1PL3 - JenaLib

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Title :   CYTOCHROME DOMAIN OF CELLOBIOSE DEHYDROGENASE, M65H MUTANT

Authors :   F. A. J. Rotsaert, B. M. Hallberg, S. De Vries, P. Moenne-Loccoz, C. Div M. H. Gold

Date :   06 Jun 03 (Deposition) - 01 Jul 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)

Keywords :   B-Type Cytochrome, Mutant, Bis-His Ligation, Beta Sandwich, Fe(Ii)- Protoporphyrin Ix, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. A. J. Rotsaert, B. M. Hallberg, S. De Vries, P. Moenne-Loccoz, C. Divne, V. Renganathan, M. H. Gold
Biophysical And Structural Analysis Of A Novel Heme B Iron Ligation In The Flavocytochrome Cellobiose Dehydrogenase.
J. Biol. Chem. V. 278 33224 2003
PubMed-ID: 12796496 | Reference-DOI: 10.1074/JBC.M302653200

Molecule 1 - CELLOBIOSE DEHYDROGENASE
	Chains	:	A, B
	EC Number	:	1.1.99.18
	Engineered	:	YES
	Expression System	:	PHANEROCHAETE CHRYSOSPORIUM
	Expression System Plasmid	:	PUGC1
	Expression System Strain	:	OGC316-7
	Expression System Taxid	:	5306
	Expression System Vector Type	:	PLASMID
	Fragment	:	CYTOCHROME TYPE B HEME DOMAIN
	Gene	:	CDH-1 AND CDH-2
	Mutation	:	YES
	Organism Scientific	:	PHANEROCHAETE CHRYSOSPORIUM
	Organism Taxid	:	5306
	Synonym	:	CDH, CELLOBIOSE-QUINONE OXIDOREDUCTASE

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 15)

No.	Name	Count	Type	Full Name
1	1PG	1	Ligand/Ion	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
2	CD	6	Ligand/Ion	CADMIUM ION
3	HEM	2	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
4	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	PCA	2	Mod. Amino Acid	PYROGLUTAMIC ACID

Biological Unit 1 (4, 5)

No.	Name	Count	Type	Full Name
1	1PG	1	Ligand/Ion	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
2	CD	-1	Ligand/Ion	CADMIUM ION
3	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	1PG	-1	Ligand/Ion	2-(2-{2-[2-(2-METHOXY-ETHOXY)-ETHOXY]-ETHOXY}-ETHOXY)-ETHANOL
2	CD	-1	Ligand/Ion	CADMIUM ION
3	HEM	1	Ligand/Ion	PROTOPORPHYRIN IX CONTAINING FE
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
5	PCA	1	Mod. Amino Acid	PYROGLUTAMIC ACID

Asymmetric Unit (13, 13)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:111 , SER A:112 , THR A:113 , NAG A:302 , HOH A:756 , HOH A:763 , HOH A:781 , GLN B:40 , THR B:136 , HOH B:1770	BINDING SITE FOR RESIDUE NAG A 301
02	AC2	SOFTWARE	PRO A:9 , NAG A:301 , HOH A:747	BINDING SITE FOR RESIDUE NAG A 302
03	AC3	SOFTWARE	ASN B:111 , NAG B:302 , HOH B:1626 , HOH B:1745	BINDING SITE FOR RESIDUE NAG B 301
04	AC4	SOFTWARE	HIS B:114 , NAG B:301	BINDING SITE FOR RESIDUE NAG B 302
05	AC5	SOFTWARE	PRO A:21 , ASP A:24 , HOH A:629 , HEM B:401 , HOH B:628	BINDING SITE FOR RESIDUE CD A 502
06	AC6	SOFTWARE	GLU A:107 , TYR A:184 , ASN A:186 , HOH A:721 , HOH A:779	BINDING SITE FOR RESIDUE CD A 503
07	AC7	SOFTWARE	GLU A:126	BINDING SITE FOR RESIDUE CD A 504
08	AC8	SOFTWARE	HEM A:401 , HOH A:1628 , PRO B:21 , ASP B:24 , HOH B:1629	BINDING SITE FOR RESIDUE CD B 1502
09	AC9	SOFTWARE	GLU B:107 , TYR B:184 , ASN B:186	BINDING SITE FOR RESIDUE CD B 1503
10	BC1	SOFTWARE	ASP A:165 , HOH A:627 , ASP B:165 , HOH B:1627	BINDING SITE FOR RESIDUE CD A 501
11	BC2	SOFTWARE	TRP A:56 , GLY A:58 , ILE A:59 , ALA A:64 , HIS A:65 , TYR A:90 , GLN A:92 , PRO A:93 , ALA A:142 , PHE A:160 , GLU A:162 , HIS A:163 , PHE A:166 , PHE A:168 , HOH A:605 , HOH A:633 , PRO B:21 , ASP B:24 , CD B:1502 , HOH B:1629 , HOH B:1637	BINDING SITE FOR RESIDUE HEM A 401
12	BC3	SOFTWARE	PRO A:21 , ASP A:24 , CD A:502 , HOH A:629 , HOH A:637 , GLY B:58 , ILE B:59 , HIS B:65 , TYR B:90 , GLN B:92 , ALA B:142 , PHE B:160 , GLU B:162 , HIS B:163 , PHE B:166 , HOH B:1605 , HOH B:1633	BINDING SITE FOR RESIDUE HEM B 401
13	BC4	SOFTWARE	PCA A:1 , HOH A:665 , PCA B:1 , HOH B:1665	BINDING SITE FOR RESIDUE 1PG A 402

Asymmetric Unit

No.	Residues
1	A:121	-	A:124
2	B:121	-	B:124

(no "Cis Peptide Bond" information available for 1PL3)

(no "SAP(SNP)/Variant" information available for 1PL3)

(no "PROSITE Motif" information available for 1PL3)

(no "Exon" information available for 1PL3)

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
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Chain A from PDB  Type:PROTEIN  Length:186
 aligned with CDH_PHACH | Q01738 from UniProtKB/Swiss-Prot  Length:773

    Alignment length:186
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198      
            CDH_PHACH    19 QSASQFTDPTTGFQFTGITDPVHDVTYGFVFPPLATSGAQSTEFIGEVVAPIASKWIGIALGGAMNNDLLLVAWANGNQIVSSTRWATGYVQPTAYTGTATLTTLPETTINSTHWKWVFRCQGCTEWNNGGGIDVTSQGVLAWAFSNVAVDDPSDPQSTFSEHTDFGFFGIDYSTAHSANYQNYLN 204
               SCOP domains d1pl3a_ A: Cytochrome domain of cellobiose dehydrogenase                                                                                                                                   SCOP domains
               CATH domains -1pl3A00 A:2-186  [code=2.60.40.1210, no name defined]                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee......eeeeeee....eeeeee.............eeeeeeee....eeeee.........eeeeeee..eeeeeeee.......ee.....eeee....ee...eeeeeeeee...............eeeeeeeee..................eeeeeeee.hhh...hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1pl3 A   1 xSASQFTDPTTGFQFTGITDPVHDVTYGFVFPPLATSGAQSTEFIGEVVAPIASKWIGIALGGAHNNDLLLVAWANGNQIVSSTRWATGYVQPTAYTGTATLTTLPETTINSTHWKWVFRCQGCTEWNNGGGIDVTSQGVLAWAFSNVAVDDPSDPQSTFSEHTDFGFFGIDYSTAHSANYQNYLN 186
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      
                            |                                                                                                                                                                                         
                            1-PCA

Chain B from PDB  Type:PROTEIN  Length:186
 aligned with CDH_PHACH | Q01738 from UniProtKB/Swiss-Prot  Length:773

    Alignment length:186
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198      
            CDH_PHACH    19 QSASQFTDPTTGFQFTGITDPVHDVTYGFVFPPLATSGAQSTEFIGEVVAPIASKWIGIALGGAMNNDLLLVAWANGNQIVSSTRWATGYVQPTAYTGTATLTTLPETTINSTHWKWVFRCQGCTEWNNGGGIDVTSQGVLAWAFSNVAVDDPSDPQSTFSEHTDFGFFGIDYSTAHSANYQNYLN 204
               SCOP domains d1pl3b_ B: Cytochrome domain of cellobiose dehydrogenase                                                                                                                                   SCOP domains
               CATH domains -1pl3B00 B:2-186  [code=2.60.40.1210, no name defined]                                                                                                                                     CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee......eeeeeee....eeeeee.............eeeeeeee....eeeee.........eeeeeee..eeeeeeee.......ee.....eeee....ee...eeeeeeeee...............eeeeeeeee..................eeeeeeee.hhh...hhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1pl3 B   1 xSASQFTDPTTGFQFTGITDPVHDVTYGFVFPPLATSGAQSTEFIGEVVAPIASKWIGIALGGAHNNDLLLVAWANGNQIVSSTRWATGYVQPTAYTGTATLTTLPETTINSTHWKWVFRCQGCTEWNNGGGIDVTSQGVLAWAFSNVAVDDPSDPQSTFSEHTDFGFFGIDYSTAHSANYQNYLN 186
                            |       10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180      
                            1-PCA

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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Class: All beta proteins (24004)

Fold: Immunoglobulin-like beta-sandwich (7299)

Superfamily: CBD9-like (9)

Family: Cytochrome domain of cellobiose dehydrogenase (4)

Protein domain: Cytochrome domain of cellobiose dehydrogenase (4)

Basidomycetes fungus (Phanerochaete chrysosporium) [TaxId: 5306] (4)

1a	d1pl3a_	A:
1b	d1pl3b_	B:

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Immunoglobulin-like (3897)

Homologous Superfamily: [code=2.60.40.1210, no name defined] (4)

Phanerochaete chrysosporium. Organism_taxid: 5306. (4)

1a	1pl3A00	A:2-186
1b	1pl3B00	B:2-186

(no "Pfam Domain" information available for 1PL3)

Asymmetric Unit(hide GO term definitions)

Chain A,B (CDH_PHACH | Q01738)

molecular function
	GO:0047735	cellobiose dehydrogenase (acceptor) activity	Catalysis of the reaction: cellobiose + acceptor = cellobiono-1,5-lactone + reduced acceptor.
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	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.
	GO:0016614	oxidoreductase activity, acting on CH-OH group of donors	Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group act as a hydrogen or electron donor and reduces a hydrogen or electron acceptor.
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:0030245	cellulose catabolic process	The chemical reactions and pathways resulting in the breakdown of cellulose, a linear beta1-4 glucan of molecular mass 50-400 kDa with the pyranose units in the -4C1 conformation.
	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.
	GO:0000272	polysaccharide catabolic process	The chemical reactions and pathways resulting in the breakdown of a polysaccharide, a polymer of many (typically more than 10) monosaccharide residues linked glycosidically.
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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	1pl3
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	1.1.99.18
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UniProtKB/Swiss-Prot
	CDH_PHACH \| Q01738	:	1d7b 1d7c 1d7d 1kdg 1naa

1d7b	CYTOCHROME DOMAIN OF CELLOBIOSE DEHYDROGENASE, PH 7.5
1d7c	CYTOCHROME DOMAIN OF CELLOBIOSE DEHYDROGENASE, PH 4.6
1d7d	CYTOCHROME DOMAIN OF CELLOBIOSE DEHYDROGENASE, HP3 FRAGMENT, PH 7.5
1kdg	CRYSTAL STRUCTURE OF THE FLAVIN DOMAIN OF CELLOBIOSE DEHYDROGENASE
1naa	TITLE CELLOBIOSE DEHYDROGENASE FLAVOPROTEIN FRAGMENT IN COMPLEX WITH CELLOBIONOLACTAM

Description

Compounds

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Chains, Units

Ligands, Modified Residues, Ions (5, 15)

Sites (13, 13)

SS Bonds (2, 2)

Cis Peptide Bonds (0, 0)

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Gene Ontology (10, 10)

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