1URX - JenaLib

Title :   CRYSTALLOGRAPHIC STRUCTURE OF BETA-AGARASE A IN COMPLEX WITH OLIGOAGAROSE

Authors :   J. Allouch, W. Helbert, B. Henrissat, M. Czjzek

Date :   12 Nov 03 (Deposition) - 04 Mar 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

Chains :   Asym./Biol. Unit : A

Keywords :   Hydrolase, Beta-Agarase, Agarose, Glycoside Hydrolase, Family 16, Double Helix, Two Binding-Sites (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Allouch, W. Helbert, B. Henrissat, M. Czjzek
Parallel Substrate Binding Sites In A Beta-Agarase Suggest A Novel Mode Of Action On Double-Helical Agarose
Structure V. 12 623 2004
PubMed-ID: 15062085 | Reference-DOI: 10.1016/J.STR.2004.02.020

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 12)

Sites (12, 12)

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:71 , TRP A:73 , GLU A:144 , GAL A:1290 , HOH A:2086 , HOH A:2335 , HOH A:2336	BINDING SITE FOR RESIDUE AAL A1289
02	AC2	SOFTWARE	TRP A:73 , GLU A:144 , ARG A:176 , AAL A:1289 , AAL A:1291 , HOH A:2206 , HOH A:2337	BINDING SITE FOR RESIDUE GAL A1290
03	AC3	SOFTWARE	TYR A:69 , TRP A:73 , TRP A:138 , GLU A:144 , PHE A:174 , ARG A:176 , GAL A:1290 , GLA A:1292 , HOH A:2337 , HOH A:2339	BINDING SITE FOR RESIDUE AAL A1291
04	AC4	SOFTWARE	ALA A:136 , TRP A:138 , SER A:147 , ASP A:149 , GLU A:152 , HIS A:172 , PHE A:174 , GLU A:254 , GLN A:256 , AAL A:1291 , HOH A:2182 , HOH A:2303 , HOH A:2339 , HOH A:2341	BINDING SITE FOR RESIDUE GLA A1292
05	AC5	SOFTWARE	ASN A:82 , TYR A:106 , GAL A:1294 , HOH A:2045	BINDING SITE FOR RESIDUE AAL A1293
06	AC6	SOFTWARE	ASN A:82 , GLN A:85 , GLN A:98 , TYR A:106 , AAL A:1293 , AAL A:1295 , HOH A:2045 , HOH A:2343 , HOH A:2344	BINDING SITE FOR RESIDUE GAL A1294
07	AC7	SOFTWARE	PRO A:84 , GLN A:85 , GLN A:96 , GLN A:98 , GAL A:1294 , GAL A:1296 , HOH A:2345 , HOH A:2346 , HOH A:2349	BINDING SITE FOR RESIDUE AAL A1295
08	AC8	SOFTWARE	TRP A:87 , GLN A:96 , ASP A:271 , AAL A:1295 , AAL A:1297 , HOH A:2348 , HOH A:2349 , HOH A:2350 , HOH A:2351 , HOH A:2352	BINDING SITE FOR RESIDUE GAL A1296
09	AC9	SOFTWARE	ASP A:271 , TRP A:277 , GAL A:1296 , GAL A:1298 , HOH A:2120	BINDING SITE FOR RESIDUE AAL A1297
10	BC1	SOFTWARE	ASN A:89 , GLN A:92 , TYR A:202 , TRP A:277 , AAL A:1297 , AAL A:1299	BINDING SITE FOR RESIDUE GAL A1298
11	BC2	SOFTWARE	LYS A:127 , GAL A:1298 , HOH A:2162	BINDING SITE FOR RESIDUE AAL A1299
12	BC3	SOFTWARE	ASP A:22 , SER A:47 , ASN A:49 , SER A:91 , ASP A:279 , HOH A:2328	BINDING SITE FOR RESIDUE CA A1300

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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)
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Chain A from PDB  Type:PROTEIN  Length:268
 aligned with AGAA_ZOBGA | G0L322 from UniProtKB/Swiss-Prot  Length:539

    Alignment length:268
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280        
           AGAA_ZOBGA    21 QDWNGIPVPANPGNGMTWQLQDNVSDSFNYTSSEGNRPTAFTSKWKPSYINGWTGPGSTIFNAPQAWTNGSQLAIQAQPAGNGKSYNGIITSKNKIQYPVYMEIKAKIMDQVLANAFWTLTDDETQEIDIMEGYGSDRGGTWFAQRMHLSHHTFIRNPFTDYQPMGDATWYYNGGTPWRSAYHRYGCYWKDPFTLEYYIDGVKVRTVTRAEIDPNNHLGGTGLNQATNIIIDCENQTDWRPAATQEELADDSKNIFWVDWIRVYKPVA 288
               SCOP domains d1urxa_ A: beta-Agarase A                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1urxA00 A:21-288  [code=2.60.120.200, no name defined]                                                                                                                                                                                                                       CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeee.hhhh............hhhhhh.ee..........................eeeeeeeee.......eeee.......eeeeeeee......eeeeeee.....eeeeeeeee.hhhhhhhhhheeeeeeeeee....eee...hhh.eee....hhhhh.eeeeeeeee..eeeeee..eeeeeehhhhhh..............eeeeeee.........hhhhhhh....eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE GH16_2  PDB: A:21-288 UniProt: 21-289                                                                                                                                                                                                                                        PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1urx A  21 QDWNGIPVPANPGNGMTWQLQDNVSDSFNYTSSEGNRPTAFTSKWKPSYINGWTGPGSTIFNAPQAWTNGSQLAIQAQPAGNGKSYNGIITSKNKIQYPVYMEIKAKIMDQVLANAFWTLTDDETQSIDIMEGYGSDRGGTWFAQRMHLSHHTFIRNPFTDYQPMGDATWYYNGGTPWRSAYHRYGCYWKDPFTLEYYIDGVKVRTVTRAEIDPNNHLGGTGLNQATNIIIDCENQTDWRPAATQEELADDSKNIFWVDWIRVYKPVA 288
                                    30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280

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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)

CATH Domains (1, 1)

Pfam Domains (0, 0)

Gene Ontology (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (AGAA_ZOBGA | G0L322)

molecular function
	GO:0033916	beta-agarase activity	Catalysis of the hydrolysis of (1->4)-beta-D-galactosidic linkages in agarose, giving the tetramer as the predominant product.
	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.
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: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.
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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