3B8V - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF ESCHERICHIA COLI ALAINE RACEMASE MUTANT E221K

Authors :   D. Wu, T. Hu, L. Zhang, H. Jiang, X. Shen

Date :   02 Nov 07 (Deposition) - 08 Jul 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Alpha/Beta Barrel, Cell Shape, Cell Wall Biogenesis/Degradation, Isomerase, Peptidoglycan Synthesis, Pyridoxal Phosphate (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Wu, T. Hu, L. Zhang, J. Chen, J. Du, J. Ding, H. Jiang, X. Shen
Residues Asp164 And Glu165 At The Substrate Entryway Function Potently In Substrate Orientation Of Alanine Racemase From E. Coli: Enzymatic Characterization With Crystal Structure Analysis
Protein Sci. V. 17 1066 2008
PubMed-ID: 18434499 | Reference-DOI: 10.1110/PS.083495908

Molecule 1 - ALANINE RACEMASE
	Chains	:	A, B, C, D
	EC Number	:	5.1.1.1
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A
	Expression System Strain	:	BL21(DE3)
	Expression System Vector Type	:	PLASMID
	Gene	:	ALR
	Mutation	:	YES
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	83333
	Strain	:	JM109

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 19)

No.	Name	Count	Type	Full Name
1	KCX	4	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
2	PLP	4	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE
3	SO4	11	Ligand/Ion	SULFATE ION

Biological Unit 1 (3, 12)

No.	Name	Count	Type	Full Name
1	KCX	2	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
2	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE
3	SO4	8	Ligand/Ion	SULFATE ION

Biological Unit 2 (3, 7)

No.	Name	Count	Type	Full Name
1	KCX	2	Mod. Amino Acid	LYSINE NZ-CARBOXYLIC ACID
2	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE
3	SO4	3	Ligand/Ion	SULFATE ION

Asymmetric Unit (14, 14)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TYR A:255 , TYR A:274 , ARG A:280 , TYR B:343	BINDING SITE FOR RESIDUE SO4 A 360
02	AC2	SOFTWARE	ARG A:19 , ARG B:266	BINDING SITE FOR RESIDUE SO4 A 361
03	AC3	SOFTWARE	ARG A:162	BINDING SITE FOR RESIDUE SO4 A 362
04	AC4	SOFTWARE	TYR A:343 , TYR B:255 , TYR B:274 , ARG B:280	BINDING SITE FOR RESIDUE SO4 B 360
05	AC5	SOFTWARE	ARG A:266 , ARG B:19	BINDING SITE FOR RESIDUE SO4 B 361
06	AC6	SOFTWARE	TYR C:255 , TYR C:274 , ALA C:302	BINDING SITE FOR RESIDUE SO4 C 360
07	AC7	SOFTWARE	ARG C:19 , ARG D:266 , ALA D:314	BINDING SITE FOR RESIDUE SO4 C 361
08	AC8	SOFTWARE	ARG C:162 , CYS C:168	BINDING SITE FOR RESIDUE SO4 C 362
09	AC9	SOFTWARE	ARG A:280 , ARG A:300 , LYS B:221	BINDING SITE FOR RESIDUE SO4 A 363
10	BC1	SOFTWARE	LYS A:221 , ARG B:280 , ARG B:300	BINDING SITE FOR RESIDUE SO4 B 363
11	BC2	SOFTWARE	LYS A:34 , TYR A:38 , HIS A:159 , ALA A:193 , SER A:194 , ARG A:209 , GLY A:211 , ILE A:212 , TYR A:343	BINDING SITE FOR RESIDUE PLP A 1001
12	BC3	SOFTWARE	LYS B:34 , TYR B:38 , HIS B:159 , ALA B:193 , SER B:194 , ARG B:209 , GLY B:211 , ILE B:212 , TYR B:343	BINDING SITE FOR RESIDUE PLP B 1001
13	BC4	SOFTWARE	LYS C:34 , TYR C:38 , LEU C:78 , HIS C:159 , ALA C:193 , SER C:194 , ARG C:209 , GLY C:211 , ILE C:212 , TYR C:343	BINDING SITE FOR RESIDUE PLP C 1001
14	BC5	SOFTWARE	LYS D:34 , TYR D:38 , HIS D:159 , ALA D:193 , SER D:194 , ARG D:209 , GLY D:211 , ILE D:212 , TYR D:343	BINDING SITE FOR RESIDUE PLP D 1001

(no "SS Bond" information available for 3B8V)

Asymmetric Unit

No.	Residues
1	Gln A:152	-	Pro A:153
2	Gln B:152	-	Pro B:153
3	Gln C:152	-	Pro C:153
4	Gln D:152	-	Pro D:153

(no "SAP(SNP)/Variant" information available for 3B8V)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALANINE_RACEMASE	PS00395	Alanine racemase pyridoxal-phosphate attachment site.	ALR1_ECOLI	31-41	4	A:31-41 B:31-41 C:31-41 D:31-41

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALANINE_RACEMASE	PS00395	Alanine racemase pyridoxal-phosphate attachment site.	ALR1_ECOLI	31-41	2	A:31-41 B:31-41 - -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ALANINE_RACEMASE	PS00395	Alanine racemase pyridoxal-phosphate attachment site.	ALR1_ECOLI	31-41	2	- - C:31-41 D:31-41

(no "Exon" information available for 3B8V)

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:359
 aligned with ALR1_ECOLI | P0A6B4 from UniProtKB/Swiss-Prot  Length:359

    Alignment length:359
                                    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       270       280       290       300       310       320       330       340       350         
           ALR1_ECOLI     1 MQAATVVINRRALRHNLQRLRELAPASKMVAVVKANAYGHGLLETARTLPDADAFGVARLEEALRLRAGGITKPVLLLEGFFDARDLPTISAQHFHTAVHNEEQLAALEEASLDEPVTVWMKLDTGMHRLGVRPEQAEAFYHRLTQCKNVRQPVNIVSHFARADEPKCGATEKQLAIFNTFCEGKPGQRSIAASGGILLWPQSHFDWVRPGIILYGVSPLEDRSTGADFGCQPVMSLTSSLIAVREHKAGEPVGYGGTWVSERDTRLGVVAMGYGDGYPRAAPSGTPVLVNGREVPIVGRVAMDMICVDLGPQAQDKAGDPVILWGEGLPVERIAEMTKVSAYELITRLTSRVAMKYVD 359
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3b8vA01  3b8vA02 A:10-217 Alanine racemase                                                                                                                                                                               3b8vA01 A:1-9,A:218-359 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeehhhhhhhhhhhhhhh...eeeeehhhhhhh.hhhhhhhhh....eeee.hhhhhhhhhhh.....eee.....hhhhhhhhhhh.eeeee.hhhhhhhhhhh.......eeee..........hhhhhhhhhhhhh.........eee...........hhhhhhhhhhhhhhh.....ee..hhhhhhhhhhhh..ee..hhhhhh........hhhhhh....eeeeeeeeeeeee....eehhhhhee....eeeeee................eeee..eeee.........eeee...........eeeee....hhhhhhhhhh.hhhhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------ALANINE_RAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b8v A   1 MQAATVVINRRALRHNLQRLRELAPASKMVAVVKANAYGHGLLETARTLPDADAFGVARLEEALRLRAGGITKPVLLLEGFFDARDLPTISAQHFHTAVHNEEQLAALEEASLDEPVTVWMkLDTGMHRLGVRPEQAEAFYHRLTQCKNVRQPVNIVSHFARADEPKCGATEKQLAIFNTFCEGKPGQRSIAASGGILLWPQSHFDWVRPGIILYGVSPLKDRSTGADFGCQPVMSLTSSLIAVREHKAGEPVGYGGTWVSERDTRLGVVAMGYGDGYPRAAPSGTPVLVNGREVPIVGRVAMDMICVDLGPQAQDKAGDPVILWGEGLPVERIAEMTKVSAYELITRLTSRVAMKYVD 359
                                    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       270       280       290       300       310       320       330       340       350         
                                                                                                                                                   122-KCX

Chain B from PDB  Type:PROTEIN  Length:359
 aligned with ALR1_ECOLI | P0A6B4 from UniProtKB/Swiss-Prot  Length:359

    Alignment length:359
                                    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       270       280       290       300       310       320       330       340       350         
           ALR1_ECOLI     1 MQAATVVINRRALRHNLQRLRELAPASKMVAVVKANAYGHGLLETARTLPDADAFGVARLEEALRLRAGGITKPVLLLEGFFDARDLPTISAQHFHTAVHNEEQLAALEEASLDEPVTVWMKLDTGMHRLGVRPEQAEAFYHRLTQCKNVRQPVNIVSHFARADEPKCGATEKQLAIFNTFCEGKPGQRSIAASGGILLWPQSHFDWVRPGIILYGVSPLEDRSTGADFGCQPVMSLTSSLIAVREHKAGEPVGYGGTWVSERDTRLGVVAMGYGDGYPRAAPSGTPVLVNGREVPIVGRVAMDMICVDLGPQAQDKAGDPVILWGEGLPVERIAEMTKVSAYELITRLTSRVAMKYVD 359
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3b8vB01  3b8vB02 B:10-217 Alanine racemase                                                                                                                                                                               3b8vB01 B:1-9,B:218-359 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                      CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeehhhhhhhhhhhhhhh...eeeeehhhhhhh.hhhhhhhhh....eeee.hhhhhhhhhhh.....eee.....hhhhhhhhhhh.eeeee.hhhhhhhhhhh.......eeee..........hhhhhhhhhhhhhh........eee...........hhhhhhhhhhhhhhh.....ee..hhhhhhhhhhhh..ee..hhhhhh........hhhhhh....eeeeeeeeeeeee....eehhhhhee....eeeeee................eeee..eeee.........eeee...........eeeee....hhhhhhhhhh.hhhhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------ALANINE_RAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b8v B   1 MQAATVVINRRALRHNLQRLRELAPASKMVAVVKANAYGHGLLETARTLPDADAFGVARLEEALRLRAGGITKPVLLLEGFFDARDLPTISAQHFHTAVHNEEQLAALEEASLDEPVTVWMkLDTGMHRLGVRPEQAEAFYHRLTQCKNVRQPVNIVSHFARADEPKCGATEKQLAIFNTFCEGKPGQRSIAASGGILLWPQSHFDWVRPGIILYGVSPLKDRSTGADFGCQPVMSLTSSLIAVREHKAGEPVGYGGTWVSERDTRLGVVAMGYGDGYPRAAPSGTPVLVNGREVPIVGRVAMDMICVDLGPQAQDKAGDPVILWGEGLPVERIAEMTKVSAYELITRLTSRVAMKYVD 359
                                    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       270       280       290       300       310       320       330       340       350         
                                                                                                                                                   122-KCX

Chain C from PDB  Type:PROTEIN  Length:355
 aligned with ALR1_ECOLI | P0A6B4 from UniProtKB/Swiss-Prot  Length:359

    Alignment length:357
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       
           ALR1_ECOLI     3 AATVVINRRALRHNLQRLRELAPASKMVAVVKANAYGHGLLETARTLPDADAFGVARLEEALRLRAGGITKPVLLLEGFFDARDLPTISAQHFHTAVHNEEQLAALEEASLDEPVTVWMKLDTGMHRLGVRPEQAEAFYHRLTQCKNVRQPVNIVSHFARADEPKCGATEKQLAIFNTFCEGKPGQRSIAASGGILLWPQSHFDWVRPGIILYGVSPLEDRSTGADFGCQPVMSLTSSLIAVREHKAGEPVGYGGTWVSERDTRLGVVAMGYGDGYPRAAPSGTPVLVNGREVPIVGRVAMDMICVDLGPQAQDKAGDPVILWGEGLPVERIAEMTKVSAYELITRLTSRVAMKYVD 359
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3b8vC013b8vC02 C:10-217 Alanine racemase                                                                                                                                                                               3b8vC01 C:3-9,C:218-359 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeehhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhh.....eeee.hhhhhhhhhhh.....eee.....hhhhhhhhhhh.eeeee.hhhhhhhhhhh.......eeee..........hhhhhhhhhhhhhh........eee...........hhhhhhhhhhhhhhh.....ee..hhhhhhhhhhhh..ee..hhhhhh........hhhhh.....eeeeeeeeeeeee....eehhhhhee....eeeeee................eeee..eeee.........eeee...........eeeee.........--....hhhhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------ALANINE_RAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b8v C   3 AATVVINRRALRHNLQRLRELAPASKMVAVVKANAYGHGLLETARTLPDADAFGVARLEEALRLRAGGITKPVLLLEGFFDARDLPTISAQHFHTAVHNEEQLAALEEASLDEPVTVWMkLDTGMHRLGVRPEQAEAFYHRLTQCKNVRQPVNIVSHFARADEPKCGATEKQLAIFNTFCEGKPGQRSIAASGGILLWPQSHFDWVRPGIILYGVSPLKDRSTGADFGCQPVMSLTSSLIAVREHKAGEPVGYGGTWVSERDTRLGVVAMGYGDGYPRAAPSGTPVLVNGREVPIVGRVAMDMICVDLGPQAQDKAGDPVILWGEGLPVERI--MTKVSAYELITRLTSRVAMKYVD 359
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332 |  |  342       352       
                                                                                                                                                 122-KCX                                                                                                                                                                                                             334  |                      
                                                                                                                                                                                                                                                                                                                                                                        337

Chain D from PDB  Type:PROTEIN  Length:353
 aligned with ALR1_ECOLI | P0A6B4 from UniProtKB/Swiss-Prot  Length:359

    Alignment length:357
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       
           ALR1_ECOLI     3 AATVVINRRALRHNLQRLRELAPASKMVAVVKANAYGHGLLETARTLPDADAFGVARLEEALRLRAGGITKPVLLLEGFFDARDLPTISAQHFHTAVHNEEQLAALEEASLDEPVTVWMKLDTGMHRLGVRPEQAEAFYHRLTQCKNVRQPVNIVSHFARADEPKCGATEKQLAIFNTFCEGKPGQRSIAASGGILLWPQSHFDWVRPGIILYGVSPLEDRSTGADFGCQPVMSLTSSLIAVREHKAGEPVGYGGTWVSERDTRLGVVAMGYGDGYPRAAPSGTPVLVNGREVPIVGRVAMDMICVDLGPQAQDKAGDPVILWGEGLPVERIAEMTKVSAYELITRLTSRVAMKYVD 359
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 3b8vD013b8vD02 D:10-217 Alanine racemase                                                                                                                                                                               3b8vD01 D:3-9,D:218-359 Lyase, Ornithine Decarboxylase; Chain A, domain 1                                                                      CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeehhhhhhhhhhhhhhh...eeeeehhhhhhhhhhhhhhhhh....eeee.hhhhhhhhhhh.....eee.....hhhhhhhhhhh.eeeee.hhhhhhhhhhh.......eeee..........hhhhhhhhhhhhh.........eee...........hhhhhhhhhhhhhhh.....ee..hhhhhhhhhhhh..ee..hhhhhh........hhhhhh....eeeeeeeeeeeee....eehhhhhee....eeeeee................eeee..eeee.........eeee...........eeeee.........----..hhhhhhhh.....eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------ALANINE_RAC------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3b8v D   3 AATVVINRRALRHNLQRLRELAPASKMVAVVKANAYGHGLLETARTLPDADAFGVARLEEALRLRAGGITKPVLLLEGFFDARDLPTISAQHFHTAVHNEEQLAALEEASLDEPVTVWMkLDTGMHRLGVRPEQAEAFYHRLTQCKNVRQPVNIVSHFARADEPKCGATEKQLAIFNTFCEGKPGQRSIAASGGILLWPQSHFDWVRPGIILYGVSPLKDRSTGADFGCQPVMSLTSSLIAVREHKAGEPVGYGGTWVSERDTRLGVVAMGYGDGYPRAAPSGTPVLVNGREVPIVGRVAMDMICVDLGPQAQDKAGDPVILWGEGLPVERI----KVSAYELITRLTSRVAMKYVD 359
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332 |    |342       352       
                                                                                                                                                 122-KCX                                                                                                                                                                                                             334  339

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 3B8V)

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Alanine racemase (53)

Escherichia coli. Organism_taxid: 83333. Strain: jm109. (6)

1a	3b8vA02	A:10-217
1b	3b8vC02	C:10-217
1c	3b8vD02	D:10-217
1d	3b8vB02	B:10-217

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Lyase, Ornithine Decarboxylase; Chain A, domain 1 (47)

Homologous Superfamily: Lyase, Ornithine Decarboxylase; Chain A, domain 1 (47)

Escherichia coli. Organism_taxid: 83333. Strain: jm109. (6)

2a	3b8vC01	C:3-9,C:218-359
2b	3b8vA01	A:1-9,A:218-359
2c	3b8vB01	B:1-9,B:218-359
2d	3b8vD01	D:3-9,D:218-359

(no "Pfam Domain" information available for 3B8V)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (ALR1_ECOLI | P0A6B4)

molecular function
	GO:0008784	alanine racemase activity	Catalysis of the reaction: L-alanine = D-alanine.
	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: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:0030170	pyridoxal phosphate binding	Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
biological process
	GO:0030632	D-alanine biosynthetic process	The chemical reactions and pathways resulting in the formation of D-alanine, the D-enantiomer of the amino acid alanine, i.e (2R)-2-aminopropanoic acid.
	GO:0006522	alanine metabolic process	The chemical reactions and pathways involving alanine, 2-aminopropanoic acid.
	GO:0071555	cell wall organization	A process that results in the assembly, arrangement of constituent parts, or disassembly of the cell wall, the rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal and most prokaryotic cells, maintaining their shape and protecting them from osmotic lysis.
	GO:0009252	peptidoglycan biosynthetic process	The chemical reactions and pathways resulting in the formation of peptidoglycans, any of a class of glycoconjugates found in bacterial cell walls.
	GO:0008360	regulation of cell shape	Any process that modulates the surface configuration of a cell.

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
		KCX	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		PLP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Gln A:152 - Pro A:153	[ RasMol ]
		Gln B:152 - Pro B:153	[ RasMol ]
		Gln C:152 - Pro C:153	[ RasMol ]
		Gln D:152 - Pro D:153	[ 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 \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites 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
	3b8v
		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
	ALR1_ECOLI \| P0A6B4
		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)
	5.1.1.1
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		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
	ALR1_ECOLI \| P0A6B4
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	ALR1_ECOLI \| P0A6B4	:	2rjg 2rjh 3b8t 3b8u 3b8w 4wr3 4xbj

2rjg	THE WILD-TYPE PROTEIN
2rjh	THE WILD-TYPE PROTEIN COMPLEXED WITH D-CYCLOSERINE
3b8t	MUTANT P219A
3b8u	MUTANT E221A
3b8w	MUTANT E221P

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 19)

Sites (14, 14)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (2, 8)

Pfam Domains (0, 0)

Gene Ontology (9, 9)

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