1EF8 - JenaLib

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Title :   CRYSTAL STRUCTURE OF METHYLMALONYL COA DECARBOXYLASE

Authors :   M. M. Benning, T. Haller, J. A. Gerlt, H. M. Holden

Date :   07 Feb 00 (Deposition) - 24 May 00 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Methylmalonyl Coa, Decarboxylase, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. M. Benning, T. Haller, J. A. Gerlt, H. M. Holden
New Reactions In The Crotonase Superfamily: Structure Of Methylmalonyl Coa Decarboxylase From Escherichia Coli.
Biochemistry V. 39 4630 2000
PubMed-ID: 10769118 | Reference-DOI: 10.1021/BI9928896
(for further references see the PDB file header)

Molecule 1 - METHYLMALONYL COA DECARBOXYLASE
	Chains	:	A, B, C
	EC Number	:	4.1.1.41
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 1)

No.	Name	Count	Type	Full Name
1	NI	1	Ligand/Ion	NICKEL (II) ION

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	NI	-1	Ligand/Ion	NICKEL (II) ION

Biological Unit 2 (0, 0)

No.	Name	Count	Type	Full Name
1	NI	-1	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HIS A:220 , HIS B:220 , HIS C:220	BINDING SITE FOR RESIDUE NI A 300

(no "SS Bond" information available for 1EF8)

(no "Cis Peptide Bond" information available for 1EF8)

(no "SAP(SNP)/Variant" information available for 1EF8)

Asymmetric Unit (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ENOYL_COA_HYDRATASE	PS00166	Enoyl-CoA hydratase/isomerase signature.	SCPB_ECOLI	100-120	3	A:100-120 B:100-120 C:100-120

Biological Unit 1 (1, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ENOYL_COA_HYDRATASE	PS00166	Enoyl-CoA hydratase/isomerase signature.	SCPB_ECOLI	100-120	3	A:100-120 B:100-120 C:100-120

Biological Unit 2 (1, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ENOYL_COA_HYDRATASE	PS00166	Enoyl-CoA hydratase/isomerase signature.	SCPB_ECOLI	100-120	6	A:100-120 B:100-120 C:100-120

(no "Exon" information available for 1EF8)

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:256
 aligned with SCPB_ECOLI | P52045 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:261
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260 
           SCPB_ECOLI     1 MSYQYVNVVTINKVAVIEFNYGRKLNALSKVFIDDLMQALSDLNRPEIRCIILRAPSGSKVFSAGHDIHELPSGGRDPLSYDDPLRQITRMIQKFPKPIISMVEGSVWGGAFEMIMSSDLIIAASTSTFSMTPVNLGVPYNLVGIHNLTRDAGFHIVKELIFTASPITAQRALAVGILNHVVEVEELEDFTLQMAHHISEKAPLAIAVIKEELRVLGEAHTMNSDEFERIQGMRRAVYDSEDYQEGMNAFLEKRKPNFVGH 261
               SCOP domains d1ef8a_ A: Methylmalonyl CoA decarboxylase                                                                                                                                                                                                                            SCOP domains
               CATH domains -1ef8A02 A:2-185 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                -----------------1ef8A01 A:203-261                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..eeeeee.hhhhh...hhhhhhhhhhhhhhh......eeeee......eee........-----......hhhhhhhhhhhhh...eeeee..eeehhhhhhhhhh.eeeee...eee.hhhhhh...hhhhhhh.....hhhhhhhhhhhh..eehhhhhhh....eeehhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------ENOYL_COA_HYDRATASE  --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ef8 A   1 MSYQYVNVVTINKVAVIEFNYGRKLNALSKVFIDDLMQALSDLNRPEIRCIILRAPSGSKVFSAGHDIHEL-----DPLSYDDPLRQITRMIQKFPKPIISMVEGSVWGGAFEMIMSSDLIIAASTSTFSMTPVNLGVPYNLVGIHNLTRDAGFHIVKELIFTASPITAQRALAVGILNHVVEVEELEDFTLQMAHHISEKAPLAIAVIKEELRVLGEAHTMNSDEFERIQGMRRAVYDSEDYQEGMNAFLEKRKPNFVGH 261
                                    10        20        30        40        50        60        70|     | 80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260 
                                                                                                 71    77

Chain B from PDB  Type:PROTEIN  Length:253
 aligned with SCPB_ECOLI | P52045 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:261
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260 
           SCPB_ECOLI     1 MSYQYVNVVTINKVAVIEFNYGRKLNALSKVFIDDLMQALSDLNRPEIRCIILRAPSGSKVFSAGHDIHELPSGGRDPLSYDDPLRQITRMIQKFPKPIISMVEGSVWGGAFEMIMSSDLIIAASTSTFSMTPVNLGVPYNLVGIHNLTRDAGFHIVKELIFTASPITAQRALAVGILNHVVEVEELEDFTLQMAHHISEKAPLAIAVIKEELRVLGEAHTMNSDEFERIQGMRRAVYDSEDYQEGMNAFLEKRKPNFVGH 261
               SCOP domains d1ef8b_ B: Methylmalonyl CoA decarboxylase                                                                                                                                                                                                                            SCOP domains
               CATH domains -1ef8B02 B:2-185 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                -----------------1ef8B01 B:203-260                                         - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..eeeeee.hhhhh...hhhhhhhhhhhhhhh......eeeee......eee.....--------......hhhhhhhhhhhhh...eeeee..eeehhhhhhhhhh.eeeee...eee.hhhhhh...hhhhhhh.....hhhhhhhhhhhh..eehhhhhhh....eeehhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------ENOYL_COA_HYDRATASE  --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ef8 B   1 MSYQYVNVVTINKVAVIEFNYGRKLNALSKVFIDDLMQALSDLNRPEIRCIILRAPSGSKVFSAGHDI--------DPLSYDDPLRQITRMIQKFPKPIISMVEGSVWGGAFEMIMSSDLIIAASTSTFSMTPVNLGVPYNLVGIHNLTRDAGFHIVKELIFTASPITAQRALAVGILNHVVEVEELEDFTLQMAHHISEKAPLAIAVIKEELRVLGEAHTMNSDEFERIQGMRRAVYDSEDYQEGMNAFLEKRKPNFVGH 261
                                    10        20        30        40        50        60       | -      | 80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260 
                                                                                              68       77

Chain C from PDB  Type:PROTEIN  Length:250
 aligned with SCPB_ECOLI | P52045 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:261
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260 
           SCPB_ECOLI     1 MSYQYVNVVTINKVAVIEFNYGRKLNALSKVFIDDLMQALSDLNRPEIRCIILRAPSGSKVFSAGHDIHELPSGGRDPLSYDDPLRQITRMIQKFPKPIISMVEGSVWGGAFEMIMSSDLIIAASTSTFSMTPVNLGVPYNLVGIHNLTRDAGFHIVKELIFTASPITAQRALAVGILNHVVEVEELEDFTLQMAHHISEKAPLAIAVIKEELRVLGEAHTMNSDEFERIQGMRRAVYDSEDYQEGMNAFLEKRKPNFVGH 261
               SCOP domains d1ef8c_ C: Methylmalonyl CoA decarboxylase                                                                                                                                                                                                                            SCOP domains
               CATH domains -1ef8C02 C:2-185 2-enoyl-CoA Hydratase; Chain A, domain 1                                                                                                                                -----------------1ef8C01 C:203-260                                         - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee..eeeeee.hhhhh...hhhhhhhhhhhhhhh......eeeee......eee....-----------....hhhhhhhhhhhhh...eeeee..eeehhhhhhhhhh.eeeee...eee.hhhhhh...hhhhhhh.....hhhhhhhhhhhh..eehhhhhhh....eeehhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------ENOYL_COA_HYDRATASE  --------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ef8 C   1 MSYQYVNVVTINKVAVIEFNYGRKLNALSKVFIDDLMQALSDLNRPEIRCIILRAPSGSKVFSAGHD-----------LSYDDPLRQITRMIQKFPKPIISMVEGSVWGGAFEMIMSSDLIIAASTSTFSMTPVNLGVPYNLVGIHNLTRDAGFHIVKELIFTASPITAQRALAVGILNHVVEVEELEDFTLQMAHHISEKAPLAIAVIKEELRVLGEAHTMNSDEFERIQGMRRAVYDSEDYQEGMNAFLEKRKPNFVGH 261
                                    10        20        30        40        50        60      |  -        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260 
                                                                                             67          79

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(

)

Folds(

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Superfamilies( (-)

)

Families(

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Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: ClpP/crotonase (207)

Superfamily: ClpP/crotonase (207)

Family: Crotonase-like (39)

Protein domain: Methylmalonyl CoA decarboxylase (2)

Escherichia coli [TaxId: 562] (2)

1a	d1ef8a_	A:
1b	d1ef8b_	B:
1c	d1ef8c_	C:

(no "Pfam Domain" information available for 1EF8)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (SCPB_ECOLI | P52045)

molecular function
	GO:0016831	carboxy-lyase activity	Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
	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.
	GO:0016829	lyase activity	Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
	GO:0004492	methylmalonyl-CoA decarboxylase activity	Catalysis of the reaction: (S)-2-methyl-3-oxopropanoyl-CoA = propanoyl-CoA + CO2.
biological process
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
cellular component
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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