1T0O - JenaLib

Title :   THE STRUCTURE OF ALPHA-GALACTOSIDASE FROM TRICHODERMA REESEI COMPLEXED WITH BETA-D-GALACTOSE

Authors :   A. M. Golubev, R. A. P. Nagem, J. R. Brandao Neto, K. N. Neustroev, E. V. E A. A. Kulminskaya, K. A. Shabalin, A. N. Savel'Ev, I. Polikarpov

Date :   12 Apr 04 (Deposition) - 12 Oct 04 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.96

Chains :   Asym./Biol. Unit : A

Keywords :   (Beta/Alpha)8 Barrel, Two Domains, Glycoprotein, Complex, Beta-D- Galactose, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. M. Golubev, R. A. P. Nagem, J. R. Brandao Neto, K. N. Neustroev, E. V. Eneyskaya, A. A. Kulminskaya, K. A. Shabalin, A. N. Savel'Ev, I. Polikarpov
Crystal Structure Of Alpha-Galactosidase From Trichoderma Reesei And Its Complex With Galactose: Implications For Catalytic Mechanism
J. Mol. Biol. V. 339 413 2004
PubMed-ID: 15136043 | Reference-DOI: 10.1016/J.JMB.2004.03.062
(for further references see the PDB file header)

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 16)

Sites (16, 16)

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	SER A:58 , MET A:59 , LYS A:60 , ASP A:61 , ASN A:71 , ARG A:74 , NAG A:501	BINDING SITE FOR RESIDUE NAG A 500
02	AC2	SOFTWARE	NAG A:500	BINDING SITE FOR RESIDUE NAG A 501
03	AC3	SOFTWARE	ASN A:157 , PHE A:243 , TRP A:331 , NAG A:601 , HOH A:1043 , HOH A:1251	BINDING SITE FOR RESIDUE NAG A 600
04	AC4	SOFTWARE	PHE A:243 , TRP A:331 , NAG A:600 , BMA A:602 , MAN A:604 , MAN A:606 , HOH A:1179	BINDING SITE FOR RESIDUE NAG A 601
05	AC5	SOFTWARE	NAG A:601 , MAN A:603 , MAN A:604	BINDING SITE FOR RESIDUE BMA A 602
06	AC6	SOFTWARE	BMA A:602 , HOH A:1025 , HOH A:1151	BINDING SITE FOR RESIDUE MAN A 603
07	AC7	SOFTWARE	ASN A:246 , NAG A:601 , BMA A:602 , MAN A:605 , MAN A:606 , HOH A:1104 , HOH A:1282	BINDING SITE FOR RESIDUE MAN A 604
08	AC8	SOFTWARE	ASN A:246 , MAN A:604 , HOH A:1167 , HOH A:1282	BINDING SITE FOR RESIDUE MAN A 605
09	AC9	SOFTWARE	SER A:242 , PHE A:243 , LYS A:244 , LEU A:245 , THR A:321 , PRO A:322 , TRP A:331 , NAG A:601 , MAN A:604 , HOH A:1000 , HOH A:1077	BINDING SITE FOR RESIDUE MAN A 606
10	BC1	SOFTWARE	VAL A:2 , ASN A:215 , ASN A:246 , ASP A:249 , PHE A:250 , TRP A:251 , NAG A:701 , HOH A:948 , HOH A:1084 , HOH A:1111 , HOH A:1182 , HOH A:1185	BINDING SITE FOR RESIDUE NAG A 700
11	BC2	SOFTWARE	VAL A:2 , LYS A:10 , ASP A:249 , PHE A:250 , TRP A:251 , NAG A:700 , BMA A:702 , HOH A:943 , HOH A:1062 , HOH A:1281	BINDING SITE FOR RESIDUE NAG A 701
12	BC3	SOFTWARE	VAL A:315 , NAG A:701 , MAN A:703 , HOH A:1062 , HOH A:1068 , HOH A:1137	BINDING SITE FOR RESIDUE BMA A 702
13	BC4	SOFTWARE	BMA A:702 , HOH A:1258	BINDING SITE FOR RESIDUE MAN A 703
14	BC5	SOFTWARE	ASP A:65 , ASN A:328 , ASN A:334 , TYR A:337 , NAG A:801 , HOH A:1003	BINDING SITE FOR RESIDUE NAG A 800
15	BC6	SOFTWARE	ILE A:327 , NAG A:800 , HOH A:1019 , HOH A:1092 , HOH A:1162	BINDING SITE FOR RESIDUE NAG A 801
16	BC7	SOFTWARE	TRP A:19 , ASP A:54 , ASP A:55 , TYR A:96 , CYS A:104 , LYS A:130 , ASP A:132 , LYS A:193 , CYS A:203 , TRP A:205 , ARG A:222 , ASP A:226 , MET A:258 , HOH A:957 , HOH A:1022	BINDING SITE FOR RESIDUE GAL A 901

SS Bonds (4, 4)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

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)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:417
 aligned with Q92456_HYPJE | Q92456 from UniProtKB/TrEMBL  Length:444

    Alignment length:417
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       
         Q92456_HYPJE    28 IVMPDGVTGKVPSLGWNSWNAYHCDIDESKFLSAAEVIVSSGLLDAGYNYVNIDDCWSMKDGRVDGHIAVNTTRFPDGIDGLAKKVHDLGLKLGIYSTAGTATCAGYPASLGYEDVDAADFADWGVDYLKYDNCNVPSDWQDEYVACAPDAVQTGPNGTCSTALEPNLAPPGYDWSTSKSAERFNAMRNALAKQSREIVLSLCIWGVADVFSWGNETGISWRMSGDISPEWGSVTHIINMNSFKMNSVGFWGHNDADILEVGNGNLTAAETRTHFALWAAMKSPLLIGTDLAQLSQENIELLKNKHLLAFNQDSVYGQPATPYKWGVNPDWTFNYTNPAEYWAGPSSKGHLVLMMNTLDHTVRKEAKWSEIPGLSAGRYEVRDVWTDKSLGCLSSYKTAVAAHDTAVILVGKKCRNW 444
               SCOP domains d1t0oa2 A:1-314 Melibiase                                                                                                                                                                                                                                                                                                 d1t0oa1 A:315-417 Melibiase                                                                             SCOP domains
               CATH domains 1t0oA01 A:1-315 Aldolase class I                                                                                                                                                                                                                                                                                           1t0oA02 A:316-417 Golgi alpha-mannosidase II                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eeeehhhhhh...hhhhhhhhhhhhhhhhhhhhh..eee........................hhhhhhhhhhhhh..eeeeeee..............hhhhhhhhhhhhh..eeeee....hhhhh.............hhhhh..............hhhhhhhhhhhhhhhhhhhh.....eeee......hhhhhhhhh..eee.......hhhhhhhhhhhhhhhhhhh....eee...........hhhhhhhhhhhhhhh...eee.......hhhhhhhhhhhhhhhhhh........eeee................eeee.....eeeeee......eeeeehhhhh.......eeeee.....eeeee..eeeee....eeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1t0o A   1 IVMPDGVTGKVPSLGWNSWNAYHCDIDESKFLSAAELIVSSGLLDAGYNYVNIDDCWSMKDGRVDGHIAPNATRFPDGIDGLAKKVHALGLKLGIYSTAGTATCAGYPASLGYEDVDAADFADWGVDYLKYDNCNVPSDWQDEYVACNPDFVKTGPNGTCTTALDPTLAPPGYDWSTSKSAERFGAMRNALAKQSHEIVLSMCIWGQADVFSWGNSTGISWRMSDDISPNWGSVTRILNLNSFKLNSVDFWGHNDADMLEVGNGNLTAAETRTHFALWAAMKSPLLIGTDLAQLSQNNINLLKNKHLLAFNQDSVYGQPATPYKWGINPDWTFNVTYPAEFWAGPSSKGHLVLMVNTLDITATKEAKWNEIPGLSAGHYEVRDVWSDKDLGCLSSYKAAVAAHDTAVILVGKKCQRW 417
                                    10        20        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       290       300       310       320       330       340       350       360       370       380       390       400       410

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 (2, 2)

CATH Domains (2, 2)

Pfam Domains (0, 0)

Gene Ontology (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (Q92456_HYPJE | Q92456)

molecular function
	GO:0004557	alpha-galactosidase activity	Catalysis of the hydrolysis of terminal, non-reducing alpha-D-galactose residues in alpha-D-galactosides, including galactose oligosaccharides, galactomannans and galactohydrolase.
	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: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.
	GO:0052692	raffinose alpha-galactosidase activity	Catalysis of the reaction: raffinose + H2O = alpha-D-galactose + sucrose.
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.

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