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Title :   CRYSTAL STRUCTURE OF THERMUS THERMOPHILUS HB8 H-PROTEIN OF THE GLYCINE CLEAVAGE SYSTEM

Authors :   T. Nakai, J. Ishijima, R. Masui, S. Kuramitsu, N. Kamiya, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   28 Feb 03 (Deposition) - 26 Aug 03 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Hybrid Barrel-Sandwich Structure, Structural Genomics, Riken Structural Genomics/Proteomics Initiative, Rsgi, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Nakai, J. Ishijima, R. Masui, S. Kuramitsu, N. Kamiya
Structure Of Thermus Thermophilus Hb8 H-Protein Of The Glycine-Cleavage System, Resolved By A Six-Dimensional Molecular-Replacement Method.
Acta Crystallogr. , Sect. D V. 59 1610 2003
PubMed-ID: 12925792 | Reference-DOI: 10.1107/S0907444903014975
(for further references see the PDB file header)

Molecule 1 - GLYCINE CLEAVAGE SYSTEM H PROTEIN
	Chains	:	A, B, C
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PET11A-GCVH
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	GCVH
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 1ONL)

(no "Site" information available for 1ONL)

(no "SS Bond" information available for 1ONL)

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

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

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BIOTINYL_LIPOYL	PS50968	Biotinyl/lipoyl domain profile.	GCSH_THET8	22-104	3	A:22-104 B:22-104 C:22-104
2	LIPOYL	PS00189	2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.	GCSH_THET8	47-76	3	A:47-76 B:47-76 C:47-76

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BIOTINYL_LIPOYL	PS50968	Biotinyl/lipoyl domain profile.	GCSH_THET8	22-104	1	A:22-104 - -
2	LIPOYL	PS00189	2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.	GCSH_THET8	47-76	1	A:47-76 - -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BIOTINYL_LIPOYL	PS50968	Biotinyl/lipoyl domain profile.	GCSH_THET8	22-104	1	- B:22-104 -
2	LIPOYL	PS00189	2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.	GCSH_THET8	47-76	1	- B:47-76 -

Biological Unit 3 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BIOTINYL_LIPOYL	PS50968	Biotinyl/lipoyl domain profile.	GCSH_THET8	22-104	1	- - C:22-104
2	LIPOYL	PS00189	2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.	GCSH_THET8	47-76	1	- - C:47-76

(no "Exon" information available for 1ONL)

Asymmetric Unit

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	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:127
 aligned with GCSH_THET8 | Q5SKW9 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:127
                                    11        21        31        41        51        61        71        81        91       101       111       121       
           GCSH_THET8     2 DIPKDRFYTKTHEWALPEGDTVLVGITDYAQDALGDVVYVELPEVGRVVEKGEAVAVVESVKTASDIYAPVAGEIVEVNLALEKTPELVNQDPYGEGWIFRLKPRDMGDLDELLDAGGYQEVLESEA 128
               SCOP domains d1onla_ A: Protein H of glycine cleavage system                                                                                 SCOP domains
               CATH domains 1onlA00 A:2-128  [code=2.40.50.100, no name defined]                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee....eeeeee..eeeeeehhhhhhhhh.eeeee......ee....eeeeeee...eeeee....eeeeee.hhhhhh.hhhhhh.......eeeee.hhhhhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------BIOTINYL_LIPOYL  PDB: A:22-104 UniProt: 22-104                                     ------------------------ PROSITE (1)
                PROSITE (2) ---------------------------------------------LIPOYL  PDB: A:47-76          ---------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1onl A   2 DIPKDRFYTKTHEWALPEGDTVLVGITDYAQDALGDVVYVELPEVGRVVEKGEAVAVVESVKTASDIYAPVAGEIVEVNLALEKTPELVNQDPYGEGWIFRLKPRDMGDLDELLDAGGYQEVLESEA 128
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain B from PDB  Type:PROTEIN  Length:127
 aligned with GCSH_THET8 | Q5SKW9 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:127
                                    11        21        31        41        51        61        71        81        91       101       111       121       
           GCSH_THET8     2 DIPKDRFYTKTHEWALPEGDTVLVGITDYAQDALGDVVYVELPEVGRVVEKGEAVAVVESVKTASDIYAPVAGEIVEVNLALEKTPELVNQDPYGEGWIFRLKPRDMGDLDELLDAGGYQEVLESEA 128
               SCOP domains d1onlb_ B: Protein H of glycine cleavage system                                                                                 SCOP domains
               CATH domains 1onlB00 B:2-128  [code=2.40.50.100, no name defined]                                                                            CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......ee....eeeeee..eeeeeehhhhhhhhh.eeeee......ee....eeeeeee...eeeee....eeeeee.hhhhhh.hhhhhh.......eeeee.hhhhhhhh.hhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------BIOTINYL_LIPOYL  PDB: B:22-104 UniProt: 22-104                                     ------------------------ PROSITE (1)
                PROSITE (2) ---------------------------------------------LIPOYL  PDB: B:47-76          ---------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1onl B   2 DIPKDRFYTKTHEWALPEGDTVLVGITDYAQDALGDVVYVELPEVGRVVEKGEAVAVVESVKTASDIYAPVAGEIVEVNLALEKTPELVNQDPYGEGWIFRLKPRDMGDLDELLDAGGYQEVLESEA 128
                                    11        21        31        41        51        61        71        81        91       101       111       121

Chain C from PDB  Type:PROTEIN  Length:127
 aligned with GCSH_THET8 | Q5SKW9 from UniProtKB/Swiss-Prot  Length:128

    Alignment length:127
                                    11        21        31        41        51        61        71        81        91       101       111       121       
           GCSH_THET8     2 DIPKDRFYTKTHEWALPEGDTVLVGITDYAQDALGDVVYVELPEVGRVVEKGEAVAVVESVKTASDIYAPVAGEIVEVNLALEKTPELVNQDPYGEGWIFRLKPRDMGDLDELLDAGGYQEVLESEA 128
               SCOP domains d1onlc_ C: Protein H of glycine cleavage system                                                                                 SCOP domains
               CATH domains 1onlC00 C:2-128  [code=2.40.50.100, no name defined]                                                                            CATH domains
           Pfam domains (1) -----GCV_H-1onlC01 C:7-127                                                                                                    - Pfam domains (1)
           Pfam domains (2) -----GCV_H-1onlC02 C:7-127                                                                                                    - Pfam domains (2)
           Pfam domains (3) -----GCV_H-1onlC03 C:7-127                                                                                                    - Pfam domains (3)
         Sec.struct. author ......ee....eeeeee..eeeeeehhhhhhhhh.eeeee......ee....eeeeeee...eeeee....eeeeee.hhhhhh.hhhhhh.......eeeee.hhhhhhhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------BIOTINYL_LIPOYL  PDB: C:22-104 UniProt: 22-104                                     ------------------------ PROSITE (1)
                PROSITE (2) ---------------------------------------------LIPOYL  PDB: C:47-76          ---------------------------------------------------- PROSITE (2)
                 Transcript ------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1onl C   2 DIPKDRFYTKTHEWALPEGDTVLVGITDYAQDALGDVVYVELPEVGRVVEKGEAVAVVESVKTASDIYAPVAGEIVEVNLALEKTPELVNQDPYGEGWIFRLKPRDMGDLDELLDAGGYQEVLESEA 128
                                    11        21        31        41        51        61        71        81        91       101       111       121

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Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: All beta proteins (24004)

Fold: Barrel-sandwich hybrid (185)

Superfamily: Single hybrid motif (49)

Family: Biotinyl/lipoyl-carrier proteins and domains (40)

Protein domain: Protein H of glycine cleavage system (11)

Thermus thermophilus [TaxId: 274] (1)

1a	d1onla_	A:
1b	d1onlb_	B:
1c	d1onlc_	C:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P) (1040)

Homologous Superfamily: [code=2.40.50.100, no name defined] (113)

Thermus thermophilus. Organism_taxid: 274. (1)

1a	1onlA00	A:2-128
1b	1onlB00	B:2-128
1c	1onlC00	C:2-128

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Hybrid (58)

Family: GCV_H (4)

Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579) (1)

1a	GCV_H-1onlC01	C:7-127
1b	GCV_H-1onlC02	C:7-127
1c	GCV_H-1onlC03	C:7-127

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (GCSH_THET8 | Q5SKW9)

biological process
	GO:0019464	glycine decarboxylation via glycine cleavage system	The chemical reactions and pathways resulting in the breakdown of glycine by oxidative cleavage to carbon dioxide, ammonia, and a methylene group, mediated by enzymes of the glycine cleavage complex.
cellular component
	GO:0005960	glycine cleavage complex	A protein complex that catalyzes the reversible oxidation of glycine. In E. coli, it has four components: dihydrolipoamide dehydrogenase, glycine dehydrogenase (decarboxylating), lipoyl-GcvH-protein and aminomethyltransferase, also known as L, P, H, and T.

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