2JDW - JenaLib

Molecule 1 - L-ARGININE:GLYCINE AMIDINOTRANSFERASE
	Cellular Location	:	INTERMEMBRANE SPACE OF MITOCHONDRIA AND CYTOPLASM
	Cell Line	:	BL21
	Chains	:	A
	EC Number	:	2.1.4.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	CYTOSOLIC
	Expression System Gene	:	AT38H
	Expression System Plasmid	:	PRSETAT38H
	Expression System Strain	:	BL21 (DE3) PLYSS
	Expression System Taxid	:	562
	Expression System Vector	:	PRSET
	Expression System Vector Type	:	PBLUESCRIPT DERIVATIVE WITH T7 EXPRESSION ELEMENTS
	Fragment	:	RESIDUES 64 - 423
	Gene	:	AT38H
	Organ	:	KIDNEY
	Organelle	:	MITOCHONDRIA
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	WITHOUT SIGNAL SEQUENCE (1-37) BUT WITH N- TERMINAL ATTACHED 6-HISTIDINE-TAG (14 RESIDUES)
	Synonym	:	TRANSAMIDINASE, AT38

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (17, 17)

Asymmetric Unit (17, 17)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_076484	I	93	V	GATM_HUMAN	Unclassified (CCDS3)	34991226	A	I	93	V
02	UniProt	VAR_076485	K	102	N	GATM_HUMAN	Unclassified (CCDS3)	376335787	A	K	102	N
03	UniProt	VAR_076486	P	105	L	GATM_HUMAN	Disease (CCDS3)	147804855	A	P	105	L
04	UniProt	VAR_020305	Q	110	H	GATM_HUMAN	Polymorphism	1288775	A	Q	110	H
05	UniProt	VAR_076487	E	181	K	GATM_HUMAN	Disease (CCDS3)	376982466	A	E	181	K
06	UniProt	VAR_076488	A	185	P	GATM_HUMAN	Disease (CCDS3)	---	A	A	185	P
07	UniProt	VAR_076489	R	189	C	GATM_HUMAN	Disease (CCDS3)	377578020	A	R	189	C
08	UniProt	VAR_069816	Y	203	S	GATM_HUMAN	Disease (CCDS3)	397514709	A	Y	203	S
09	UniProt	VAR_076490	A	208	T	GATM_HUMAN	Disease (CCDS3)	374059924	A	A	208	T
10	UniProt	VAR_076491	S	231	C	GATM_HUMAN	Polymorphism	202225656	A	S	231	C
11	UniProt	VAR_076492	D	234	G	GATM_HUMAN	Polymorphism	146057680	A	D	234	G
12	UniProt	VAR_076493	R	282	H	GATM_HUMAN	Disease (CCDS3)	371447931	A	R	282	H
13	UniProt	VAR_076494	L	329	V	GATM_HUMAN	Disease (CCDS3)	373802463	A	L	329	V
14	UniProt	VAR_076495	P	346	L	GATM_HUMAN	Disease (CCDS3)	142814307	A	P	346	L
15	UniProt	VAR_071789	R	413	Q	GATM_HUMAN	Disease (CCDS3)	---	A	R	413	Q
16	UniProt	VAR_071790	R	413	W	GATM_HUMAN	Disease (CCDS3)	---	A	R	413	W
17	UniProt	VAR_076496	R	415	Q	GATM_HUMAN	Unclassified (CCDS3)	374592247	A	R	415	Q

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (17, 34)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_076484	I	93	V	GATM_HUMAN	Unclassified (CCDS3)	34991226	A	I	93	V
02	UniProt	VAR_076485	K	102	N	GATM_HUMAN	Unclassified (CCDS3)	376335787	A	K	102	N
03	UniProt	VAR_076486	P	105	L	GATM_HUMAN	Disease (CCDS3)	147804855	A	P	105	L
04	UniProt	VAR_020305	Q	110	H	GATM_HUMAN	Polymorphism	1288775	A	Q	110	H
05	UniProt	VAR_076487	E	181	K	GATM_HUMAN	Disease (CCDS3)	376982466	A	E	181	K
06	UniProt	VAR_076488	A	185	P	GATM_HUMAN	Disease (CCDS3)	---	A	A	185	P
07	UniProt	VAR_076489	R	189	C	GATM_HUMAN	Disease (CCDS3)	377578020	A	R	189	C
08	UniProt	VAR_069816	Y	203	S	GATM_HUMAN	Disease (CCDS3)	397514709	A	Y	203	S
09	UniProt	VAR_076490	A	208	T	GATM_HUMAN	Disease (CCDS3)	374059924	A	A	208	T
10	UniProt	VAR_076491	S	231	C	GATM_HUMAN	Polymorphism	202225656	A	S	231	C
11	UniProt	VAR_076492	D	234	G	GATM_HUMAN	Polymorphism	146057680	A	D	234	G
12	UniProt	VAR_076493	R	282	H	GATM_HUMAN	Disease (CCDS3)	371447931	A	R	282	H
13	UniProt	VAR_076494	L	329	V	GATM_HUMAN	Disease (CCDS3)	373802463	A	L	329	V
14	UniProt	VAR_076495	P	346	L	GATM_HUMAN	Disease (CCDS3)	142814307	A	P	346	L
15	UniProt	VAR_071789	R	413	Q	GATM_HUMAN	Disease (CCDS3)	---	A	R	413	Q
16	UniProt	VAR_071790	R	413	W	GATM_HUMAN	Disease (CCDS3)	---	A	R	413	W
17	UniProt	VAR_076496	R	415	Q	GATM_HUMAN	Unclassified (CCDS3)	374592247	A	R	415	Q

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

PROSITE Motifs (0, 0)

Exons (8, 8)

Asymmetric Unit (8, 8)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000396659	1b	ENSE00001879768	chr15:45670979-45670583	397	GATM_HUMAN	1-23	23	0	-	-
1.2	ENST00000396659	2	ENSE00001120580	chr15:45669017-45668799	219	GATM_HUMAN	24-96	73	1	A:64-96	33
1.3	ENST00000396659	3	ENSE00001303602	chr15:45661719-45661524	196	GATM_HUMAN	97-162	66	1	A:97-162	66
1.4	ENST00000396659	4	ENSE00001120562	chr15:45660458-45660268	191	GATM_HUMAN	162-225	64	1	A:162-225	64
1.5	ENST00000396659	5	ENSE00001120554	chr15:45658706-45658569	138	GATM_HUMAN	226-271	46	1	A:226-271	46
1.6	ENST00000396659	6	ENSE00001120548	chr15:45658408-45658244	165	GATM_HUMAN	272-326	55	1	A:272-326	55
1.7	ENST00000396659	7	ENSE00001120538	chr15:45657058-45656995	64	GATM_HUMAN	327-348	22	1	A:327-348	22
1.8	ENST00000396659	8	ENSE00001120526	chr15:45656214-45656098	117	GATM_HUMAN	348-387	40	1	A:348-387	40
1.9b	ENST00000396659	9b	ENSE00001847421	chr15:45654419-45653322	1098	GATM_HUMAN	387-423	37	1	A:387-423	37

Sequences/Alignments

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:360
 aligned with GATM_HUMAN | P50440 from UniProtKB/Swiss-Prot  Length:423

    Alignment length:360
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423
           GATM_HUMAN    64 CPVSSYNEWDPLEEVIVGRAENACVPPFTIEVKANTYEKYWPFYQKQGGHYFPKDHLKKAVAEIEEMCNILKTEGVTVRRPDPIDWSLKYKTPDFESTGLYSAMPRDILIVVGNEIIEAPMAWRSRFFEYRAYRSIIKDYFHRGAKWTTAPKPTMADELYNQDYPIHSVEDRHKLAAQGKFVTTEFEPCFDAADFIRAGRDIFAQRSQVTNYLGIEWMRRHLAPDYRVHIISFKDPNPMHIDATFNIIGPGIVLSNPDRPCHQIDLFKKAGWTIITPPTPIIPDDHPLWMSSKWLSMNVLMLDEKRVMVDANEVPIQKMFEKLGITTIKVNIRNANSLGGGFHCWTCDVRRRGTLQSYLD 423
               SCOP domains d2jdwa_ A: L-arginine: glycine amidinotransferase                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains 2jdwA00 A:64-423 L-arginine/glycine Amidinotransferase; Chain A                                                                                                                                                                                                                                                                                                          CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Amidinotransf-2jdwA01 A:246-414                                                                                                                                          --------- Pfam domains
         Sec.struct. author ..........eeeeeee............hhhhhh..hhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...eeee........eee....eee......hhhheeee..eeee.....hhh..hhhh.hhhhhhhhh...eeee.......hhh.........hhhhhhhhhh.............hhheeee..eeee.......hhhhhhhhhhh....eeee..............eeeee..eeee........hhhhhh...eee.................hhhhh..eeee..eeeee...hhhhhhhhh...eeeee..hhhhhh.......eee.eee........ Sec.struct. author
             SAPs(SNPs) (1) -----------------------------V--------N--L----H----------------------------------------------------------------------K---P---C-------------S----T----------------------C--G-----------------------------------------------H----------------------------------------------V----------------L------------------------------------------------------------------Q-Q-------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------W---------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.2  PDB: A:64-96           Exon 1.3  PDB: A:97-162 UniProt: 97-162                           ---------------------------------------------------------------Exon 1.5  PDB: A:226-271 UniProt: 226-271     Exon 1.6  PDB: A:272-326 UniProt: 272-326              Exon 1.7              --------------------------------------Exon 1.9b  PDB: A:387-423             Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------Exon 1.4  PDB: A:162-225 UniProt: 162-225                       --------------------------------------------------------------------------------------------------------------------------Exon 1.8  PDB: A:348-387                ------------------------------------ Transcript 1 (2)
                 2jdw A  64 CPVSSYNEWDPLEEVIVGRAENACVPPFTIEVKANTYEKYWPFYQKQGGHYFPKDHLKKAVAEIEEMCNILKTEGVTVRRPDPIDWSLKYKTPDFESTGLYSAMPRDILIVVGNEIIEAPMAWRSRFFEYRAYRSIIKDYFHRGAKWTTAPKPTMADELYNQDYPIHSVEDRHKLAAQGKFVTTEFEPCFDAADFIRAGRDIFAQRSQVTNYLGIEWMRRHLAPDYRVHIISFKDPNPMHIDATFNIIGPGIVLSNPDRPCHQIDLFKKAGWTIITPPTPIIPDDHPLWMSSKWLSMNVLMLDEKRVMVDANEVPIQKMFEKLGITTIKVNIRNANSLGGGFHCWTCDVRRRGTLQSYLD 423
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423

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 '\|'

Classification and Annotation

SCOP Domains (1, 1)

CATH Domains (1, 1)

Pfam Domains (1, 1)

Gene Ontology (11, 11)

Asymmetric Unit(hide GO term definitions)

Chain A (GATM_HUMAN | P50440)

molecular function
	GO:0015067	amidinotransferase activity	Catalysis of the reversible transfer of an amidino group to an acceptor.
	GO:0015068	glycine amidinotransferase activity	Catalysis of the reaction: L-arginine + glycine = L-ornithine + guanidinoacetate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0006601	creatine biosynthetic process	The chemical reactions and pathways resulting in the formation of creatine, N-[amino(imino)methyl]-N-methylglycine. Creatine is formed by a process beginning with amidino group transfer from L-arginine to glycine to form guanidinoacetate, followed by methyl group transfer from S-adenosyl-L-methionine to guanidinoacetate; it is then is phosphorylated to form a pool that stores high energy phosphate for the replenishment of ATP during periods of high, or fluctuating energy demand. In animals, most creatine is transported to and used in muscle.
	GO:0006600	creatine metabolic process	The chemical reactions and pathways involving creatine (N-(aminoiminomethyl)-N-methylglycine), a compound synthesized from the amino acids arginine, glycine, and methionine that occurs in muscle.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0070062	extracellular exosome	A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005743	mitochondrial inner membrane	The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
	GO:0005758	mitochondrial intermembrane space	The region between the inner and outer lipid bilayers of the mitochondrial envelope.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

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Access by PDB/NDB ID
	2jdw
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	GATM_HUMAN \| P50440
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	2.1.4.1
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	612718
		Disease Information	:	OMIM

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Description

Compounds