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Title :   METHYLMALONYL-COA MUTASE, SUBSTRATE-FREE STATE (POOR QUALITY STRUCTURE)

Authors :   P. R. Evans, F. Mancia

Date :   04 Dec 97 (Deposition) - 18 Mar 98 (Release) - 24 Oct 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

Chains :   Asym./Biol. Unit : A,B

Keywords :   Complex (Isomerase-Deoxyadenosine), Isomerase, Mutase, Intramolecular Transferase, Complex (Isomerase-Deoxyadenosine) Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   F. Mancia, P. R. Evans
Conformational Changes On Substrate Binding To Methylmalony Coa Mutase And New Insights Into The Free Radical Mechanism
Structure V. 6 711 1998
PubMed-ID: 9655823 | Reference-DOI: 10.1016/S0969-2126(98)00073-2
(for further references see the PDB file header)

Molecule 1 - METHYLMALONYL-COA MUTASE
	Chains	:	A
	EC Number	:	5.4.99.2
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	CYTOPLASM
	Expression System Gene	:	MUTA, MUTB
	Expression System Plasmid	:	PMEX2
	Expression System Taxid	:	562
	Expression System Vector	:	PT7-7
	Expression System Vector Type	:	PLASMID
	Gene	:	MUTA, MUTB
	Organism Scientific	:	PROPIONIBACTERIUM FREUDENREICHII SUBSP. SHERMANII
	Organism Taxid	:	1752
	Other Details	:	THE 2 GENES MUTA (BETA CHAIN) AND MUTB (ALPHA CHAIN) ARE COEXPRESSED FROM THE SAME PLASMID
	Strain	:	NCIB 9885

Molecule 2 - METHYLMALONYL-COA MUTASE
	Chains	:	B
	EC Number	:	5.4.99.2
	Engineered	:	YES
	Expression System	:	K38 PGP1-2
	Expression System Cellular Location	:	CYTOPLASM
	Expression System Gene	:	MUTA, MUTB
	Expression System Plasmid	:	PMEX2
	Expression System Vector	:	PT7-7
	Expression System Vector Type	:	PLASMID
	Gene	:	MUTA, MUTB
	Organism Scientific	:	PROPIONIBACTERIUM FREUDENREICHII SUBSP. SHERMANII
	Organism Taxid	:	1752
	Other Details	:	THE 2 GENES MUTA (BETA CHAIN) AND MUTB (ALPHA CHAIN) ARE COEXPRESSED FROM THE SAME PLASMID
	Strain	:	NCIB 9885

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	ADN	1	Ligand/Ion	ADENOSINE
2	B12	1	Ligand/Ion	COBALAMIN

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:119 , VAL A:206 , ARG A:207 , GLU A:247 , GLY A:333 , TRP A:334 , GLU A:370 , ALA A:371 , ILE A:372 , ALA A:373 , GLN A:454 , ASP A:608 , GLY A:609 , HIS A:610 , ASP A:611 , ARG A:612 , GLY A:613 , ILE A:617 , TYR A:621 , GLY A:653 , SER A:655 , LEU A:657 , GLY A:685 , GLY A:686 , TYR A:705 , THR A:706 , PRO A:707 , THR A:709 , ADN A:801	BINDING SITE FOR RESIDUE B12 A 800
2	AC2	SOFTWARE	TYR A:89 , TYR A:243 , GLU A:247 , GLY A:333 , TRP A:334 , B12 A:800	BINDING SITE FOR RESIDUE ADN A 801

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

Asymmetric/Biological Unit

No.	Residues
1	Pro A:68	-	Pro A:69
2	Ala B:91	-	Pro B:92

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

Asymmetric/Biological Unit (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	METMALONYL_COA_MUTASE	PS00544	Methylmalonyl-CoA mutase signature.	MUTA_PROFR	377-402	1	B:377-402
1	METMALONYL_COA_MUTASE	PS00544	Methylmalonyl-CoA mutase signature.	MUTB_PROFR	381-406	1	A:381-406
2	B12_BINDING	PS51332	B12-binding domain profile.	MUTB_PROFR	597-728	1	A:597-728

(no "Exon" information available for 3REQ)

Asymmetric/Biological 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:725
 aligned with MUTB_PROFR | P11653 from UniProtKB/Swiss-Prot  Length:728

    Alignment length:725
                                    13        23        33        43        53        63        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       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723     
           MUTB_PROFR     4 LPRFDSVDLGNAPVPADAARRFEELAAKAGTGEAWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKLRASLDA 728
               SCOP domains d3reqa1 A:4-560 Methylmalonyl-CoA mutase alpha subunit, domain 1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             d3reqa2 A:561-728 Methylmalonyl-CoA mutase alpha subunit, C-terminal domain                                                                                              SCOP domains
               CATH domains ----------------------------------3reqA01 A:38-559  [code=3.20.20.240, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     ---3reqA02 A:563-726  [code=3.40.50.280, no name defined]                                                                                                              -- CATH domains
               Pfam domains ----------------------------------MM_CoA_mutase-3reqA02 A:38-559                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            --------------------------------------B12-binding-3reqA01 A:598-712                                                                                      ---------------- Pfam domains
         Sec.struct. author .................hhhhhhhhhhhh...................hhh..........................................hhhhhhhhhhhh....eee...hhhhh......................hhhhhhhh.........eee.....hhhhhhhhhhhhh..........eee....hhhhh........hhhhhhhhh....hhhhh.......eee.hhhhhh...hhhhhhhhhhhhhhhhhhh......hhhh....eeeeee...hhhhhhhhhhhhhhhhhhhhhh....hhh...eeeeee.........hhhhhhhhhhhhhhhhhh...eee............hhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhh....hhhhh.hhhhhhhhhhhhhhhhhhh..........................hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..........hhhhhhhhhhh...hhhhhhhhhhhh............hhhhhh...hhhhhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhh..eeee........hhhhhhh.....eeeeee....hhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhh............hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------METMALONYL_COA_MUTASE     ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                PROSITE (1) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------B12_BINDING  PDB: A:597-728 UniProt: 597-728                                                                                         PROSITE (1)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3req A   4 LPRFDSVDLGNAPVPADAARRFEELAAKAGTGEAWETAEQIPVGTLFNEDVYKDMDWLDTYAGIPPFVHGPYATMYAFRPWTIRQYAGFSTAKESNAFYRRNLAAGQKGLSVAFDLPTHRGYDSDNPRVAGDVGMAGVAIDSIYDMRELFAGIPLDQMSVSMTMNGAVLPILALYVVTAEEQGVKPEQLAGTIQNDILKEFMVRNTYIYPPQPSMRIISEIFAYTSANMPKWNSISISGYHMQEAGATADIEMAYTLADGVDYIRAGESVGLNVDQFAPRLSFFWGIGMNFFMEVAKLRAARMLWAKLVHQFGPKNPKSMSLRTHSQTSGWSLTAQDVYNNVVRTCIEAMAATQGHTQSLHTNSLDEAIALPTDFSARIARNTQLFLQQESGTTRVIDPWSGSAYVEELTWDLARKAWGHIQEVEKVGGMAKAIEKGIPKMRIEEAAARTQARIDSGRQPLIGVNKYRLEHEPPLDVLKVDNSTVLAEQKAKLVKLRAERDPEKVKAALDKITWAAGNPDDKDPDRNLLKLCIDAGRAMATVGEMSDALEKVFGRYTAQIRTISGVYSKEVKNTPEVEEARELVEEFEQAEGRRPRILLAKMGQDGHDRGQKVIATAYADLGFDVDVGPLFQTPEETARQAVEADVHVVGVSSLAGGHLTLVPALRKELDKLGRPDILITVGGVIPEQDFDELRKDGAVEIYTPGTVIPESAISLVKKLRASLDA 728
                                    13        23        33        43        53        63        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       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583       593       603       613       623       633       643       653       663       673       683       693       703       713       723

Chain B from PDB  Type:PROTEIN  Length:620
 aligned with MUTA_PROFR | P11652 from UniProtKB/Swiss-Prot  Length:638

    Alignment length:622
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635  
           MUTA_PROFR    16 LTPTTLSLAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKRLTVHTVDGIDIVPMYRPKDAPKKLGYPGVAPFTRGTTVRNGDMDAWDVRALHEDPDEKFTRKAILEGLERGVTSLLLRVDPDAIAPEHLDEVLSDVLLEMTKVEVFSRYDQGAAAEALVSVYERSDKPAKDLALNLGLDPIAFAALQGTEPDLTVLGDWVRRLAKFSPDSRAVTIDANIYHNAGAGDVAELAWALATGAEYVRALVEQGFTATEAFDTINFRVTATHDQFLTIARLRALREAWARIGEVFGVDEDKRGARQNAITSWRDVTREDPYVNILRGSIATFSASVGGAESITTLPFTQALGLPEDDFPLRIARNTGIVLAEEVNIGRVNDPAGGSYYVESLTRSLADAAWKEFQEVEKLGGMSKAVMTEHVTKVLDACNAERAKRLANRKQPITAVSEFPMIGARSIETKPFPAAPARKGLAWHRDSEVFEQLMDRSTSVSERPKVFLACLGTRRDFGGREGFSSPVWHIAGIDTPQVEGGTTAEIVEAFKKSGAQVADLCSSAKVYAQQGLEVAKALKAAGAKALYLSGAFKEFGDDAAEAEKLIDGRLFMGMDVVDTLSSTLDILGVA 637
               SCOP domains d3reqb1 B:16-475 Methylmalonyl-CoA mutase beta subunit, domain 1                                                                                                                                                                                                                                                                                                                                                                                                            d3reqb2 B:476-637 Methylmalonyl-CoA mutase beta subunit, C-terminal dom  ain                                                                                       SCOP domains
               CATH domains -----------------------------------------------3reqB01 B:63-499  [code=3.20.20.240, no name defined]                                                                                                                                                                                                                                                                                                                                                                                                3reqB02 B:500-636  [code=3.40.50.280, no name d  efined]                                                                                 - CATH domains
               Pfam domains ---------------------------------MM_CoA_mutase-3reqB01 B:49-519                                                                                                                                                                                                                                                                                                                                                                                                                                                         ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhhhhhh...........hhhhhhhh...............hhh.............................eeee....hhhhhhhhhhhhhh...eeeee.......hhh..hhh........eeeee.......hhhhhhhhhh................hhhhhhhh........hhhhhhh..........eeee.hhhhhh...hhhhhhhhhhhhhhhhhhhhh....hhhhhh.eeeeeee...hhhhhhhhhhhhhhhhhhhhhh..........eeeee.........hhhhhhhhhhhhhhhhh....eee..............hhhhhhhhhhhhhhh..............hhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhh.......................................hhhhhhhhhhhh.......eeee...hhhhhhhhhhhhhhhhhh........--......hhhhhh...eeeee..hhhhhhhhhhhhhhhhhh...eeeee..hhh....hhhhhhh..eee.....hhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------METMALONYL_COA_MUTASE     ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3req B  16 LTPTTLSLAGDFPKATEEQWEREVEKVLNRGRPPEKQLTFAECLKRLTVHTVDGIDIVPMYRPKDAPKKLGYPGVAPFTRGTTVRNGDMDAWDVRALHEDPDEKFTRKAILEGLERGVTSLLLRVDPDAIAPEHLDEVLSDVLLEMTKVEVFSRYDQGAAAEALVSVYERSDKPAKDLALNLGLDPIGFAALQGTEPDLTVLGDWVRRLAKFSPDSRAVTIDANIYHNAGAGDVAELAWALATGAEYVRALVEQGFTATEAFDTINFRVTATHDQFLTIARLRALREAWARIGEVFGVDEDKRGARQNAITSWRELTREDPYVNILRGSIATFSASVGGAESITTLPFTQALGLPEDDFPLRIARNTGIVLAEEVNIGRVNDPAGGSYYVESLTRSLADAAWKEFQEVEKLGGMSKAVMTEHVTKVLDACNAERAKRLANRKQPITAVSEFPMIGARSIETKPFPAAPARKGLAWHRDSEVFEQLMDRSTSVSERPKVFLACLGTRRDFGGREGFSSPVWHIAGIDTPQVE--TTAEIVEAFKKSGAQVADLCSSAKVYAQQGLEVAKALKAAGAKALYLSGAFKEFGDDAAEAEKLIDGRLFMGMDVVDTLSSTLDILGVA 637
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545|  |   555       565       575       585       595       605       615       625       635  
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            546  |                                                                                        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               549

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/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.280, no name defined] (23)

Shermanii (Propionibacterium freudenreichii subsp) (7)

1a	3reqB02	B:500-636
1b	3reqA02	A:563-726

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: [code=3.20.20.240, no name defined] (12)

Shermanii (Propionibacterium freudenreichii subsp) (7)

2a	3reqB01	B:63-499
2b	3reqA01	A:38-559

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (MUTB_PROFR | P11653)

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.
	GO:0031419	cobalamin binding	Interacting selectively and non-covalently with cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
	GO:0016866	intramolecular transferase activity	Catalysis of the transfer of a functional group from one position to another within a single molecule.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004494	methylmalonyl-CoA mutase activity	Catalysis of the reaction: (R)-methylmalonyl-CoA = succinyl-CoA.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
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.

Chain B (MUTA_PROFR | P11652)

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.
	GO:0031419	cobalamin binding	Interacting selectively and non-covalently with cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
	GO:0016866	intramolecular transferase activity	Catalysis of the transfer of a functional group from one position to another within a single molecule.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0004494	methylmalonyl-CoA mutase activity	Catalysis of the reaction: (R)-methylmalonyl-CoA = succinyl-CoA.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0019652	lactate fermentation to propionate and acetate	The anaerobic enzymatic conversion of lactate to propionate, concomitant with the oxidation of lactate to acetate and CO2 and yielding energy in the form of adenosine triphosphate (ATP).
	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.

Asymmetric/Biological Unit
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	MUTA_PROFR \| P11652	:	1e1c 1req 2req 4req 5req 6req 7req
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Description

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