3GXK - JenaLib

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Biological Unit 4 (Jmol Viewer)

Title :   THE CRYSTAL STRUCTURE OF G-TYPE LYSOZYME FROM ATLANTIC COD (GADUS MORHUA L.) IN COMPLEX WITH NAG OLIGOMERS SHEDS NEW LIGHT ON SUBSTRATE BINDING AND THE CATALYTIC MECHANISM. NATIVE STRUCTURE TO 1.9

Authors :   R. Helland, R. L. Larsen, S. Finstad, P. Kyomuhendo, A. N. Larsen

Date :   02 Apr 09 (Deposition) - 20 Oct 09 (Release) - 20 Oct 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)

Keywords :   Atlantic Cod, Fish Lysozyme, Crystal Structure, Active Site Residues, Substrate Binding Sites, Surface Potential, Muramidase Activity, Immune System, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   R. Helland, R. L. Larsen, S. Finstad, P. Kyomuhendo, A. N. Larsen
Crystal Structures Of G-Type Lysozyme From Atlantic Cod Shed New Light On Substrate Binding And The Catalytic Mechanism.
Cell. Mol. Life Sci. V. 66 2585 2009
PubMed-ID: 19543850 | Reference-DOI: 10.1007/S00018-009-0063-X
(for further references see the PDB file header)

Molecule 1 - GOOSE-TYPE LYSOZYME 1
	Chains	:	A, B, C, D
	EC Number	:	3.2.1.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET151/D-TOPO GLYS
	Expression System Strain	:	BL21 STAR (DE3)
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 31-217
	Gene	:	LYSOZYME
	Organism Common	:	ATLANTIC COD
	Organism Scientific	:	GADUS MORHUA
	Organism Taxid	:	8049

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 2)

No.	Name	Count	Type	Full Name
1	CO	2	Ligand/Ion	COBALT (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION

Biological Unit 3 (0, 0)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION

Biological Unit 4 (0, 0)

No.	Name	Count	Type	Full Name
1	CO	-1	Ligand/Ion	COBALT (II) ION

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	not defined	GLU A:106 , HIS B:35
2	AC2	not defined	HIS C:35 , GLU D:106

(no "SS Bond" information available for 3GXK)

Asymmetric Unit

No.	Residues
1	Thr A:84	-	Pro A:85
2	Thr B:84	-	Pro B:85
3	Gly C:4	-	Tyr C:5
4	Gly D:4	-	Tyr D:5
5	Thr D:84	-	Pro D:85

(no "SAP(SNP)/Variant" information available for 3GXK)

(no "PROSITE Motif" information available for 3GXK)

(no "Exon" information available for 3GXK)

Asymmetric 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:185
 aligned with B9TU22_GADMO | B9TU22 from UniProtKB/TrEMBL  Length:217

    Alignment length:185
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212     
         B9TU22_GADMO    33 YGDITQVETSGASSKTSRQDKLEYDGVRASHTMAQTDAGRMEKYKSFINNVAKKHVVDPAVIAAIISRESRAGNVIFNTTPPGWGDNYNGFGLMQVDKRYHEPRGAWNSEEHIDQATGILVNFIQLIQKKFPSWSTEQQLKGGIAAYNTGDGRVESYESVDSRTTGKDYSNDVVARAQWYKKNGF 217
               SCOP domains d3gxka_ A: automated matches                                                                                                                                                              SCOP domains
               CATH domains 3gxkA00 A:5-189  [code=1.10.530.10, no name defined]                                                                                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh.....hhhhhhhh....hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhh............ee....ee....ee...........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gxk A   5 YGDITQVETSGASSKTSRQDKLEYDGVRASHTMAQTDAGRMEKYKSFINNVAKKHVVDPAVIAAIISRESRAGNVIFNTTPPGWGDNYNGFGLMQVDKRYHEPRGAWNSEEHIDQATGILVNFIQLIQKKFPSWSTEQQLKGAIAAYNTGDGRVESYESVDSRTTGKDYSNDVVARAQWYKKNGF 189
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184

Chain B from PDB  Type:PROTEIN  Length:183
 aligned with B9TU22_GADMO | B9TU22 from UniProtKB/TrEMBL  Length:217

    Alignment length:183
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214   
         B9TU22_GADMO    35 DITQVETSGASSKTSRQDKLEYDGVRASHTMAQTDAGRMEKYKSFINNVAKKHVVDPAVIAAIISRESRAGNVIFNTTPPGWGDNYNGFGLMQVDKRYHEPRGAWNSEEHIDQATGILVNFIQLIQKKFPSWSTEQQLKGGIAAYNTGDGRVESYESVDSRTTGKDYSNDVVARAQWYKKNGF 217
               SCOP domains d3gxkb_ B: automated matches                                                                                                                                                            SCOP domains
               CATH domains 3gxkB00 B:7-189  [code=1.10.530.10, no name defined]                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh.....hhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh.........ee....ee....ee...........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gxk B   7 DITQVETSGASSKTSRQDKLEYDGVRASHTMAQTDAGRMEKYKSFINNVAKKHVVDPAVIAAIISRESRAGNVIFNTTPPGWGDNYNGFGLMQVDKRYHEPRGAWNSEEHIDQATGILVNFIQLIQKKFPSWSTEQQLKGAIAAYNTGDGRVESYESVDSRTTGKDYSNDVVARAQWYKKNGF 189
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186

Chain C from PDB  Type:PROTEIN  Length:174
 aligned with B9TU22_GADMO | B9TU22 from UniProtKB/TrEMBL  Length:217

    Alignment length:187
                                    40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       
         B9TU22_GADMO    31 VGYGDITQVETSGASSKTSRQDKLEYDGVRASHTMAQTDAGRMEKYKSFINNVAKKHVVDPAVIAAIISRESRAGNVIFNTTPPGWGDNYNGFGLMQVDKRYHEPRGAWNSEEHIDQATGILVNFIQLIQKKFPSWSTEQQLKGGIAAYNTGDGRVESYESVDSRTTGKDYSNDVVARAQWYKKNGF 217
               SCOP domains d3gxkc_ C: automated matches                                                                                                                                                                SCOP domains
               CATH domains 3gxkC00 C:3-189  [code=1.10.530.10, no name defined]                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.....hhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhh...-------------..ee....ee...........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gxk C   3 VGYGDITQVETSGASSKTSRQDKLEYDGVRASHTMAQTDAGRMEKYKSFINNVAKKHVVDPAVIAAIISRESRAGN-------------YNGFGLMQVDKRYHEPRGAWNSEEHIDQATGILVNFIQLIQKKFPSWSTEQQLKGAIAAYNTGDGRVESYESVDSRTTGKDYSNDVVARAQWYKKNGF 189
                                    12        22        32        42        52        62        72     |   -        92       102       112       122       132       142       152       162       172       182       
                                                                                                      78            92

Chain D from PDB  Type:PROTEIN  Length:186
 aligned with B9TU22_GADMO | B9TU22 from UniProtKB/TrEMBL  Length:217

    Alignment length:186
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211      
         B9TU22_GADMO    32 GYGDITQVETSGASSKTSRQDKLEYDGVRASHTMAQTDAGRMEKYKSFINNVAKKHVVDPAVIAAIISRESRAGNVIFNTTPPGWGDNYNGFGLMQVDKRYHEPRGAWNSEEHIDQATGILVNFIQLIQKKFPSWSTEQQLKGGIAAYNTGDGRVESYESVDSRTTGKDYSNDVVARAQWYKKNGF 217
               SCOP domains d3gxkd_ D: automated matches                                                                                                                                                               SCOP domains
               CATH domains 3gxkD00 D:4-189  [code=1.10.530.10, no name defined]                                                                                                                                       CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhh.....hhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.hhhhhhhhhhhhhh............ee....ee....ee...........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3gxk D   4 GYGDITQVETSGASSKTSRQDKLEYDGVRASHTMAQTDAGRMEKYKSFINNVAKKHVVDPAVIAAIISRESRAGNVIFNTTPPGWGDNYNGFGLMQVDKRYHEPRGAWNSEEHIDQATGILVNFIQLIQKKFPSWSTEQQLKGAIAAYNTGDGRVESYESVDSRTTGKDYSNDVVARAQWYKKNGF 189
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a+b) (23004)

Fold: Lysozyme-like (1361)

Superfamily: Lysozyme-like (1361)

Family: G-type lysozyme (8)

Protein domain: automated matches (4)

Atlantic cod (Gadus morhua) [TaxId: 8049] (2)

1a	d3gxka_	A:
1b	d3gxkb_	B:
1c	d3gxkc_	C:
1d	d3gxkd_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Lysozyme (1131)

Homologous Superfamily: [code=1.10.530.10, no name defined] (605)

Atlantic cod (Gadus morhua) (2)

1a	3gxkC00	C:3-189
1b	3gxkB00	B:7-189
1c	3gxkA00	A:5-189
1d	3gxkD00	D:4-189

(no "Pfam Domain" information available for 3GXK)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (B9TU22_GADMO | B9TU22)

molecular function
	GO:0003796	lysozyme activity	Catalysis of the hydrolysis of the beta-(1->4) linkages between N-acetylmuramic acid and N-acetyl-D-glucosamine residues in a peptidoglycan.
biological process
	GO:0016998	cell wall macromolecule catabolic process	The chemical reactions and pathways resulting in the breakdown of macromolecules that form part of a cell wall.
	GO:0009253	peptidoglycan catabolic process	The chemical reactions and pathways resulting in the breakdown of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.

Asymmetric Unit
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	Cis Peptide Bonds
		Gly C:4 - Tyr C:5	[ RasMol ]
		Gly D:4 - Tyr D:5	[ RasMol ]
		Thr A:84 - Pro A:85	[ RasMol ]
		Thr B:84 - Pro B:85	[ RasMol ]
		Thr D:84 - Pro D:85	[ RasMol ]

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	3gxk
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	B9TU22_GADMO \| B9TU22	:	3gxr

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (1, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

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