 3)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (3, 3)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2E22)

(-) Gene Ontology  (12, 12)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (XANLY_BACGL | Q9AQS0)
molecular function
    GO:0005509    calcium ion binding    Interacting selectively and non-covalently with calcium ions (Ca2+).
    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:0016837    carbon-oxygen lyase activity, acting on polysaccharides    Catalysis of the cleavage of a carbon-oxygen bond by the elimination of an alcohol from a polysaccharide.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0005537    mannose binding    Interacting selectively and non-covalently with mannose, a monosaccharide hexose, stereoisomeric with glucose, that occurs naturally only in polymerized forms called mannans.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0047492    xanthan lyase activity    Catalysis of the reaction: xanthan = oligosaccharide with 4-deoxy-alpha-L-threo-hex-4-enuronosyl end + pyruvylate mannose. This reaction is the eliminative cleavage of the terminal beta-D-mannosyl-beta-D-1,4-glucuronosyl linkage of the side-chain of the polysaccharide xanthan, leaving a 4-deoxy-alpha-L-threo-hex-4-enuronosyl group at the terminus of the side-chain.
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:0005976    polysaccharide metabolic process    The chemical reactions and pathways involving a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
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.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.

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 Related Entries

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

UniProtKB/Swiss-Prot
        XANLY_BACGL | Q9AQS0: 1j0m 1j0n 1x1h 1x1i 1x1j 2e24

(-) Related Entries Specified in the PDB File

1j0m THE SAME PROTEIN WITHOUT LIGAND
1j0n THE SAME PROTEIN IN COMPLEX WITH CA
1x1h MUTANT (N194A) OF THE SAME PROTEIN
1x1i MUTANT (N194A) OF THE SAME PROTEIN IN COMPLEX WITH A PRODUCT
1x1j MUTANT (N194A) OF THE SAME PROTEIN IN COMPLEX WITH A SUBSTRATE
2e24 MUTANT (R612A) OF THE SAME PROTEIN