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(-) Description

Title :  THE X-RAY STRUCTURE OF THE STREPTOMYCES COELICOLOR A3 CHONDROITIN AC LYASE Y253A MUTANT
 
Authors :  Z. H. Elmabrouk, E. J. Taylor, F. Vincent, N. L. Smith, J. P. Turkenburg, G. J. Davies, G. W. Black
Date :  04 Dec 09  (Deposition) - 18 Aug 10  (Release) - 29 Mar 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hyaluronate Lyase, Lyase, Chondroitin Lyase, Family 8 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. H. Elmabrouk, F. Vincent, M. Zhang, N. L. Smith, J. P. Turkenburg, S. J. Charnock, G. W. Black, E. J. Taylor
Crystal Structures Of A Family 8 Polysaccharide Lyase Revea Open And Highly Occluded Substrate-Binding Cleft Conformations.
Proteins V. 79 965 2011
PubMed-ID: 21287626  |  Reference-DOI: 10.1002/PROT.22938

(-) Compounds

Molecule 1 - PUTATIVE SECRETED LYASE
    Chains: A, B
    EC Number: 4.2.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET28A (NOVAGEN)
    Expression System Vector Type: PLASMID
    Fragment: RESIDUES 33-776
    Mutation: YES
    Organism Scientific: STREPTOMYCES COELICOLOR
    Organism Taxid: 100226
    Other Details: GERMAN COLLECTION OF MICROORGANISMS (DSM) DSM NO. 40783
    Strain: A3(2)
    Synonym: PL8

 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  (1, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1MG1Ligand/IonMAGNESIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR B:478 , HOH B:2215 , HOH B:2225 , HOH B:2269 , HOH B:2270BINDING SITE FOR RESIDUE MG B 1766

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2X03)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:48 -Pro A:49
2Asp A:82 -Pro A:83
3Glu B:48 -Pro B:49
4Asp B:82 -Pro B:83

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2X03)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2X03)

(-) Exons   (0, 0)

(no "Exon" information available for 2X03)

(-) 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:742
 aligned with O86516_STRCO | O86516 from UniProtKB/TrEMBL  Length:776

    Alignment length:742
                                    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       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774  
         O86516_STRCO    35 ADPYDALRRRWLGITLGTGYDPAAEPYASRLAETGERAREHRATMAPTPTSLWPGHPFDPPAGITFAYGRLWTMTEAYVQEGTGATGDPALLADILRGLDHLSATVYHPATTRYGNWWEWQIGSPRLLMDITAALYDHLGADRVAAACAAVDHFVPDAMLGAYTGTSTGANRVDLCRSVALRGVLGRAPAKIALARDALSPVFPYVTKGDGLYADGSFVQHTWVAYSGTYGQVMLDGLGRLFTLLAGSEWEVTDPGRQLVLDSVEHAYAPLIHDGLVMDTVNGRAISRGYLKSDDLHVMRSDHFHGQQLIAAMAVLAGGASNAERERWHARIKGWIERDTVTPVLTAPQFPVADLTRLHAIADAPGEAAPEPVGHHLFAAMDRAVHRRPAFTAGLAMASDRIAHYECGNGENPRGWHTGAGMLTWWANGTRADQYTDWFWPTVDWYRLPGTTVSTKRLADRAGGEWGAPKPDVRWVGGATDGEYAAVGQHLKGLGSTLEARKSWFFLDDAVVCLGAGITCADGVPVETVVDNRNLGEGGTQALVRGRHWAHLEGHGGWIVPGGALRTLREDRTGAWSDINTTSTTERRTRRWQTLWLDHGTDPAGADYVYTVMPGASRAALARRAADRHWLTVLANDDRRQAVSVPSLGLTAANFWQAGTAGPLTTTAGASVLVRRRGRTATLRVSEPPRTGEALEIVWDHPVGAVLRADETVEILATGRRLHLRVTPGVVCTTHECEVTLS 776
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2x03A01 A:24-394  [code=1.50.10.100, no name defined]                                                                                                                                                                                                                                                                                                                              2x03A02 A:395-650  [code=2.70.98.10, no name defined]                                                                                                                                                                                                           ------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhh.....eee..ee...hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.........hhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.......ee.....eee...eehhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh.ee..ee.hhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhh.........eeeeehhh.eeeee...eeeeee.........................eeeeee........................eee.....................eeeee....eeeeeeee......eeeeeeee....eeeeeeeee.....eeeeeeeeee........ee....eeee...eeee......eeeeeeeeee.hhh.......eeeeeeeeeeeeeee....eeeeeeeee..hhhhhhhhhhh....eeeee...eeeeeehhh.eeeeee...eee..eee...eeeeeeee..eeeeeee........eeeee...eeeeeee...eeeee....eeeee........eeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x03 A  24 ADPYDALRRRWLGITLGTGYDPAAEPYASRLAETGERAREHRATMAPTPTSLWPGHPFDPPAGITFAYGRLWTMTEAYVQEGTGATGDPALLADILRGLDHLSATVYHPATTRYGNWWEWQIGSPRLLMDITAALYDHLGADRVAAACAAVDHFVPDAMLGAYTGTSTGANRVDLCRSVALRGVLGRAPAKIALARDALSPVFPYVTKGDGLYADGSFVQHTWVAYSGTAGQVMLDGLGRLFTLLAGSEWEVTDPGRQLVLDSVEHAYAPLIHDGLVMDTVNGRAISRGYLKSDDLHVMRSDHFHGQQLIAAMAVLAGGASNAERERWHARIKGWIERDTVTPVLTAPQFPVADLTRLHAIADAPGEAAPEPVGHHLFAAMDRAVHRRPAFTAGLAMASDRIAHYECGNGENPRGWHTGAGMLTWWANGTRADQYTDWFWPTVDWYRLPGTTVSTKRLADRAGGEWGAPKPDVRWVGGATDGEYAAVGQHLKGLGSTLEARKSWFFLDDAVVCLGAGITCADGVPVETVVDNRNLGEGGTQALVRGRHWAHLEGHGGWIVPGGALRTLREDRTGAWSDINTTSTTERRTRRWQTLWLDHGTDPAGADYVYTVMPGASRAALARRAADRHWLTVLANDDRRQAVSVPSLGLTAANFWQAGTAGPLTTTAGASVLVRRRGRTATLRVSEPPRTGEALEIVWDHPVGAVLRADETVEILATGRRLHLRVTPGVVCTTHECEVTLS 765
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763  


Chain B from PDB  Type:PROTEIN  Length:743
 aligned with O86516_STRCO | O86516 from UniProtKB/TrEMBL  Length:776

    Alignment length:743
                                    43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723       733       743       753       763       773   
         O86516_STRCO    34 TADPYDALRRRWLGITLGTGYDPAAEPYASRLAETGERAREHRATMAPTPTSLWPGHPFDPPAGITFAYGRLWTMTEAYVQEGTGATGDPALLADILRGLDHLSATVYHPATTRYGNWWEWQIGSPRLLMDITAALYDHLGADRVAAACAAVDHFVPDAMLGAYTGTSTGANRVDLCRSVALRGVLGRAPAKIALARDALSPVFPYVTKGDGLYADGSFVQHTWVAYSGTYGQVMLDGLGRLFTLLAGSEWEVTDPGRQLVLDSVEHAYAPLIHDGLVMDTVNGRAISRGYLKSDDLHVMRSDHFHGQQLIAAMAVLAGGASNAERERWHARIKGWIERDTVTPVLTAPQFPVADLTRLHAIADAPGEAAPEPVGHHLFAAMDRAVHRRPAFTAGLAMASDRIAHYECGNGENPRGWHTGAGMLTWWANGTRADQYTDWFWPTVDWYRLPGTTVSTKRLADRAGGEWGAPKPDVRWVGGATDGEYAAVGQHLKGLGSTLEARKSWFFLDDAVVCLGAGITCADGVPVETVVDNRNLGEGGTQALVRGRHWAHLEGHGGWIVPGGALRTLREDRTGAWSDINTTSTTERRTRRWQTLWLDHGTDPAGADYVYTVMPGASRAALARRAADRHWLTVLANDDRRQAVSVPSLGLTAANFWQAGTAGPLTTTAGASVLVRRRGRTATLRVSEPPRTGEALEIVWDHPVGAVLRADETVEILATGRRLHLRVTPGVVCTTHECEVTLS 776
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2x03B01 B:23-394  [code=1.50.10.100, no name defined]                                                                                                                                                                                                                                                                                                                               2x03B02 B:395-650  [code=2.70.98.10, no name defined]                                                                                                                                                                                                           ------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -----------Lyase_8_N-2x03B03 B:34-357                                                                                                                                                                                                                                                                                                          ---------------------------------Lyase_8-2x03B01 B:391-645                                                                                                                                                                                                                                      --------Lyase_8_C-2x03B05 B:654-734                                                      ------------------------------- Pfam domains (1)
           Pfam domains (2) -----------Lyase_8_N-2x03B04 B:34-357                                                                                                                                                                                                                                                                                                          ---------------------------------Lyase_8-2x03B02 B:391-645                                                                                                                                                                                                                                      --------Lyase_8_C-2x03B06 B:654-734                                                      ------------------------------- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.......eee..ee...hhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.......ee.....eee...ee...hhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhh.ee..ee.hhhhhhhhhh............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhh...hhhhhhhhhhhhhh.........eeeeehhh.eeeee...eeeeee.................hhhhh...eeeeee........................eee.....................eeeee....eeeeeeee......eeeeeeee....eeeeeeeee.....eeeeeeeeeeee......eeee..eeee...eeee......eeeeeeeeee.hhh.......eeeeeeeeeeeeeee....eeeeeeeee..hhhhhhhhhhh....eeeee...eeeeeehhh.eeeeee...eee..eee...eeeeeeee..eeeeeee........eeeee...eeeeeee...eeeee....eeeee........eeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2x03 B  23 TADPYDALRRRWLGITLGTGYDPAAEPYASRLAETGERAREHRATMAPTPTSLWPGHPFDPPAGITFAYGRLWTMTEAYVQEGTGATGDPALLADILRGLDHLSATVYHPATTRYGNWWEWQIGSPRLLMDITAALYDHLGADRVAAACAAVDHFVPDAMLGAYTGTSTGANRVDLCRSVALRGVLGRAPAKIALARDALSPVFPYVTKGDGLYADGSFVQHTWVAYSGTAGQVMLDGLGRLFTLLAGSEWEVTDPGRQLVLDSVEHAYAPLIHDGLVMDTVNGRAISRGYLKSDDLHVMRSDHFHGQQLIAAMAVLAGGASNAERERWHARIKGWIERDTVTPVLTAPQFPVADLTRLHAIADAPGEAAPEPVGHHLFAAMDRAVHRRPAFTAGLAMASDRIAHYECGNGENPRGWHTGAGMLTWWANGTRADQYTDWFWPTVDWYRLPGTTVSTKRLADRAGGEWGAPKPDVRWVGGATDGEYAAVGQHLKGLGSTLEARKSWFFLDDAVVCLGAGITCADGVPVETVVDNRNLGEGGTQALVRGRHWAHLEGHGGWIVPGGALRTLREDRTGAWSDINTTSTTERRTRRWQTLWLDHGTDPAGADYVYTVMPGASRAALARRAADRHWLTVLANDDRRQAVSVPSLGLTAANFWQAGTAGPLTTTAGASVLVRRRGRTATLRVSEPPRTGEALEIVWDHPVGAVLRADETVEILATGRRLHLRVTPGVVCTTHECEVTLS 765
                                    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       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762
   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 2X03)

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (3, 6)

Asymmetric Unit
(-)
Clan: Gal_mutarotase (81)
(-)
Clan: Hy-ly_N (15)
(-)
Clan: no clan defined [family: Lyase_8_C] (15)

(-) Gene Ontology  (7, 7)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (O86516_STRCO | O86516)
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: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: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.
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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  2x03
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 Related Entries

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

UniProtKB/TrEMBL
        O86516_STRCO | O86516: 2wco 2wda

(-) Related Entries Specified in the PDB File

2wco STRUCTURES OF THE STREPTOMYCES COELICOLOR A3( 2) HYALURONAN LYASE IN COMPLEX WITH OLIGOSACCHARIDE SUBSTRATES AND AN INHIBITOR
2wda THE X-RAY STRUCTURE OF THE STREPTOMYCES COELICOLOR A3 CHONDROITIN AC LYASE IN COMPLEX WITH CHONDROITIN SULPHATE