3SBY - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF SEMET-SUBSTITUTED APO-MMACHC (1-244), A HUMAN B12 PROCESSING ENZYME

Authors :   M. Koutmos, C. Gherasim, J. L. Smith, R. Banerjee

Date :   06 Jun 11 (Deposition) - 22 Jun 11 (Release) - 25 Apr 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.71

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

Keywords :   Mmachc, Cblc, Cobalamin, Flavin, Glutathione, Flavin Reductase, Oxidoreductase, Maturase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Koutmos, C. Gherasim, J. L. Smith, R. Banerjee
Structural Basis Of Multifunctionality In A Vitamin B12-Processing Enzyme.
J. Biol. Chem. V. 286 29780 2011
PubMed-ID: 21697092 | Reference-DOI: 10.1074/JBC.M111.261370

Molecule 1 - METHYLMALONIC ACIDURIA AND HOMOCYSTINURIA TYPE C PROTEIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B(+)
	Expression System Strain	:	BL21
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Fragment	:	12 BINDING DOMAIN, RESIDUES 1-244
	Gene	:	MMACHC
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 13)

No.	Name	Count	Type	Full Name
1	MSE	13	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 1 (1, 7)

No.	Name	Count	Type	Full Name
1	MSE	7	Mod. Amino Acid	SELENOMETHIONINE

Biological Unit 2 (1, 6)

No.	Name	Count	Type	Full Name
1	MSE	6	Mod. Amino Acid	SELENOMETHIONINE

(no "Site" information available for 3SBY)

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

Asymmetric Unit

No.	Residues
1	Arg A:112	-	Pro A:113
2	Arg B:112	-	Pro B:113

Asymmetric Unit (14, 28)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_024770	Q	27	R	MMAC_HUMAN	Disease (MMAHCC)	546099787	A/B	Q	27	R
02	UniProt	VAR_024771	L	116	P	MMAC_HUMAN	Disease (MMAHCC)	121918240	A/B	L	116	P
03	UniProt	VAR_024772	H	122	R	MMAC_HUMAN	Disease (MMAHCC)	---	A/B	H	122	R
04	UniProt	VAR_024773	Y	130	H	MMAC_HUMAN	Disease (MMAHCC)	372670428	A/B	Y	130	H
05	UniProt	VAR_024774	G	147	A	MMAC_HUMAN	Disease (MMAHCC)	140522266	A/B	G	147	A
06	UniProt	VAR_024775	G	147	D	MMAC_HUMAN	Disease (MMAHCC)	140522266	A/B	G	147	D
07	UniProt	VAR_024776	G	156	D	MMAC_HUMAN	Disease (MMAHCC)	---	A/B	G	156	D
08	UniProt	VAR_024777	W	157	C	MMAC_HUMAN	Disease (MMAHCC)	---	A/B	W	157	C
09	UniProt	VAR_024778	R	161	G	MMAC_HUMAN	Disease (MMAHCC)	---	A/B	R	161	G
10	UniProt	VAR_024779	R	161	Q	MMAC_HUMAN	Disease (MMAHCC)	121918243	A/B	R	161	Q
11	UniProt	VAR_024780	R	189	S	MMAC_HUMAN	Disease (MMAHCC)	200895671	A/B	R	189	S
12	UniProt	VAR_024781	L	193	P	MMAC_HUMAN	Disease (MMAHCC)	---	A/B	L	193	P
13	UniProt	VAR_024782	R	206	P	MMAC_HUMAN	Disease (MMAHCC)	---	A/B	R	206	P
14	UniProt	VAR_024783	R	206	W	MMAC_HUMAN	Disease (MMAHCC)	---	A/B	R	206	W

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

Biological Unit 1 (14, 14)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_024770	Q	27	R	MMAC_HUMAN	Disease (MMAHCC)	546099787	A	Q	27	R
02	UniProt	VAR_024771	L	116	P	MMAC_HUMAN	Disease (MMAHCC)	121918240	A	L	116	P
03	UniProt	VAR_024772	H	122	R	MMAC_HUMAN	Disease (MMAHCC)	---	A	H	122	R
04	UniProt	VAR_024773	Y	130	H	MMAC_HUMAN	Disease (MMAHCC)	372670428	A	Y	130	H
05	UniProt	VAR_024774	G	147	A	MMAC_HUMAN	Disease (MMAHCC)	140522266	A	G	147	A
06	UniProt	VAR_024775	G	147	D	MMAC_HUMAN	Disease (MMAHCC)	140522266	A	G	147	D
07	UniProt	VAR_024776	G	156	D	MMAC_HUMAN	Disease (MMAHCC)	---	A	G	156	D
08	UniProt	VAR_024777	W	157	C	MMAC_HUMAN	Disease (MMAHCC)	---	A	W	157	C
09	UniProt	VAR_024778	R	161	G	MMAC_HUMAN	Disease (MMAHCC)	---	A	R	161	G
10	UniProt	VAR_024779	R	161	Q	MMAC_HUMAN	Disease (MMAHCC)	121918243	A	R	161	Q
11	UniProt	VAR_024780	R	189	S	MMAC_HUMAN	Disease (MMAHCC)	200895671	A	R	189	S
12	UniProt	VAR_024781	L	193	P	MMAC_HUMAN	Disease (MMAHCC)	---	A	L	193	P
13	UniProt	VAR_024782	R	206	P	MMAC_HUMAN	Disease (MMAHCC)	---	A	R	206	P
14	UniProt	VAR_024783	R	206	W	MMAC_HUMAN	Disease (MMAHCC)	---	A	R	206	W

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

Biological Unit 2 (14, 14)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_024770	Q	27	R	MMAC_HUMAN	Disease (MMAHCC)	546099787	B	Q	27	R
02	UniProt	VAR_024771	L	116	P	MMAC_HUMAN	Disease (MMAHCC)	121918240	B	L	116	P
03	UniProt	VAR_024772	H	122	R	MMAC_HUMAN	Disease (MMAHCC)	---	B	H	122	R
04	UniProt	VAR_024773	Y	130	H	MMAC_HUMAN	Disease (MMAHCC)	372670428	B	Y	130	H
05	UniProt	VAR_024774	G	147	A	MMAC_HUMAN	Disease (MMAHCC)	140522266	B	G	147	A
06	UniProt	VAR_024775	G	147	D	MMAC_HUMAN	Disease (MMAHCC)	140522266	B	G	147	D
07	UniProt	VAR_024776	G	156	D	MMAC_HUMAN	Disease (MMAHCC)	---	B	G	156	D
08	UniProt	VAR_024777	W	157	C	MMAC_HUMAN	Disease (MMAHCC)	---	B	W	157	C
09	UniProt	VAR_024778	R	161	G	MMAC_HUMAN	Disease (MMAHCC)	---	B	R	161	G
10	UniProt	VAR_024779	R	161	Q	MMAC_HUMAN	Disease (MMAHCC)	121918243	B	R	161	Q
11	UniProt	VAR_024780	R	189	S	MMAC_HUMAN	Disease (MMAHCC)	200895671	B	R	189	S
12	UniProt	VAR_024781	L	193	P	MMAC_HUMAN	Disease (MMAHCC)	---	B	L	193	P
13	UniProt	VAR_024782	R	206	P	MMAC_HUMAN	Disease (MMAHCC)	---	B	R	206	P
14	UniProt	VAR_024783	R	206	W	MMAC_HUMAN	Disease (MMAHCC)	---	B	R	206	W

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

(no "PROSITE Motif" information available for 3SBY)

(no "Exon" information available for 3SBY)

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:218
 aligned with MMAC_HUMAN | Q9Y4U1 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:229
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220         
           MMAC_HUMAN     1 MEPKVAELKQKIEDTLCPFGFEVYPFQVAWYNELLPPAFHLPLPGPTLAFLVLSTPAMFDRALKPFLQSCHLRMLTDPVDQCVAYHLGRVRESLPELQIEIIADYEVHPNRRPKILAQTAAHVAGAAYYYQRQDVEADPWGNQRISGVCIHPRFGGWFAIRGVVLLPGIEVPDLPPRKPHDCVPTRADRIALLEGFNFHWRDWTYRDAVTPQERYSEEQKAYFSTPPAQ 229
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh...eeeeeeehhhhhhhhhhhhh......eeeeeeee..hhhhhh..............hhhhhhhhhhhhhhhhhh.....eeee.hhh........hhhhhhhhh...eee....-----------..eee........eeeeeeeeeeee..............hhhhhhhhhhhhhh.....hhhhh.......hhhhhhhhh..... Sec.struct. author
             SAPs(SNPs) (1) --------------------------R----------------------------------------------------------------------------------------P-----R-------H----------------A--------DC---G---------------------------S---P------------P----------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) --------------------------------------------------------------------------------------------------------------------------------------------------D-------------Q--------------------------------------------W----------------------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3sby A   1 mEPKVAELKQKIEDTLCPFGFEVYPFQVAWYNELLPPAFHLPLPGPTmAFLVLSTPAmFDRALKPFLQSCHLRmLTDPVDQCmAYHLGRVRESLPELQIEIIADYEmHPNRRPKILAQTAAHVAGAAYYYQRQD-----------SGVCIHPRFGGWFAIRGVmLLPGIEVPDLPPRKPHDCVPTRADRIALLEGFNFHWRDWTYRDAVTPQERYSEEQKAYFSTPPAQ 229
                            |       10        20        30        40       |50       |60        70   |    80  |     90       100      |110       120       130   |     -     | 150       160   |   170       180       190       200       210       220         
                            |                                             48-MSE    58-MSE          74-MSE   83-MSE                 107-MSE                    134         146               164-MSE                                                             
                            1-MSE

Chain B from PDB  Type:PROTEIN  Length:228
 aligned with MMAC_HUMAN | Q9Y4U1 from UniProtKB/Swiss-Prot  Length:282

    Alignment length:228
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224        
           MMAC_HUMAN     5 VAELKQKIEDTLCPFGFEVYPFQVAWYNELLPPAFHLPLPGPTLAFLVLSTPAMFDRALKPFLQSCHLRMLTDPVDQCVAYHLGRVRESLPELQIEIIADYEVHPNRRPKILAQTAAHVAGAAYYYQRQDVEADPWGNQRISGVCIHPRFGGWFAIRGVVLLPGIEVPDLPPRKPHDCVPTRADRIALLEGFNFHWRDWTYRDAVTPQERYSEEQKAYFSTPPAQRLA 232
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhh...eeeeeeehhhhhh.............eeeeeeee..hhhhhhhhhhh.........hhhhhhhhhhhhhhhh.......eeee.hhh........hhhhhhhhh...eeehhhhh............eee........eeeeeeeeeeee..............hhhhhhhhhhhhhhh..hhhhhhh.......hhhhhhhhhhhhhhh.. Sec.struct. author
             SAPs(SNPs) (1) ----------------------R----------------------------------------------------------------------------------------P-----R-------H----------------A--------DC---G---------------------------S---P------------P-------------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ----------------------------------------------------------------------------------------------------------------------------------------------D-------------Q--------------------------------------------W-------------------------- SAPs(SNPs) (2)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3sby B   5 VAELKQKIEDTLCPFGFEVYPFQVAWYNELLPPAFHLPLPGPTmAFLVLSTPAmFDRALKPFLQSCHLRmLTDPVDQCmAYHLGRVRESLPELQIEIIADYEmHPNRRPKILAQTAAHVAGAAYYYQRQDVEADPWGNQRISGVCIHPRFGGWFAIRGVmLLPGIEVPDLPPRKPHDCVPTRADRIALLEGFNFHWRDWTYRDAVTPQERYSEEQKAYFSTPPAQRLA 232
                                    14        24        34        44   |    54   |    64        74        84        94       104  |    114       124       134       144       154       164       174       184       194       204       214       224        
                                                                      48-MSE    58-MSE          74-MSE   83-MSE                 107-MSE                                                  164-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 '\|'

(no "SCOP Domain" information available for 3SBY)

(no "CATH Domain" information available for 3SBY)

(no "Pfam Domain" information available for 3SBY)

Asymmetric Unit(hide GO term definitions)

Chain A,B (MMAC_HUMAN | Q9Y4U1)

molecular function
	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:0033787	cyanocobalamin reductase (cyanide-eliminating) activity	Catalysis of the reaction: cob(I)alamin + hydrogen cyanide + NADP(+) = cyanocob(III)alamin + H(+) + NADPH.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	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:0009236	cobalamin biosynthetic process	The chemical reactions and pathways resulting in the formation of cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
	GO:0009235	cobalamin metabolic process	The chemical reactions and pathways involving cobalamin (vitamin B12), a water-soluble vitamin characterized by possession of a corrin nucleus containing a cobalt atom.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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.

Asymmetric Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		MSE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
(no "Sites" information available for 3sby)

	Cis Peptide Bonds
		Arg A:112 - Pro A:113	[ RasMol ]
		Arg B:112 - Pro B:113	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	3sby
		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
	MMAC_HUMAN \| Q9Y4U1
		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)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	277400
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	MMAC_HUMAN \| Q9Y4U1
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	MMAC_HUMAN \| Q9Y4U1	:	3sbz 3sc0 3som 5uos

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 13)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (14, 28)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (10, 10)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File