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Title :   STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE IN COMPLEX WITH TETRASACCHARIDE HYALURONAN SUBSTRATE

Authors :   M. J. Jedrzejas, L. V. Mello, B. L. De Groot, S. Li

Date :   05 Jun 02 (Deposition) - 07 Aug 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.53

Chains :   Asym./Biol. Unit : A

Keywords :   Protein-Carbohydrate Complex, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. J. Jedrzejas, L. V. Mello, B. L. De Groot, S. Li
Mechanism Of Hyaluronan Degradation By Streptococcus Pneumoniae Hyaluronate Lyase. Structures Of Complexes With The Substrate.
J. Biol. Chem. V. 277 28287 2002
PubMed-ID: 11991948 | Reference-DOI: 10.1074/JBC.M112009200

Molecule 1 - HYALURONATE LYASE
	Chains	:	A
	EC Number	:	4.2.2.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET21
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organism Scientific	:	STREPTOCOCCUS PNEUMONIAE
	Organism Taxid	:	1313
	Synonym	:	HYALURONIDASE

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	BDP	2	Ligand/Ion	BETA-D-GLUCOPYRANURONIC ACID
2	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:291 , ARG A:336 , HIS A:399 , GLN A:808 , BDP A:1001 , HOH A:1509 , HOH A:1515 , HOH A:1516	BINDING SITE FOR RESIDUE NAG A 1000
2	AC2	SOFTWARE	ASN A:290 , TRP A:291 , TRP A:292 , ASN A:349 , HIS A:399 , PHE A:408 , ARG A:462 , ASN A:580 , NAG A:1000 , NAG A:1002	BINDING SITE FOR RESIDUE BDP A 1001
3	AC3	SOFTWARE	TRP A:292 , PHE A:408 , ARG A:462 , ARG A:466 , BDP A:1001 , BDP A:1003 , HOH A:1397 , HOH A:1398 , HOH A:1399 , HOH A:1403 , HOH A:1619	BINDING SITE FOR RESIDUE NAG A 1002
4	AC4	SOFTWARE	ARG A:243 , ARG A:300 , ARG A:466 , GLU A:477 , NAG A:1002 , HOH A:1347 , HOH A:1348 , HOH A:1394 , HOH A:1395 , HOH A:1621	BINDING SITE FOR RESIDUE BDP A 1003

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

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

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

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

(no "Exon" information available for 1LXK)

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:719
 aligned with HYSA_STRPN | Q54873 from UniProtKB/Swiss-Prot  Length:1066

    Alignment length:719
                                   297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537       547       557       567       577       587       597       607       617       627       637       647       657       667       677       687       697       707       717       727       737       747       757       767       777       787       797       807       817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997         
          HYSA_STRPN    288 KDAYTDRLDDWNGIIAGNQYYDSKNEQMAKLNQELEGKVADSLSSISSQADRTYLWEKFSNYKTSANLTATYRKLEEMAKQVTNPSSRYYQDETVVRTVRDSMEWMHKHVYNSEKSIVGNWWDYEIGTPRAINNTLSLMKEYFSDEEIKKYTDVIEKFVPDPEHFRKTTDNPFKALGGNLVDMGRVKVIAGLLRKDDQEISSTIRSIEQVFKLVDQGEGFYQDGSYIDHTNVAYTGAYGNVLIDGLSQLLPVIQKTKNPIDKDKMQTMYHWIDKSFAPLLVNGELMDMSRGRSISRANSEGHVAAVEVLRGIHRIADMSEGETKQCLQSLVKTIVQSDSYYDVFKNLKTYKDISLMQSLLSDAGVASVPRPSYLSAFNKMDKTAMYNAEKGFGFGLSLFSSRTLNYEHMNKENKRGWYTSDGMFYLYNGDLSHYSDGYWPTVNPYKMPGTTETDAKRADSDTGKVLPSAFVGTSKLDDANATATMDFTNWNQTLTAHKSWFMLKDKIAFLGSNIQNTSTDTAATTIDQRKLESGNPYKVYVNDKEASLTEQEKDYPETQSVFLESFDSKKNIGYFFFKKSSISMSKALQKGAWKDINEGQSDKEVENEFLTISQAHKQNRDSYGYMLIPNVDRATFNQMIKELESSLIENNETLQSVYDAKQGVWGIVKYDDSVSTISNQFQVLKRGVYTIRKEGDEYKIAYYNPETQESAPDQEVFKK 1006
               SCOP domains d1lxka1 A:171-540 Hyaluronate lyase                                                                                                                                                                                                                                                                                                                                               d1lxka3 A:541-814 Hyaluronate lyase                                                                                                                                                                                                                                               d1lxka2 A:815-889 Hyaluronate lyase                                         SCOP domains
               CATH domains 1lxkA02 A:171-542  [code=1.50.10.100, no name defined]                                                                                                                                                                                                                                                                                                                              -----1lxkA01 A:548-804  [code=2.70.98.10, no name defined]                                                                                                                                                                                                            1lxkA03 A:805-889 Chondroitinase Ac; Chain A, domain 3                                CATH domains
               Pfam domains ----------Lyase_8_N-1lxkA02 A:181-503                                                                                                                                                                                                                                                                                                        ---------------------------------Lyase_8-1lxkA01 A:537-807                                                                                                                                                                                                                                                      -------Lyase_8_C-1lxkA03 A:815-887                                              -- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.........hhhhh....hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....ee.......ee.hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......ee.....eee...ee...hhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.ee..ee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhh.hhhhhhhhhhhhhh..........eeeeehhh.eeeeee....eeeeee.........................eeeee.........hhhhhhhhhhh...eee.................eeeee....eeeeeeeee.....eeeeeeeeee...eeeeeeeeee.....eeeeeeeee.......eeee..ee.......eeeeeeeeeeee..hhhh.eeeeeeeeeeeeeeeeeeeehhhhhh.......eeeeeeeeeeee....eeeeeeeee..hhhhhhhhhhhh...eeee...eeeeee....eeeeee.....eee...eee...eeeeeeee..eeeeeee........hhhhhee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1lxk A  171 KDTYTDRLDDWNGIIAGNQYYDSKNDQMAKLNQELEGKVADSLSSISSQADRIYLWEKFSNYKTSANLTATYRKLEEMAKQVTNPSSRYYQDETVVRTVRDSMEWMHKHVYNSEKSIVGNWWDYEIGTPRAINNTLSLMKEYFSDEEIKKYTDVIEKFVPDPEHFRKTTDNPFKALGGNLVDMGRVKVIAGLLRKDDQEISSTIRSIEQVFKLVDQGEGFYQDGSYIDHTNVAYTGAFGNVLIDGLSQLLPVIQKTKNPIDKDKMQTMYHWIDKSFAPLLVNGELMDMSRGRSISRANSEGHVAAVEVLRGIHRIADMSEGETKQRLQSLVKTIVQSDSYYDVFKNLKTYKDISLMQSLLSDAGVASVPRTSYLSAFNKMDKTAMYNAEKGFGFGLSLFSSRTLNYEHMNKENKRGWYTSDGMFYLYNGDLSHYSDGYWPTVNPYKMPGTTETDAKRADSDTGKVLPSAFVGTSKLDDANATATMDFTNWNQTLTAHKSWFMLKDKIAFLGSNIQNTSTDTAATTIDQRKLESSNPYKVYVNDKEASLTEQEKDYPETQSVFLESSDSKKNIGYFFFKKSSISMSKALQKGAWKDINEGQSDKEVENEFLTISQAHKQNGDSYGYMLIPNVDRATFNQMIKELESSLIENNETLQSVYDAKQGVWGIVKYDDSVSTISNQFQVLKRGVYTIRKEGDEYKIAYYNPETQESAPDQEVFKK  889
                                   180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830       840       850       860       870       880

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 '\|'

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Gal_mutarotase (81)

Family: Lyase_8 (15)

Streptococcus pneumoniae (11)

Lyase_8-1lxkA01

A:537-807

Clan: Hy-ly_N (15)

Family: Lyase_8_N (15)

Streptococcus pneumoniae (11)

Lyase_8_N-1lxkA02

A:181-503

Clan: no clan defined [family: Lyase_8_C] (15)

Family: Lyase_8_C (15)

Streptococcus pneumoniae (11)

Lyase_8_C-1lxkA03

A:815-887

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (HYSA_STRPN | Q54873)

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:0005618	cell wall	The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
	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.

Asymmetric/Biological Unit
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1c82	1C82 IS THE MECHANISM OF HYALURONAN BINDING AND DEGRADATION: STRUCTURE OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE IN COMPLEX WITH HYALURONIC ACID DISACCHARIDE AT 1.7 A RESOLUTION
1egu	1EGU IS THE CRYSTAL STRUCTURE OF STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE AT 1.56 A RESOLUTION
1loh	1LOH IS STREPTOCOCCUS PNEUMONIAE HYALURONATE LYASE IN COMPLEX WITH HEXASACCHARIDE HYALURONAN SUBSTRATE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

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