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Asym./Biol. Unit (Jmol Viewer)

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Title :   STRUCTURAL BASIS FOR STEREO SELECTIVITY IN THE (R)- AND (S)-HYDROXYPROPYLETHANE THIOSULFONATE DEHYDROGENASES

Authors :   A. M. Krishnakumar, B. P. Nocek, D. D. Clark, S. A. Ensign, J. W. Peters

Date :   19 Feb 06 (Deposition) - 26 Jul 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.80

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

Keywords :   Nad, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. M. Krishnakumar, B. P. Nocek, D. D. Clark, S. A. Ensign, J. W. Peters
Structural Basis For Stereoselectivity In The (R)- And (S)-Hydroxypropylthioethanesulfonate Dehydrogenases.
Biochemistry V. 45 8831 2006
PubMed-ID: 16846226 | Reference-DOI: 10.1021/BI0603569

Molecule 1 - 2-(R)-HYDROXYPROPYL-COM DEHYDROGENASE
	Chains	:	A, B, C, D
	EC Number	:	1.1.1.268
	Organism Scientific	:	XANTHOBACTER AUTOTROPHICUS
	Organism Taxid	:	78245
	Strain	:	PY2
	Synonym	:	R-HPCD, R-HPCDH, ALIPHATIC EPOXIDE CARBOXYLATION COMPONENT III

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 8)

No.	Name	Count	Type	Full Name
1	KPC	4	Ligand/Ion	(2-[2-KETOPROPYLTHIO]ETHANESULFONATE
2	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:9 , SER A:11 , SER A:12 , GLY A:13 , ASN A:14 , ASP A:33 , LEU A:34 , ALA A:59 , ASP A:60 , VAL A:61 , ASN A:87 , ALA A:88 , GLY A:89 , ILE A:140 , ALA A:141 , TYR A:155 , LYS A:159 , PRO A:185 , GLY A:186 , MET A:187 , ILE A:188 , THR A:190 , PRO A:191 , MET A:192 , THR A:193 , HOH A:2166 , HOH A:2244 , HOH A:2245 , HOH A:2246	BINDING SITE FOR RESIDUE NAD A1251
2	AC2	SOFTWARE	THR A:91 , SER A:142 , VAL A:143 , ALA A:144 , PHE A:149 , ARG A:152 , TYR A:155 , MET A:192 , TRP A:195 , ARG A:196 , HOH A:2166	BINDING SITE FOR RESIDUE KPC A1252
3	AC3	SOFTWARE	GLY B:9 , SER B:11 , SER B:12 , GLY B:13 , ASN B:14 , ASP B:33 , LEU B:34 , ALA B:59 , ASP B:60 , VAL B:61 , ASN B:87 , ALA B:88 , GLY B:89 , VAL B:113 , ILE B:140 , ALA B:141 , TYR B:155 , LYS B:159 , PRO B:185 , GLY B:186 , MET B:187 , ILE B:188 , THR B:190 , PRO B:191 , MET B:192 , KPC B:1252 , HOH B:2015 , HOH B:2128 , HOH B:2170 , HOH B:2243	BINDING SITE FOR RESIDUE NAD B1251
4	AC4	SOFTWARE	THR B:91 , PHE B:149 , ARG B:152 , TYR B:155 , MET B:187 , MET B:192 , THR B:193 , ARG B:196 , NAD B:1251 , HOH B:2170	BINDING SITE FOR RESIDUE KPC B1252
5	AC5	SOFTWARE	SER C:11 , SER C:12 , GLY C:13 , ASN C:14 , ASP C:33 , LEU C:34 , ALA C:59 , ASP C:60 , VAL C:61 , ASN C:87 , ALA C:88 , GLY C:89 , VAL C:113 , ILE C:140 , ALA C:141 , TYR C:155 , LYS C:159 , PRO C:185 , GLY C:186 , MET C:187 , ILE C:188 , THR C:190 , PRO C:191 , MET C:192 , THR C:193 , KPC C:1252 , HOH C:2015 , HOH C:2095 , HOH C:2118 , HOH C:2131 , HOH C:2201	BINDING SITE FOR RESIDUE NAD C1251
6	AC6	SOFTWARE	THR C:91 , PHE C:149 , ARG C:152 , TYR C:155 , GLY C:186 , MET C:187 , MET C:192 , THR C:193 , TRP C:195 , ARG C:196 , NAD C:1251 , HOH C:2131	BINDING SITE FOR RESIDUE KPC C1252
7	AC7	SOFTWARE	GLY D:9 , SER D:11 , SER D:12 , GLY D:13 , ASN D:14 , ASP D:33 , LEU D:34 , ALA D:59 , ASP D:60 , VAL D:61 , ASN D:87 , ALA D:88 , GLY D:89 , VAL D:113 , ILE D:140 , ALA D:141 , TYR D:155 , LYS D:159 , PRO D:185 , GLY D:186 , ILE D:188 , THR D:190 , PRO D:191 , MET D:192 , THR D:193 , KPC D:1252 , HOH D:2011 , HOH D:2222 , HOH D:2223 , HOH D:2225	BINDING SITE FOR RESIDUE NAD D1251
8	AC8	SOFTWARE	THR D:91 , PHE D:149 , ARG D:152 , TYR D:155 , GLY D:186 , MET D:187 , MET D:192 , THR D:193 , TRP D:195 , ARG D:196 , NAD D:1251 , HOH D:2225	BINDING SITE FOR RESIDUE KPC D1252

(no "SS Bond" information available for 2CFC)

(no "Cis Peptide Bond" information available for 2CFC)

(no "SAP(SNP)/Variant" information available for 2CFC)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	HCDR_XANP2	142-170	4	A:142-170 B:142-170 C:142-170 D:142-170

(no "Exon" information available for 2CFC)

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
	(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:250
 aligned with HCDR_XANP2 | Q56840 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:250
                                    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
           HCDR_XANP2     1 MSRVAIVTGASSGNGLAIATRFLARGDRVAALDLSAETLEETARTHWHAYADKVLRVRADVADEGDVNAAIAATMEQFGAIDVLVNNAGITGNSEAGVLHTTPVEQFDKVMAVNVRGIFLGCRAVLPHMLLQGAGVIVNIASVASLVAFPGRSAYTTSKGAVLQLTKSVAVDYAGSGIRCNAVCPGMIETPMTQWRLDQPELRDQVLARIPQKEIGTAAQVADAVMFLAGEDATYVNGAALVMDGAYTAI 250
               SCOP domains d2cfca_ A: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains 2cfcA00 A:1-250 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhh..hhh.eeeee....hhhhhhhhhhhhhhhhh...eeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.......hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.........eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:142-170    -------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cfc A   1 MSRVAIVTGASSGNGLAIATRFLARGDRVAALDLSAETLEETARTHWHAYADKVLRVRADVADEGDVNAAIAATMEQFGAIDVLVNNAGITGNSEAGVLHTTPVEQFDKVMAVNVRGIFLGCRAVLPHMLLQGAGVIVNIASVASLVAFPGRSAYTTSKGAVLQLTKSVAVDYAGSGIRCNAVCPGMIETPMTQWRLDQPELRDQVLARIPQKEIGTAAQVADAVMFLAGEDATYVNGAALVMDGAYTAI 250
                                    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

Chain B from PDB  Type:PROTEIN  Length:250
 aligned with HCDR_XANP2 | Q56840 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:250
                                    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
           HCDR_XANP2     1 MSRVAIVTGASSGNGLAIATRFLARGDRVAALDLSAETLEETARTHWHAYADKVLRVRADVADEGDVNAAIAATMEQFGAIDVLVNNAGITGNSEAGVLHTTPVEQFDKVMAVNVRGIFLGCRAVLPHMLLQGAGVIVNIASVASLVAFPGRSAYTTSKGAVLQLTKSVAVDYAGSGIRCNAVCPGMIETPMTQWRLDQPELRDQVLARIPQKEIGTAAQVADAVMFLAGEDATYVNGAALVMDGAYTAI 250
               SCOP domains d2cfcb_ B: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains 2cfcB00 B:1-250 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhh...eeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.......hhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:142-170    -------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cfc B   1 MSRVAIVTGASSGNGLAIATRFLARGDRVAALDLSAETLEETARTHWHAYADKVLRVRADVADEGDVNAAIAATMEQFGAIDVLVNNAGITGNSEAGVLHTTPVEQFDKVMAVNVRGIFLGCRAVLPHMLLQGAGVIVNIASVASLVAFPGRSAYTTSKGAVLQLTKSVAVDYAGSGIRCNAVCPGMIETPMTQWRLDQPELRDQVLARIPQKEIGTAAQVADAVMFLAGEDATYVNGAALVMDGAYTAI 250
                                    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

Chain C from PDB  Type:PROTEIN  Length:250
 aligned with HCDR_XANP2 | Q56840 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:250
                                    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
           HCDR_XANP2     1 MSRVAIVTGASSGNGLAIATRFLARGDRVAALDLSAETLEETARTHWHAYADKVLRVRADVADEGDVNAAIAATMEQFGAIDVLVNNAGITGNSEAGVLHTTPVEQFDKVMAVNVRGIFLGCRAVLPHMLLQGAGVIVNIASVASLVAFPGRSAYTTSKGAVLQLTKSVAVDYAGSGIRCNAVCPGMIETPMTQWRLDQPELRDQVLARIPQKEIGTAAQVADAVMFLAGEDATYVNGAALVMDGAYTAI 250
               SCOP domains d2cfcc_ C: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains 2cfcC00 C:1-250 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhh...hhh.eeeee....hhhhhhhhhhhhhhhhh...eeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee..ee...hhhhhhhhhhhhhhhh.......eehhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: C:142-170    -------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cfc C   1 MSRVAIVTGASSGNGLAIATRFLARGDRVAALDLSAETLEETARTHWHAYADKVLRVRADVADEGDVNAAIAATMEQFGAIDVLVNNAGITGNSEAGVLHTTPVEQFDKVMAVNVRGIFLGCRAVLPHMLLQGAGVIVNIASVASLVAFPGRSAYTTSKGAVLQLTKSVAVDYAGSGIRCNAVCPGMIETPMTQWRLDQPELRDQVLARIPQKEIGTAAQVADAVMFLAGEDATYVNGAALVMDGAYTAI 250
                                    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

Chain D from PDB  Type:PROTEIN  Length:250
 aligned with HCDR_XANP2 | Q56840 from UniProtKB/Swiss-Prot  Length:250

    Alignment length:250
                                    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
           HCDR_XANP2     1 MSRVAIVTGASSGNGLAIATRFLARGDRVAALDLSAETLEETARTHWHAYADKVLRVRADVADEGDVNAAIAATMEQFGAIDVLVNNAGITGNSEAGVLHTTPVEQFDKVMAVNVRGIFLGCRAVLPHMLLQGAGVIVNIASVASLVAFPGRSAYTTSKGAVLQLTKSVAVDYAGSGIRCNAVCPGMIETPMTQWRLDQPELRDQVLARIPQKEIGTAAQVADAVMFLAGEDATYVNGAALVMDGAYTAI 250
               SCOP domains d2cfcd_ D: automated matches                                                                                                                                                                                                                               SCOP domains
               CATH domains 2cfcD00 D:1-250 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                        CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee...hhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhhhh...eeee...........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.............hhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: D:142-170    -------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2cfc D   1 MSRVAIVTGASSGNGLAIATRFLARGDRVAALDLSAETLEETARTHWHAYADKVLRVRADVADEGDVNAAIAATMEQFGAIDVLVNNAGITGNSEAGVLHTTPVEQFDKVMAVNVRGIFLGCRAVLPHMLLQGAGVIVNIASVASLVAFPGRSAYTTSKGAVLQLTKSVAVDYAGSGIRCNAVCPGMIETPMTQWRLDQPELRDQVLARIPQKEIGTAAQVADAVMFLAGEDATYVNGAALVMDGAYTAI 250
                                    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

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(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: automated matches (447)

Protein domain: automated matches (447)

Xanthobacter autotrophicus [TaxId: 78245] (3)

1a	d2cfca_	A:
1b	d2cfcc_	C:
1c	d2cfcd_	D:
1d	d2cfcb_	B:

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: NAD(P)-binding Rossmann-like Domain (1244)

Xanthobacter autotrophicus. Organism_taxid: 78245. Strain: py2 (1)

1a	2cfcA00	A:1-250
1b	2cfcB00	B:1-250
1c	2cfcC00	C:1-250
1d	2cfcD00	D:1-250

(no "Pfam Domain" information available for 2CFC)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (HCDR_XANP2 | Q56840)

molecular function
	GO:0050574	2-(R)-hydroxypropyl-CoM dehydrogenase activity	Catalysis of the reaction: 2-(R)-hydroxypropyl-coenzyme M + NAD(+) = 2-oxopropyl-coenzyme M + H(+) + NADH.
	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.
biological process
	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.
	GO:0042208	propylene catabolic process	The chemical reactions and pathways resulting in the breakdown of propylene, an alkene produced by catalytic or thermal cracking of hydrocarbons or as a by-product of petroleum refining.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2cfc)

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	2cfc
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Ligands, Modified Residues, Ions (2, 8)

Sites (8, 8)

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