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Title :   CRYSTAL STRUCTURE OF GLYCINE CLEAVAGE SYSTEM H PROTEIN (TM0212) FROM THERMOTOGA MARITIMA AT 1.65 A RESOLUTION

Authors :   Joint Center For Structural Genomics (Jcsg)

Date :   03 May 05 (Deposition) - 10 May 05 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.65

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

Keywords :   Tm0212, Glycine Cleavage System H Protein, Structural Genomics, Joint Center For Structural Genomics, Jcsg, Protein Structure Initiative, Psi, Glycine Cleavage H-Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Joint Center For Structural Genomics (Jcsg)
Crystal Structure Of Glycine Cleavage System H Protein (Tm0212) From Thermotoga Maritima At 1. 65 A Resolution
To Be Published
PubMed: search

Molecule 1 - GLYCINE CLEAVAGE SYSTEM H PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GCVH
	Organism Scientific	:	THERMOTOGA MARITIMA
	Organism Taxid	:	2336

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 5)

No.	Name	Count	Type	Full Name
1	MSE	4	Mod. Amino Acid	SELENOMETHIONINE
2	NA	1	Ligand/Ion	SODIUM ION

Biological Unit 1 (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
2	NA	-1	Ligand/Ion	SODIUM ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	MSE	2	Mod. Amino Acid	SELENOMETHIONINE
2	NA	-1	Ligand/Ion	SODIUM ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:5 , ASP A:113 , HOH A:135 , LYS B:5 , ASP B:113	BINDING SITE FOR RESIDUE NA A 125

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

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

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

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BIOTINYL_LIPOYL	PS50968	Biotinyl/lipoyl domain profile.	GCSH_THEMA	19-101	2	A:19-101 B:19-101
2	LIPOYL	PS00189	2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.	GCSH_THEMA	44-73	2	A:44-73 B:44-73

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_THEMA	19-101	1	A:19-101 -
2	LIPOYL	PS00189	2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.	GCSH_THEMA	44-73	1	A:44-73 -

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_THEMA	19-101	1	- B:19-101
2	LIPOYL	PS00189	2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.	GCSH_THEMA	44-73	1	- B:44-73

Biological Unit 3 (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BIOTINYL_LIPOYL	PS50968	Biotinyl/lipoyl domain profile.	GCSH_THEMA	19-101	2	A:19-101 B:19-101
2	LIPOYL	PS00189	2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.	GCSH_THEMA	44-73	2	A:44-73 B:44-73

(no "Exon" information available for 1ZKO)

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:128
 aligned with GCSH_THEMA | Q9WY55 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:128
                                 1                                                                                                                          
                                 |   5        15        25        35        45        55        65        75        85        95       105       115        
           GCSH_THEMA     - -----MKMKKYTKTHEWVSIEDKVATVGITNHAQEQLGDVVYVDLPEVGREVKKGEVVASIESVKAAADVYAPLSGKIVEVNEKLDTEPELINKDPEGEGWLFKMEISDEGELEDLLDEQAYQEFCAQ 123
               SCOP domains d1zkoa_ A: Protein H of glycine cleavage system                                                                                  SCOP domains
               CATH domains 1zkoA00 A:-4-123  [code=2.40.50.100, no name defined]                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee....eeeeee..eeeeeehhhhhhhhh.eeeee......ee....eeeeeee...eeeee....eeeeee.hhhhhhhhhhhhh.......eeeee.hhhhhhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------BIOTINYL_LIPOYL  PDB: A:19-101 UniProt: 19-101                                     ---------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------LIPOYL  PDB: A:44-73          -------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zko A  -4 HHHHHLKmKKYTKTHEWVSIEDKVATVGITNHAQEQLGDVVYVDLPEVGREVKKGEVVASIESVKAAADVYAPLSGKIVEVNEKLDTEPELINKDPEGEGWLFKmEISDEGELEDLLDEQAYQEFCAQ 123
                                   | 5        15        25        35        45        55        65        75        85        95    |  105       115        
                                   3-MSE                                                                                          100-MSE

Chain B from PDB  Type:PROTEIN  Length:128
 aligned with GCSH_THEMA | Q9WY55 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:128
                                 1                                                                                                                          
                                 |   5        15        25        35        45        55        65        75        85        95       105       115        
           GCSH_THEMA     - -----MKMKKYTKTHEWVSIEDKVATVGITNHAQEQLGDVVYVDLPEVGREVKKGEVVASIESVKAAADVYAPLSGKIVEVNEKLDTEPELINKDPEGEGWLFKMEISDEGELEDLLDEQAYQEFCAQ 123
               SCOP domains d1zkob_ B: Protein H of glycine cleavage system                                                                                  SCOP domains
               CATH domains 1zkoB00 B:-4-123  [code=2.40.50.100, no name defined]                                                                            CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeeee....eeeeee..eeeeeehhhhhhhhh.eeeee......ee....eeeeeee...eeeee....eeeeee.hhhhhhhhhhhhh.......eeeee.hhhhhhhh.hhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------BIOTINYL_LIPOYL  PDB: B:19-101 UniProt: 19-101                                     ---------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------LIPOYL  PDB: B:44-73          -------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1zko B  -4 HHHHHLKmKKYTKTHEWVSIEDKVATVGITNHAQEQLGDVVYVDLPEVGREVKKGEVVASIESVKAAADVYAPLSGKIVEVNEKLDTEPELINKDPEGEGWLFKmEISDEGELEDLLDEQAYQEFCAQ 123
                                   | 5        15        25        35        45        55        65        75        85        95    |  105       115        
                                   3-MSE                                                                                          100-MSE

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: 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)

Thermotoga maritima [TaxId: 2336] (1)

1a	d1zkoa_	A:
1b	d1zkob_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

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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)

Thermotoga maritima. Organism_taxid: 2336. (2)

1a	1zkoA00	A:-4-123
1b	1zkoB00	B:-4-123

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (GCSH_THEMA | Q9WY55)

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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