2WQ8 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   GLYCAN LABELLING USING ENGINEERED VARIANTS OF GALACTOSE OXIDASE OBTAINED BY DIRECTED EVOLUTION

Authors :   J. G. Rannes, A. Ioannou, S. C. Willies, C. Behrens, G. J. Grogan, S. L. Fl N. J. Turner

Date :   14 Aug 09 (Deposition) - 01 Sep 10 (Release) - 15 Jun 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.19

Chains :   Asym./Biol. Unit : A

Keywords :   Oxidoreductase, Kelch Repeat, Metal-Binding, Glycoengineering, Directed Evolution (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. B. Rannes, A. Ioannou, S. C. Willies, G. Grogan, C. Behrens, S. L. Flitsch, N. J. Turner
Glycoprotein Labeling Using Engineered Variants Of Galactose Oxidase Obtained By Directed Evolution.
J. Am. Chem. Soc. V. 133 8436 2011
PubMed-ID: 21526835 | Reference-DOI: 10.1021/JA2018477

Molecule 1 - GALACTOSE OXIDASE
	Chains	:	A
	EC Number	:	1.1.3.9
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET16B
	Expression System Strain	:	BL21 (DE3)
	Expression System Taxid	:	469008
	Mutation	:	YES
	Organism Scientific	:	GIBBERELLA ZEAE
	Organism Taxid	:	5518
	Other Details	:	THIO-ETHER BOND BETWEEN CYS228 SG AND TYR272 CE1
	Synonym	:	GAO, GOASE, GO

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (5, 16)

No.	Name	Count	Type	Full Name
1	ACY	2	Ligand/Ion	ACETIC ACID
2	CA	1	Ligand/Ion	CALCIUM ION
3	CU	1	Ligand/Ion	COPPER (II) ION
4	EDO	9	Ligand/Ion	1,2-ETHANEDIOL
5	GOL	3	Ligand/Ion	GLYCEROL

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	PHE A:227 , CYS A:228 , TYR A:272 , TYR A:495 , HIS A:496 , HIS A:581 , ACY A:1642	BINDING SITE FOR RESIDUE CU A1640
02	AC2	SOFTWARE	LYS A:29 , ASP A:32 , ASN A:34 , THR A:37 , ALA A:141 , GLU A:142	BINDING SITE FOR RESIDUE CA A1641
03	AC3	SOFTWARE	TYR A:272 , PHE A:290 , TYR A:495 , HIS A:496 , CU A:1640	BINDING SITE FOR RESIDUE ACY A1642
04	AC4	SOFTWARE	ARG A:371 , ALA A:378 , ALA A:381 , THR A:398 , GLY A:400 , ASN A:413 , ALA A:414 , HIS A:415 , EDO A:1644	BINDING SITE FOR RESIDUE ACY A1643
05	AC5	SOFTWARE	ALA A:378 , PRO A:379 , ALA A:381 , GLY A:400 , GLY A:401 , THR A:411 , ASN A:413 , ACY A:1643 , HOH A:2375	BINDING SITE FOR RESIDUE EDO A1644
06	AC6	SOFTWARE	ASN A:385 , ALA A:386 , VAL A:387 , THR A:443 , SER A:444 , THR A:582 , GLN A:587 , EDO A:1646 , HOH A:2333	BINDING SITE FOR RESIDUE EDO A1645
07	AC7	SOFTWARE	THR A:443 , SER A:497 , ILE A:498 , SER A:499 , ALA A:579 , THR A:580 , HIS A:581 , THR A:582 , VAL A:583 , EDO A:1645 , HOH A:2376	BINDING SITE FOR RESIDUE EDO A1646
08	AC8	SOFTWARE	ILE A:475 , GLN A:486 , PHE A:528 , PRO A:530 , ASN A:531 , TYR A:532 , GOL A:1655 , HOH A:2377	BINDING SITE FOR RESIDUE EDO A1647
09	AC9	SOFTWARE	PRO A:72 , TRP A:81 , ILE A:82 , TRP A:105 , PHE A:106 , ASP A:108 , LYS A:112 , ALA A:132 , HOH A:2378	BINDING SITE FOR RESIDUE EDO A1648
10	BC1	SOFTWARE	HIS A:334 , ALA A:335 , TRP A:336 , GLY A:384 , THR A:582 , VAL A:583 , HOH A:2379 , HOH A:2380	BINDING SITE FOR RESIDUE EDO A1649
11	BC2	SOFTWARE	LEU A:158 , ASN A:314 , TYR A:436 , TYR A:484 , LYS A:485	BINDING SITE FOR RESIDUE EDO A1650
12	BC3	SOFTWARE	PRO A:156 , GLY A:157 , LEU A:158 , GLY A:159 , ARG A:160 , ASN A:531 , GLY A:538	BINDING SITE FOR RESIDUE EDO A1651
13	BC4	SOFTWARE	PRO A:591 , LEU A:592 , THR A:593 , GLN A:605 , PRO A:607	BINDING SITE FOR RESIDUE EDO A1652
14	BC5	SOFTWARE	VAL A:268 , PHE A:295 , GLU A:296 , ASN A:298 , GLY A:299 , SER A:311	BINDING SITE FOR RESIDUE GOL A1653
15	BC6	SOFTWARE	HIS A:40 , ARG A:73 , ASN A:79 , HOH A:2015 , HOH A:2381	BINDING SITE FOR RESIDUE GOL A1654
16	BC7	SOFTWARE	TYR A:484 , GLN A:486 , ASN A:531 , EDO A:1647 , HOH A:2382	BINDING SITE FOR RESIDUE GOL A1655

Asymmetric/Biological Unit

No.	Residues
1	A:18	-	A:27
2	A:515	-	A:518

Asymmetric/Biological Unit

No.	Residues
1	Pro A:51	-	Pro A:52
2	Gly A:162	-	Pro A:163
3	Gly A:349	-	Pro A:350

(no "SAP(SNP)/Variant" information available for 2WQ8)

(no "PROSITE Motif" information available for 2WQ8)

(no "Exon" information available for 2WQ8)

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:639
 aligned with GAOA_GIBZA | P0CS93 from UniProtKB/Swiss-Prot  Length:680

    Alignment length:639
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671         
           GAOA_GIBZA    42 ASAPIGSAISRNNWAVTCDSAQSGNECNKAIDGNKDTFWHTFYGANGDPKPPHTYTIDMKTTQNVNGLSMLPRQDGNQNGWIGRHEVYLSSDGTNWGSPVASGSWFADSTTKYSNFETRPARYVRLVAITEANGQPWTSIAEINVFQASSYTAPQPGLGRWGPTIDLPIVPAAAAIEPTSGRVLMWSSYRNDAFGGSPGGITLTSSWDPSTGIVSDRTVTVTKHDMFCPGISMDGNGQIVVTGGNDAKKTSLYDSSSDSWIPGPDMQVARGYQSSATMSDGRVFTIGGSWSGGVFEKNGEVYSPSSKTWTSLPNAKVNPMLTADKQGLYRSDNHAWLFGWKKGSVFQAGPSTAMNWYYTSGSGDVKSAGKRQSNRGVAPDAMCGNAVMYDAVKGKILTFGGSPDYQDSDATTNAHIITLGEPGTSPNTVFASNGLYFARTFHTSVVLPDGSTFITGGQRRGIPFEDSTPVFTPEIYVPEQDTFYKQNPNSIVRVYHSISLLLPDGRVFNGGGGLCGDCTTNHFDAQIFTPNYLYNSNGNLATRPKITRTSTQSVKVGGRITISTDSSISKASLIRYGTATHTVNTDQRRIPLTLTNNGGNSYSFQVPSDSGVALPGYWMLFVMNSAGVPSVASTIRVTQ 680
               SCOP domains d2wq8a1 A:1-150 automated matches                                                                                                                     d2wq8a2 A:151-537 automated matches                                                                                                                                                                                                                                                                                                                                                                d2wq8a3 A:538-639 automated matches                                                                    SCOP domains
               CATH domains 2wq8A01 A:1-153 Galactose-binding domain-like                                                                                                            2wq8A02 A:154-541 Galactose oxidase, central domain                                                                                                                                                                                                                                                                                                                                                 2wq8A03 A:542-639 Immunoglobulins                                                                  CATH domains
               Pfam domains ------------F5_F8_type_C-2wq8A02 A:13-143                                                                                                      -------------------------------------------------------------------------------------------------------------------------------Kelch_1-2wq8A01 A:271-316                     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DUF1929-2wq8A03 A:543-637                                                                      -- Pfam domains
         Sec.struct. author ..............eeee.......hhhhhhh......ee............eeeeeeeeeeeee...eee.............eeeeee..........ee.........ee.....eeeeeeeeee..........ee.eee...................eee......eeee......eeee...............eeeeee......eeeeee............ee.....eee.........eeee....eee............eeee.....eeee..............eee....eee......hhhhh...............ee......eee.......eee.......eee..................eee.......eee................eeee........eeee............eeee.....eeee..................eeeehhhheeee..............ee.....eee..............eeeee.hhhh............eeee...eee....eeeee.....eeeeee...ee........eee...ee....eeee.............eeeeee.........eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wq8 A   1 ASAPIGSAIPRNNWAVTCDSAQSGNECNKAIDGNKDTFWHTFYGANGDPKPPHTYTIDMKTTQNVNGLSVLPRQDGNQNGWIGRHEVYLSSDGTNWGSPVASGSWFADSTTKYSNFETRPARYVRLVAITEANGQPWTSIAEINVFQASSYTAPQPGLGRWGPTIDLPIVPAAAAIEPTSGRVLMWSSYRNDAFEGSPGGITLTSSWDPSTGIVSDRTVTVTKHDMFCPGISMDGNGQIVVTGGNDAKKTSLYDSSSDSWIPGPDMQVARGYQSSATMSDGRVFTIGGSFSGGVFEKNGEVYSPSSKTWTSLPNAKVNPMLTADKQGLYKSDNHAWLFGWKKGSVFQAGPSTAMNWYYTSGSGDVKSAGKRQSNRGVAPDAMCGNAVMYDAVKGKILTFGGSPDYTDSDATTNAHIITLGEPGTSPNTVFASNGLYFARTFHTSVVLPDGSTFITGGQRRGIIFEDSTPVFTPEIYVPEQDTFYKQNPNSIVRAYHSISLLLPDGRVFNGGGGLCGDCTTNHFDAQIFTPNYLYDSNGNLATRPKITRTSTQSVKVGGRITISTDSSISKASLIRYGTATHTVNTDQRRIPLTLTNNGGNSYSFQVPSDSGVALPGYWMLFVMNSAGVPSVASTIRVTQ 639
                                    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       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630

Chain A from PDB  Type:PROTEIN  Length:639
 aligned with GAOA_GIBZE | I1S2N3 from UniProtKB/Swiss-Prot  Length:680

    Alignment length:639
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671         
           GAOA_GIBZE    42 ASAPIGSAISRNNWAVTCDSAQSGNECNKAIDGNKDTFWHTFYGANGDPKPPHTYTIDMKTTQNVNGLSMLPRQDGNQNGWIGRHEVYLSSDGTNWGSPVASGSWFADSTTKYSNFETRPARYVRLVAVTEANGQPWTSIAEINVFQASSYTAPQPGLGRWGPTIDLPIVPAAAAIEPTSGRVLMWSSYRNDAFGGSPGGITLTSSWDPSTGIVSDRTVTVTKHDMFCPGISMDGNGQIVVTGGNDAKKTSLYDSSSDSWIPGPDMQVARGYQSSATMSDGRVFTIGGSWSGGVFEKNGEVYSPSSKTWTSLPNAKVNPMLTADKQGLYRSDNHAWLFGWKKGSVFQAGPSTAMNWYYTSGSGDVKSAGKRQSNRGVAPDAMCGNAVMYDAVKGKILTFGGSPDYQDSDATTNAHIITLGEPGTSPNTVFASNGLYFARTFHTSVVLPDGSTFITGGQRRGIPFEDSTPVFTPEIYVPEQDTFYKQNPNSIVRVYHSISLLLPDGRVFNGGGGLCGDCTTNHFDAQIFTPNYLYNSNGNLATRPKITRTSTQSVKVGGRITISTDSSITKASLIRYGTATHTVNTDQRRIPLTLTNNGGNSYSFQVPSDSGVALPGYWMLFVMNSAGVPSVASTIRVTQ 680
               SCOP domains d2wq8a1 A:1-150 automated matches                                                                                                                     d2wq8a2 A:151-537 automated matches                                                                                                                                                                                                                                                                                                                                                                d2wq8a3 A:538-639 automated matches                                                                    SCOP domains
               CATH domains 2wq8A01 A:1-153 Galactose-binding domain-like                                                                                                            2wq8A02 A:154-541 Galactose oxidase, central domain                                                                                                                                                                                                                                                                                                                                                 2wq8A03 A:542-639 Immunoglobulins                                                                  CATH domains
               Pfam domains ------------F5_F8_type_C-2wq8A02 A:13-143                                                                                                      -------------------------------------------------------------------------------------------------------------------------------Kelch_1-2wq8A01 A:271-316                     ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DUF1929-2wq8A03 A:543-637                                                                      -- Pfam domains
         Sec.struct. author ..............eeee.......hhhhhhh......ee............eeeeeeeeeeeee...eee.............eeeeee..........ee.........ee.....eeeeeeeeee..........ee.eee...................eee......eeee......eeee...............eeeeee......eeeeee............ee.....eee.........eeee....eee............eeee.....eeee..............eee....eee......hhhhh...............ee......eee.......eee.......eee..................eee.......eee................eeee........eeee............eeee.....eeee..................eeeehhhheeee..............ee.....eee..............eeeee.hhhh............eeee...eee....eeeee.....eeeeee...ee........eee...ee....eeee.............eeeeee.........eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wq8 A   1 ASAPIGSAIPRNNWAVTCDSAQSGNECNKAIDGNKDTFWHTFYGANGDPKPPHTYTIDMKTTQNVNGLSVLPRQDGNQNGWIGRHEVYLSSDGTNWGSPVASGSWFADSTTKYSNFETRPARYVRLVAITEANGQPWTSIAEINVFQASSYTAPQPGLGRWGPTIDLPIVPAAAAIEPTSGRVLMWSSYRNDAFEGSPGGITLTSSWDPSTGIVSDRTVTVTKHDMFCPGISMDGNGQIVVTGGNDAKKTSLYDSSSDSWIPGPDMQVARGYQSSATMSDGRVFTIGGSFSGGVFEKNGEVYSPSSKTWTSLPNAKVNPMLTADKQGLYKSDNHAWLFGWKKGSVFQAGPSTAMNWYYTSGSGDVKSAGKRQSNRGVAPDAMCGNAVMYDAVKGKILTFGGSPDYTDSDATTNAHIITLGEPGTSPNTVFASNGLYFARTFHTSVVLPDGSTFITGGQRRGIIFEDSTPVFTPEIYVPEQDTFYKQNPNSIVRAYHSISLLLPDGRVFNGGGGLCGDCTTNHFDAQIFTPNYLYDSNGNLATRPKITRTSTQSVKVGGRITISTDSSISKASLIRYGTATHTVNTDQRRIPLTLTNNGGNSYSFQVPSDSGVALPGYWMLFVMNSAGVPSVASTIRVTQ 639
                                    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       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630

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(hide GO term definitions)

Chain A (GAOA_GIBZA | P0CS93)

molecular function
	GO:0045480	galactose oxidase activity	Catalysis of the reaction: D-galactose + O2 = D-galacto-hexodialdose + hydrogen peroxide.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
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.

Chain A (GAOA_GIBZE | I1S2N3)

molecular function
	GO:0045480	galactose oxidase activity	Catalysis of the reaction: D-galactose + O2 = D-galacto-hexodialdose + hydrogen peroxide.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
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.

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Gly A:162 - Pro A:163	[ RasMol ]
		Gly A:349 - Pro A:350	[ RasMol ]
		Pro A:51 - Pro A:52	[ RasMol ]

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	2wq8
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	GAOA_GIBZA \| P0CS93
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	GAOA_GIBZE \| I1S2N3
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	1.1.3.9
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	GAOA_GIBZA \| P0CS93
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1gof	GALACTOSE OXIDASE (PH 4.5)
1gog	GALACTOSE OXIDASE (PH 7.0)
1goh	GALACTOSE OXIDASE (APO FORM)
1k3i	CRYSTAL STRUCTURE OF THE PRECURSOR OF GALACTOSE OXIDASE
1t2x	GLACTOSE OXIDASE C383S MUTANT IDENTIFIED BY DIRECTEDEVOLUTION
2jkx	GALACTOSE OXIDASE. MATGO. COPPER FREE, EXPRESSED IN PICHIA PASTORIS.
2vz1	PREMAT-GALACTOSE OXIDASE
2vz3	BLEACHED GALACTOSE OXIDASE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 16)

Sites (16, 16)

SS Bonds (2, 2)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (3, 3)

CATH Domains (3, 3)

Pfam Domains (3, 3)

Gene Ontology (5, 10)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File