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(-) Description

Title :  CRYSTAL STRUCTURE OF STREPTOCOCCUS AGALACTIAE HYALURONATE LYASE COMPLEXED WITH HEXASACCHARIDE UNIT OF HYALURONAN
 
Authors :  L. V. Mello, B. L. De Groot, S. Li, M. J. Jedrzejas
Date :  05 Jun 02  (Deposition) - 30 Oct 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Streptococcus Agalactiae, Protein-Carbohydrate Complex, Hyaluronan, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. V. Mello, B. L. De Groot, S. Li, M. J. Jedrzejas
Structure And Flexibility Of Streptococcus Agalactiae Hyaluronate Lyase Complex With Its Substrate. Insights Into The Mechanism Of Processive Degradation Of Hyaluronan.
J. Biol. Chem. V. 277 36678 2002
PubMed-ID: 12130645  |  Reference-DOI: 10.1074/JBC.M205140200

(-) Compounds

Molecule 1 - HYALURONATE LYASE
    Chains: A
    EC Number: 4.2.2.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: HYL
    Organism Scientific: STREPTOCOCCUS AGALACTIAE
    Organism Taxid: 1311
    Synonym: HYALURONIDASE, HYASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric/Biological Unit (2, 6)
No.NameCountTypeFull Name
1BDP3Ligand/IonBETA-D-GLUCOPYRANURONIC ACID
2NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:371 , ARG A:416 , BDP A:2001BINDING SITE FOR RESIDUE NAG A 2000
2AC2SOFTWARETRP A:371 , NAG A:2000 , NAG A:2002BINDING SITE FOR RESIDUE BDP A 2001
3AC3SOFTWAREASN A:370 , TRP A:372 , TYR A:488 , ARG A:542 , BDP A:2001 , BDP A:2003BINDING SITE FOR RESIDUE NAG A 2002
4AC4SOFTWARETRP A:372 , ARG A:380 , HOH A:1026 , NAG A:2002 , NAG A:2004BINDING SITE FOR RESIDUE BDP A 2003
5AC5SOFTWAREARG A:380 , BDP A:2003 , BDP A:2005BINDING SITE FOR RESIDUE NAG A 2004
6AC6SOFTWAREGLU A:557 , ARG A:560 , ASN A:596 , LYS A:598 , HOH A:1178 , NAG A:2004BINDING SITE FOR RESIDUE BDP A 2005

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1LXM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1LXM)

(-) Exons   (0, 0)

(no "Exon" information available for 1LXM)

(-) 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:794
 aligned with HYSA_STRA3 | Q53591 from UniProtKB/Swiss-Prot  Length:984

    Alignment length:812
                                   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       772       782       792       802       812       822       832       842       852       862       872       882       892       902       912       922       932       942       952       962       972       982  
           HYSA_STRA3   173 HPQPVTTQIEESVNTALNKNYVFNKADYQYTLTNPSLGKIVGGILYPNATGSTTVKISDKSGKIIKEVPLSVTASTEDKFTKLLDKWNDVTIGNHVYDTNDSNMQKINQKLDETNAKNIKTIKLDSNHTFLWKDLDNLNNSAQLTATYRRLEDLAKQITNPHSTIYKNEKAIRTVKESLAWLHQNFYNVNKDIEGSANWWDFEIGVPRSITATLALMNNYFTDAEIKTYTDPIEHFVPDAGYFRKTLDNPFKALGGNLVDMGRVKIIEGLLRKDNTIIEKTSHSLKNLFTTATKAEGFYADGSYIDHTNVAYTGAYGNVLIDGLTQLLPIIQETDYKISNQELDMVYKWINQSFLPLIVKGELMDMSRGRSISREAASSHAAAVEVLRGFLRLANMSNEERNLDLKSTIKTIITSNKFYNVFNNLKSYSDIANMNKMLNDSTVATKPLKSNLSTFNSMDRLAYYNAEKDFGFALSLHSKRTLNYEGMNDENTRDWYTGDGMFYLYNSDQSHYSNHFWPTVNPYKMAGTTEKDAKREDTTKEFMSKHSKDAKEKTGQVTGTSDFVGSVKLNDHFALAAMDFTNWDRTLTAQKGWVILNDKIVFLGSNIKNTNGIGNVSTTIDQRKDDSKTPYTTYVNGKTIDLKQASSQQFTDTKSVFLESKEPGRNIGYIFFKNSTIDIERKEQTGTWNSINRTSKNTSIVSNPFITISQKHDNKGDSYGYMMVPNIDRTSFDKLANSKEVELLENSSKQQVIYDKNSQTWAVIKHDNQESLINNQFKMNKAGLYLVQKVGNDYQNVYYQPQTMTKTDQLAI 984
               SCOP domains d1lxma2 A:173-248 Hyaluronate lyase precatalytic domain                     d1lxma1 A:249-619 Hyaluronate lyase                                                                                                                                                                                                                                                                                                                                                d1lxma4 A:620-911 Hyaluronate lyase                                                                                                                                                                                                                                                                 d1lxma3 A:912-984 Hyaluronate lyase                                       SCOP domains
               CATH domains 1lxmA04 A:173-248 E set domains; domain 4                                   1lxmA02 A:249-622  [code=1.50.10.100, no name defined]                                                                                                                                                                                                                                                                                                                                -----1lxmA01 A:628-902  [code=2.70.98.10, no name defined]                                                                                                                                                                                                                              1lxmA03 A:903-981 Chondroitinase Ac; Chain A, domain 3                         --- CATH domains
               Pfam domains --------------------------------------------------------------------------------------Lyase_8_N-1lxmA02 A:259-583                                                                                                                                                                                                                                                                                                          ---------------------------------Lyase_8-1lxmA01 A:617-905                                                                                                                                                                                                                                                                        -------Lyase_8_C-1lxmA03 A:913-984                                              Pfam domains
         Sec.struct. author ............eeee....ee......eeee.hhh.eeee..eeee...eeeeeeee.....eeeeeeeeee....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.........hhhhh...hhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.......ee..hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.......ee.....eee...ee...hhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhh.ee..ee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh...hhhhhh.hhhhhhhhhhhhh...........eeeeehhh.eeeeee....eeeeee.................hhhhh...eeeee.........hhhhhh........eee..........--------..............eeeeeee..eeeeeeeee......eeeeeeeee..eeeeeeeeee.......eeeeeeeee.......eeee..ee.------..eeeeeeeeeee.......eeeeeeeeeeeeeeeeeeeehhhhhh........eeeeeeeeeee..----.eeeeeee..hhhhhhhhhh...eeeeee...eeeeee....eeeeee.....eee...eee...eeeeeee....eeeeeee....eeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1lxm A 173 HPQPVTTQIEKSVNTALNKNYVFNKADYQYTLTNPSLGKIVGGILYPNATGSTTVKISDKSGKIIKEVPLSVTASTEDNFTKLLDKWNDVTIGNYVYDTNDSNMQKLNQKLDETNAKNIEAIKLDSNRTFLWKDLDNLNNSAQLTATYRRLEDLAKQITNPHSTIYKNEKAIRTVKESLAWLHQNFYNVNKDIEGSANWWDFEIGVPRSITGTLSLMNNYFTDAEIKTYTDPIEHFVPDAEYFRKTLVNPFKALGGNLVDMGRVKIIEGLLRKDNTIIEKTSHSLKNLFTTATKAEGFYADGSYIDHTNVAYTGAYGNVLIDGLTQLLPIIQETDYKISNQELDMVYKWINQSFLPLIVKGELMDMSRGRSISREAASSHAAAVEVLRGFLRLANMSNEERNLDLKSTIKTIITSNKFYNVFNNLKSYSDIANMNKLLNDSTVATKPLKSNLSTFNSMDRLAYYNAKKDFGFALSLHSKRTLNYEGMNDENTRGWYTGDGMFYIYNSDQSHYSNHFWPTVNPYKMAGTTEKDAKREDTTKE--------AKEKTGQVTGTSDFVGSVKLNDHFALAAMDFTNWDRTLTAQKGWVILNDKIVFLGSNIKNTNGIGNVSTTIDQRKDDSKTPYTTYVNGKTI------SQQFTDTKSVFLESKEPGRNIGYIFFKNSTIDIERKEQTGTWNSINRTSKNTSIVSNPFITISQKHD----SYGYMMVPNIDRTSFDKLANSKEVELLENSSKQQVIYDKNSQTWAVIKHDNQESLINNQFKMNKAGLYLVQKVGNDYQNVYYQPQTMTKTDQLAI 984
                                   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       772       782       792       802       812      |822       832       842       852       862       872       882  |    892       902       912       922       932       942       952       962       972       982  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                      713      722                                                                                       812    819                                                               885  890
   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  (4, 4)

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

(-) CATH Domains  (4, 4)

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

(-) Pfam Domains  (3, 3)

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

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (HYSA_STRA3 | Q53591)
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:0030340    hyaluronate lyase activity    Catalysis of the reaction: hyaluronate = n 3-(4-deoxy-beta-D-gluc-4-enuronosyl)-N-acetyl-D-glucosamine.
    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.
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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 Related Entries

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

UniProtKB/Swiss-Prot
        HYSA_STRA3 | Q53591: 1f1s 1i8q

(-) Related Entries Specified in the PDB File

1f1s 1F1S IS THE CRYSTAL STRUCTURE OF STREPTOCOCCUS AGALACTIAE HYALURONATE LYASE AT 2.1 ANGSTROM RESOLUTION
1i8q 1I8Q IS THE CRYSTAL STRUCTURE OF STREPTOCOCCUS AGALACTIAE HYALURONATE LYASE COMPLEXED WITH ENZYME PRODUCT, UNSATURATED DISACCHARIDE HYALURONAN