3KPD - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE CBS DOMAIN PAIR OF PROTEIN MJ0100 IN COMPLEX WITH 5 -METHYLTHIOADENOSINE AND S-ADENOSYL-L-METHIONINE.

Authors :   M. Lucas, I. Oyenarte, I. G. Garcia, E. A. Arribas, J. A. Encinar, D. Kortazar, J. A. Fernandez, J. M. Mato, M. L. Martinez-Chantar, L. A. Martinez-Cruz

Date :   16 Nov 09 (Deposition) - 12 Jan 10 (Release) - 02 Mar 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.91

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

Keywords :   Cbs Domain; S-Adenosylmethionine; Conformational Change, Cbs Domain, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Lucas, J. A. Encinar, E. A. Arribas, I. Oyenarte, I. G. Garcia, D. Kortazar, J. A. Fernandez, J. M. Mato, M. L. Martinez-Chantar, L. A. Martinez-Cruz
Binding Of S-Methyl-5'-Thioadenosine And S-Adenosyl-L-Methionine To Protein Mj0100 Triggers An Open-To-Closed Conformational Change In Its Cbs Motif Pair.
J. Mol. Biol. V. 396 800 2010
PubMed-ID: 20026078 | Reference-DOI: 10.1016/J.JMB.2009.12.012

Molecule 1 - UNCHARACTERIZED PROTEIN MJ0100
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET101D
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	MJ0100
	Organism Common	:	METHANOCOCCUS JANNASCHII
	Organism Scientific	:	METHANOCALDOCOCCUS JANNASCHII
	Organism Taxid	:	2190

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 7)

No.	Name	Count	Type	Full Name
1	MTA	5	Ligand/Ion	5'-DEOXY-5'-METHYLTHIOADENOSINE
2	SAM	2	Ligand/Ion	S-ADENOSYLMETHIONINE

Biological Unit 1 (1, 4)

No.	Name	Count	Type	Full Name
1	MTA	4	Ligand/Ion	5'-DEOXY-5'-METHYLTHIOADENOSINE
2	SAM	-1	Ligand/Ion	S-ADENOSYLMETHIONINE

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	MTA	1	Ligand/Ion	5'-DEOXY-5'-METHYLTHIOADENOSINE
2	SAM	2	Ligand/Ion	S-ADENOSYLMETHIONINE

Biological Unit 3 (1, 4)

No.	Name	Count	Type	Full Name
1	MTA	4	Ligand/Ion	5'-DEOXY-5'-METHYLTHIOADENOSINE
2	SAM	-1	Ligand/Ion	S-ADENOSYLMETHIONINE

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	THR B:436 , TRP B:438 , ASP B:439 , LYS B:442 , THR B:456 , ASN B:458 , VAL B:459 , ILE B:460 , ASN B:479 , ILE B:480 , SER B:481 , GLY B:482 , PRO B:484 , MTA C:1 , ASN C:418 , ASN C:420 , GLU C:499	BINDING SITE FOR RESIDUE SAM B 1000
2	AC2	SOFTWARE	ASN B:418 , ASN B:420 , GLU B:499 , TRP C:438 , ASP C:439 , THR C:456 , ASN C:458 , VAL C:459 , ILE C:460 , ASN C:479 , ILE C:480 , SER C:481 , GLY C:482 , VAL C:483 , PRO C:484	BINDING SITE FOR RESIDUE SAM C 1000
3	AC3	SOFTWARE	SER A:395 , ILE A:399 , ASN A:418 , ILE A:419 , HIS A:421 , PRO A:423 , ILE A:495 , THR A:497 , GLU A:499 , ASP A:500	BINDING SITE FOR RESIDUE MTA A 1
4	AC4	SOFTWARE	ILE A:434 , TRP A:438 , ASP A:439 , THR A:456 , ASN A:458 , VAL A:459 , ILE A:460 , ASN A:479 , ILE A:480 , GLY A:482	BINDING SITE FOR RESIDUE MTA A 2
5	AC5	SOFTWARE	SAM B:1000 , SER C:395 , PRO C:397 , PRO C:398 , ILE C:399 , ASN C:418 , ILE C:419 , ASN C:420 , HIS C:421 , PRO C:423 , ILE C:495 , THR C:497 , GLU C:499 , ASP C:500	BINDING SITE FOR RESIDUE MTA C 1
6	AC6	SOFTWARE	SER D:395 , PRO D:397 , ILE D:399 , ASN D:418 , ILE D:419 , HIS D:421 , PRO D:423 , ASN D:479 , ILE D:495 , THR D:497 , ASP D:500	BINDING SITE FOR RESIDUE MTA D 1
7	AC7	SOFTWARE	ILE D:434 , THR D:436 , TRP D:438 , ASP D:439 , THR D:456 , ASN D:458 , ILE D:460 , TYR D:478 , ASN D:479 , ILE D:480 , GLY D:482 , PRO D:484	BINDING SITE FOR RESIDUE MTA D 2

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

(no "Cis Peptide Bond" information available for 3KPD)

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

Asymmetric Unit (1, 8)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CBS	PS51371	CBS domain profile.	Y100_METJA	394-450 455-509	8	A:394-450 B:394-450 C:394-450 D:394-450 A:455-506 B:455-508 C:455-506 D:455-506

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CBS	PS51371	CBS domain profile.	Y100_METJA	394-450 455-509	4	A:394-450 - - - A:455-506 - - -

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CBS	PS51371	CBS domain profile.	Y100_METJA	394-450 455-509	4	- B:394-450 C:394-450 - - B:455-508 C:455-506 -

Biological Unit 3 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	CBS	PS51371	CBS domain profile.	Y100_METJA	394-450 455-509	4	- - - D:394-450 - - - D:455-506

(no "Exon" information available for 3KPD)

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:119
 aligned with Y100_METJA | Q57564 from UniProtKB/Swiss-Prot  Length:509

    Alignment length:119
                                   397       407       417       427       437       447       457       467       477       487       497         
           Y100_METJA   388 TLVKDILSKPPITAHSNISIMEAAKILIKHNINHLPIVDEHGKLVGIITSWDIAKALAQNKKTIEEIMTRNVITAHEDEPVDHVAIKMSKYNISGVPVVDDYRRVVGIVTSEDISRLFG 506
               SCOP domains d3kpda_ A: automated matches                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh............hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhh...............ee...hhhhhhhhhhhh...eeeee.....eeeeeehhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------CBS  PDB: A:394-450 UniProt: 394-450                     ----CBS  PDB: A:455-506 UniProt: 455-509                 PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3kpd A 388 TLVKDILSKPPITAHSNISIMEAAKILIKHNINHLPIVDEHGKLVGIITSWDIAKALAQNKKTIEEIMTRNVITAHEDEPVDHVAIKMSKYNISGVPVVDDYRRVVGIVTSEDISRLFG 506
                                   397       407       417       427       437       447       457       467       477       487       497

Chain B from PDB  Type:PROTEIN  Length:121
 aligned with Y100_METJA | Q57564 from UniProtKB/Swiss-Prot  Length:509

    Alignment length:121
                                   397       407       417       427       437       447       457       467       477       487       497       507 
           Y100_METJA   388 TLVKDILSKPPITAHSNISIMEAAKILIKHNINHLPIVDEHGKLVGIITSWDIAKALAQNKKTIEEIMTRNVITAHEDEPVDHVAIKMSKYNISGVPVVDDYRRVVGIVTSEDISRLFGGK 508
               SCOP domains d3kpdb_ B: automated matches                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................hhhhhhhhhhhh...eeeee.....eeeeeehhhhhhhhhh...hhhhhh......ee...hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------CBS  PDB: B:394-450 UniProt: 394-450                     ----CBS  PDB: B:455-508 UniProt: 455-509                   PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kpd B 388 TLVKDILSKPPITAHSNISIMEAAKILIKHNINHLPIVDEHGKLVGIITSWDIAKALAQNKKTIEEIMTRNVITAHEDEPVDHVAIKMSKYNISGVPVVDDYRRVVGIVTSEDISRLFGGK 508
                                   397       407       417       427       437       447       457       467       477       487       497       507

Chain C from PDB  Type:PROTEIN  Length:119
 aligned with Y100_METJA | Q57564 from UniProtKB/Swiss-Prot  Length:509

    Alignment length:119
                                   397       407       417       427       437       447       457       467       477       487       497         
           Y100_METJA   388 TLVKDILSKPPITAHSNISIMEAAKILIKHNINHLPIVDEHGKLVGIITSWDIAKALAQNKKTIEEIMTRNVITAHEDEPVDHVAIKMSKYNISGVPVVDDYRRVVGIVTSEDISRLFG 506
               SCOP domains d3kpdc_ C: automated matches                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhh...........hhhhhhhhhhhh...eeeee.....eeeeeehhhhhhhhhh....................hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------CBS  PDB: C:394-450 UniProt: 394-450                     ----CBS  PDB: C:455-506 UniProt: 455-509                 PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3kpd C 388 TLVKDILSKPPITAHSNISIMEAAKILIKHNINHLPIVDEHGKLVGIITSWDIAKALAQNKKTIEEIMTRNVITAHEDEPVDHVAIKMSKYNISGVPVVDDYRRVVGIVTSEDISRLFG 506
                                   397       407       417       427       437       447       457       467       477       487       497

Chain D from PDB  Type:PROTEIN  Length:119
 aligned with Y100_METJA | Q57564 from UniProtKB/Swiss-Prot  Length:509

    Alignment length:119
                                   397       407       417       427       437       447       457       467       477       487       497         
           Y100_METJA   388 TLVKDILSKPPITAHSNISIMEAAKILIKHNINHLPIVDEHGKLVGIITSWDIAKALAQNKKTIEEIMTRNVITAHEDEPVDHVAIKMSKYNISGVPVVDDYRRVVGIVTSEDISRLFG 506
               SCOP domains d3kpdd_ D: automated matches                                                                                            SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------------------------------------------------------------CBS-3kpdD01 D:451-506                                    Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------CBS-3kpdD02 D:451-506                                    Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------CBS-3kpdD03 D:451-506                                    Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------CBS-3kpdD04 D:451-506                                    Pfam domains (4)
           Pfam domains (5) ---------------------------------------------------------------CBS-3kpdD05 D:451-506                                    Pfam domains (5)
           Pfam domains (6) ---------------------------------------------------------------CBS-3kpdD06 D:451-506                                    Pfam domains (6)
           Pfam domains (7) ---------------------------------------------------------------CBS-3kpdD07 D:451-506                                    Pfam domains (7)
           Pfam domains (8) ---------------------------------------------------------------CBS-3kpdD08 D:451-506                                    Pfam domains (8)
         Sec.struct. author .............ee...hhhhhhhhhhhh...eeeee.....eeeeeehhhhhhhhhh...hhhhhh......ee...hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------CBS  PDB: D:394-450 UniProt: 394-450                     ----CBS  PDB: D:455-506 UniProt: 455-509                 PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------- Transcript
                 3kpd D 388 TLVKDILSKPPITAHSNISIMEAAKILIKHNINHLPIVDEHGKLVGIITSWDIAKALAQNKKTIEEIMTRNVITAHEDEPVDHVAIKMSKYNISGVPVVDDYRRVVGIVTSEDISRLFG 506
                                   397       407       417       427       437       447       457       467       477       487       497

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: CBS-domain pair (75)

Superfamily: CBS-domain pair (75)

Family: automated matches (25)

Protein domain: automated matches (25)

Methanocaldococcus jannaschii [TaxId: 2190] (3)

1a	d3kpda_	A:
1b	d3kpdb_	B:
1c	d3kpdc_	C:
1d	d3kpdd_	D:

(no "CATH Domain" information available for 3KPD)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: CBS] (51)

Family: CBS (51)

Methanocaldococcus jannaschii (strain ATCC 43067 / DSM 2661 / JAL-1 / JCM 10045 / NBRC 100440) (Meth (4)

1a	CBS-3kpdD01	D:451-506
1b	CBS-3kpdD02	D:451-506
1c	CBS-3kpdD03	D:451-506
1d	CBS-3kpdD04	D:451-506
1e	CBS-3kpdD05	D:451-506
1f	CBS-3kpdD06	D:451-506
1g	CBS-3kpdD07	D:451-506
1h	CBS-3kpdD08	D:451-506

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (Y100_METJA | Q57564)

molecular function
	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.

Asymmetric Unit
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	3kpd
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	Y100_METJA \| Q57564
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	Y100_METJA \| Q57564
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	Y100_METJA \| Q57564	:	3kpb 3kpc

Description

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Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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SAPs(SNPs)/Variants (0, 0)

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